101
|
Warmerdam DO, Alonso‐de Vega I, Wiegant WW, van den Broek B, Rother MB, Wolthuis RMF, Freire R, van Attikum H, Medema RH, Smits VAJ. PHF6 promotes non-homologous end joining and G2 checkpoint recovery. EMBO Rep 2020; 21:e48460. [PMID: 31782600 PMCID: PMC6944915 DOI: 10.15252/embr.201948460] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
The cellular response to DNA breaks is influenced by chromatin compaction. To identify chromatin regulators involved in the DNA damage response, we screened for genes that affect recovery following DNA damage using an RNAi library of chromatin regulators. We identified genes involved in chromatin remodeling, sister chromatid cohesion, and histone acetylation not previously associated with checkpoint recovery. Among these is the PHD finger protein 6 (PHF6), a gene mutated in Börjeson-Forssman-Lehmann syndrome and leukemic cancers. We find that loss of PHF6 dramatically compromises checkpoint recovery in G2 phase cells. Moreover, PHF6 is rapidly recruited to sites of DNA lesions in a PARP-dependent manner and required for efficient DNA repair through classical non-homologous end joining. These results indicate that PHF6 is a novel DNA damage response regulator that promotes end joining-mediated repair, thereby stimulating timely recovery from the G2 checkpoint.
Collapse
Affiliation(s)
- Daniël O Warmerdam
- CRISPR PlatformCancer Center AmsterdamAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Division of Cell BiologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Ignacio Alonso‐de Vega
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaTenerifeSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaTenerifeSpain
| | - Wouter W Wiegant
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Bram van den Broek
- Division of Cell BiologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- BioImaging FacilityThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Magdalena B Rother
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Rob MF Wolthuis
- Section of OncogeneticsDepartment of Clinical GeneticsVrije Universiteit Amsterdam, Cancer Center AmsterdamAmsterdam UMCAmsterdamThe Netherlands
| | - Raimundo Freire
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaTenerifeSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaTenerifeSpain
- Universidad Fernando Pessoa CanariasLas Palmas de Gran CanariaSpain
| | - Haico van Attikum
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - René H Medema
- Division of Cell BiologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Veronique AJ Smits
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaTenerifeSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaTenerifeSpain
- Universidad Fernando Pessoa CanariasLas Palmas de Gran CanariaSpain
| |
Collapse
|
102
|
Bagger FO, Probst V. Single Cell Sequencing in Cancer Diagnostics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:175-193. [PMID: 32949400 DOI: 10.1007/978-981-15-4494-1_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Personalized medicine has been driven by improvements in genomic sequencing and analysis. For several diseases, in particular cancers, it has for nearly a decade been standard clinical practice to analyze the genome and expression of the genes of patients. The results are reflected directly in the treatment plan for the patient, in targeted medical inventions. This specialized mode of diagnostics has been restricted to account for averaged trends in the tumor. The approach sharply contrasts our knowledge on heterogeneity within tumors. Several studies further describe how treatment against one tumor subclone in some cases merely serves to provide space and support for uncontrolled growth of more aggressive subclones. In this chapter, we describe current possibilities for implementation of single cell sequencing of malignomas in clinic, as well as discuss hands-on practical advice for single cell routine diagnostics that allows for full delineation of tumor clonality.
Collapse
Affiliation(s)
- Frederik Otzen Bagger
- Department of Genomic Medicine, Rigshospitalet, Centre of Diagnostics, Section 4113, Copenhagen, Denmark.
| | - Victoria Probst
- Department of Genomic Medicine, Rigshospitalet, Centre of Diagnostics, Section 4113, Copenhagen, Denmark
| |
Collapse
|
103
|
Rai R, Gu P, Broton C, Kumar-Sinha C, Chen Y, Chang S. The Replisome Mediates A-NHEJ Repair of Telomeres Lacking POT1-TPP1 Independently of MRN Function. Cell Rep 2019; 29:3708-3725.e5. [PMID: 31825846 PMCID: PMC7001145 DOI: 10.1016/j.celrep.2019.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 09/22/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023] Open
Abstract
Telomeres use shelterin to protect chromosome ends from activating the DNA damage sensor MRE11-RAD50-NBS1 (MRN), repressing ataxia-telangiectasia, mutated (ATM) and ATM and Rad3-related (ATR) dependent DNA damage checkpoint responses. The MRE11 nuclease is thought to be essential for the resection of the 5' C-strand to generate the microhomologies necessary for alternative non-homologous end joining (A-NHEJ) repair. In the present study, we uncover DNA damage signaling and repair pathways engaged by components of the replisome complex to repair dysfunctional telomeres. In cells lacking MRN, single-stranded telomeric overhangs devoid of POT1-TPP1 do not recruit replication protein A (RPA), ATR-interacting protein (ATRIP), and RAD 51. Rather, components of the replisome complex, including Claspin, Proliferating cell nuclear antigen (PCNA), and Downstream neighbor of SON (DONSON), initiate DNA-PKcs-mediated p-CHK1 activation and A-NHEJ repair. In addition, Claspin directly interacts with TRF2 and recruits EXO1 to newly replicated telomeres to promote 5' end resection. Our data indicate that MRN is dispensable for the repair of dysfunctional telomeres lacking POT1-TPP1 and highlight the contributions of the replisome in telomere repair.
Collapse
Affiliation(s)
- Rekha Rai
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA.
| | - Peili Gu
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA
| | - Cayla Broton
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Tri-Institutional MD/PhD Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Yong Chen
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Sandy Chang
- Departments of Laboratory Medicine, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 330 Cedar St., New Haven, CT 06520, USA.
| |
Collapse
|
104
|
Álvarez-Escribano I, Sasse C, Bok JW, Na H, Amirebrahimi M, Lipzen A, Schackwitz W, Martin J, Barry K, Gutiérrez G, Cea-Sánchez S, Marcos AT, Grigoriev IV, Keller NP, Braus GH, Cánovas D. Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants. BMC Biol 2019; 17:88. [PMID: 31711484 PMCID: PMC6844060 DOI: 10.1186/s12915-019-0702-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/19/2019] [Indexed: 01/19/2023] Open
Abstract
Background Aspergillus spp. comprises a very diverse group of lower eukaryotes with a high relevance for industrial applications and clinical implications. These multinucleate species are often cultured for many generations in the laboratory, which can unknowingly propagate hidden genetic mutations. To assess the likelihood of such events, we studied the genome stability of aspergilli by using a combination of mutation accumulation (MA) lines and whole genome sequencing. Results We sequenced the whole genomes of 30 asexual and 10 sexual MA lines of three Aspergillus species (A. flavus, A. fumigatus and A. nidulans) and estimated that each MA line accumulated mutations for over 4000 mitoses during asexual cycles. We estimated mutation rates of 4.2 × 10−11 (A. flavus), 1.1 × 10−11 (A. fumigatus) and 4.1 × 10−11 (A. nidulans) per site per mitosis, suggesting that the genomes are very robust. Unexpectedly, we found a very high rate of GC → TA transversions only in A. flavus. In parallel, 30 asexual lines of the non-homologous end-joining (NHEJ) mutants of the three species were also allowed to accumulate mutations for the same number of mitoses. Sequencing of these NHEJ MA lines gave an estimated mutation rate of 5.1 × 10−11 (A. flavus), 2.2 × 10−11 (A. fumigatus) and 4.5 × 10−11 (A. nidulans) per base per mitosis, which is slightly higher than in the wild-type strains and some ~ 5–6 times lower than in the yeasts. Additionally, in A. nidulans, we found a NHEJ-dependent interference of the sexual cycle that is independent of the accumulation of mutations. Conclusions We present for the first time direct counts of the mutation rate of filamentous fungal species and find that Aspergillus genomes are very robust. Deletion of the NHEJ machinery results in a slight increase in the mutation rate, but at a rate we suggest is still safe to use for biotechnology purposes. Unexpectedly, we found GC→TA transversions predominated only in the species A. flavus, which could be generated by the hepatocarcinogen secondary metabolite aflatoxin. Lastly, a strong effect of the NHEJ mutation in self-crossing was observed and an increase in the mutations of the asexual lines was quantified.
Collapse
Affiliation(s)
- Isidro Álvarez-Escribano
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.,Present Address: Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
| | - Christoph Sasse
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Göttingen, Germany
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Gabriel Gutiérrez
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
| | - Sara Cea-Sánchez
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
| | - Ana T Marcos
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.,Present Address: Instituto para el Estudio de la Reproducción Humana (Inebir), Avda de la Cruz Roja 1, 41009, Sevilla, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Göttingen, Germany
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.
| |
Collapse
|
105
|
Tsegay PS, Lai Y, Liu Y. Replication Stress and Consequential Instability of the Genome and Epigenome. Molecules 2019; 24:molecules24213870. [PMID: 31717862 PMCID: PMC6864812 DOI: 10.3390/molecules24213870] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
Cells must faithfully duplicate their DNA in the genome to pass their genetic information to the daughter cells. To maintain genomic stability and integrity, double-strand DNA has to be replicated in a strictly regulated manner, ensuring the accuracy of its copy number, integrity and epigenetic modifications. However, DNA is constantly under the attack of DNA damage, among which oxidative DNA damage is the one that most frequently occurs, and can alter the accuracy of DNA replication, integrity and epigenetic features, resulting in DNA replication stress and subsequent genome and epigenome instability. In this review, we summarize DNA damage-induced replication stress, the formation of DNA secondary structures, peculiar epigenetic modifications and cellular responses to the stress and their impact on the instability of the genome and epigenome mainly in eukaryotic cells.
Collapse
Affiliation(s)
- Pawlos S. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA;
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA;
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Correspondence:
| |
Collapse
|
106
|
Haynes B, Gajan A, Nangia-Makker P, Shekhar MP. RAD6B is a major mediator of triple negative breast cancer cisplatin resistance: Regulation of translesion synthesis/Fanconi anemia crosstalk and BRCA1 independence. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165561. [PMID: 31639439 DOI: 10.1016/j.bbadis.2019.165561] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/26/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022]
Abstract
Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype with few therapy options besides chemotherapy. Although platinum-based drugs have shown initial activity in BRCA1-mutated TNBCs, chemoresistance remains a challenge. Here we show that RAD6B (UBE2B), a principal mediator of translesion synthesis (TLS), is overexpressed in BRCA1 wild-type and mutant TNBCs, and RAD6B overexpression correlates with poor survival. Pretreatment with a RAD6-selective inhibitor, SMI#9, enhanced cisplatin chemosensitivity of BRCA1 wild-type and mutant TNBCs. SMI#9 attenuated cisplatin-induced PCNA monoubiquitination (TLS marker), FANCD2 (Fanconi anemia (FA) activation marker), and TLS polymerase POL η. SMI#9-induced decreases in γH2AX levels were associated with concomitant inhibition of H2AX monoubiquitination, suggesting a key role for RAD6 in modulating cisplatin-induced γH2AX via H2AX monoubiquitination. Concordantly, SMI#9 inhibited γH2AX, POL η and FANCD2 foci formation. RAD51 foci formation was unaffected by SMI#9, however, its recruitment to double-strand breaks was inhibited. Using the DR-GFP-based assay, we showed that RAD6B silencing or SMI#9 treatment impairs homologous recombination (HR) in HR-proficient cells. DNA fiber assays confirmed that restart of cisplatin-stalled replicating forks is inhibited by SMI#9 in both BRCA1 wild-type and mutant TNBC cells. Consistent with the in vitro data, SMI#9 and cisplatin combination treatment inhibited BRCA1 wild-type and mutant TNBC growth as compared to controls. These RAD6B activities are unaffected by BRCA1 status of TNBCs suggesting that the RAD6B function in TLS/FA crosstalk could occur in HR-dependent and independent modes. Collectively, these data implicate RAD6 as an important therapeutic target for TNBCs irrespective of their BRCA1 status.
Collapse
Affiliation(s)
- Brittany Haynes
- Karmanos Cancer Institute, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA
| | - Ambikai Gajan
- Karmanos Cancer Institute, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA
| | - Pratima Nangia-Makker
- Karmanos Cancer Institute, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA
| | - Malathy P Shekhar
- Karmanos Cancer Institute, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Pathology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA.
| |
Collapse
|
107
|
Jiménez M, Urtasun R, Elizalde M, Azkona M, Latasa MU, Uriarte I, Arechederra M, Alignani D, Bárcena-Varela M, Álvarez-Sola G, Colyn L, Santamaría E, Sangro B, Rodriguez-Ortigosa C, Fernández-Barrena MG, Ávila MA, Berasain C. Splicing events in the control of genome integrity: role of SLU7 and truncated SRSF3 proteins. Nucleic Acids Res 2019; 47:3450-3466. [PMID: 30657957 PMCID: PMC6468163 DOI: 10.1093/nar/gkz014] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/21/2018] [Accepted: 01/08/2019] [Indexed: 12/13/2022] Open
Abstract
Genome instability is related to disease development and carcinogenesis. DNA lesions are caused by genotoxic compounds but also by the dysregulation of fundamental processes like transcription, DNA replication and mitosis. Recent evidence indicates that impaired expression of RNA-binding proteins results in mitotic aberrations and the formation of transcription-associated RNA-DNA hybrids (R-loops), events strongly associated with DNA injury. We identify the splicing regulator SLU7 as a key mediator of genome stability. SLU7 knockdown results in R-loops formation, DNA damage, cell-cycle arrest and severe mitotic derangements with loss of sister chromatid cohesion (SCC). We define a molecular pathway through which SLU7 keeps in check the generation of truncated forms of the splicing factor SRSF3 (SRp20) (SRSF3-TR). Behaving as dominant negative, or by gain-of-function, SRSF3-TR impair the correct splicing and expression of the splicing regulator SRSF1 (ASF/SF2) and the crucial SCC protein sororin. This unique function of SLU7 was found in cancer cells of different tissue origin and also in the normal mouse liver, demonstrating a conserved and fundamental role of SLU7 in the preservation of genome integrity. Therefore, the dowregulation of SLU7 and the alterations of this pathway that we observe in the cirrhotic liver could be involved in the process of hepatocarcinogenesis.
Collapse
Affiliation(s)
- Maddalen Jiménez
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Raquel Urtasun
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain
| | - María Elizalde
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - María Azkona
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - M Ujue Latasa
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Iker Uriarte
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - María Arechederra
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Diego Alignani
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,Cytometry Unit, CIMA, University of Navarra, Pamplona 31008, Spain
| | | | - Gloria Álvarez-Sola
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Leticia Colyn
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain
| | - Eva Santamaría
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Bruno Sangro
- Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain.,Hepatology Unit, Navarra University Clinic, Pamplona 31008, Spain
| | - Carlos Rodriguez-Ortigosa
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Maite G Fernández-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Matías A Ávila
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Carmen Berasain
- Hepatology Program, CIMA, University of Navarra, Pamplona 31008, Spain.,Instituto de Investigaciones Sanitarias de Navarra-IdiSNA, Pamplona 31008, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid 28029, Spain
| |
Collapse
|
108
|
Abstract
New therapies that promote antitumour immunity have been recently developed. Most of these immunomodulatory approaches have focused on enhancing T-cell responses, either by targeting inhibitory pathways with immune checkpoint inhibitors, or by targeting activating pathways, as with chimeric antigen receptor T cells or bispecific antibodies. Although these therapies have led to unprecedented successes, only a minority of patients with cancer benefit from these treatments, highlighting the need to identify new cells and molecules that could be exploited in the next generation of immunotherapy. Given the crucial role of innate immune responses in immunity, harnessing these responses opens up new possibilities for long-lasting, multilayered tumour control.
Collapse
|
109
|
Replication Stress Response Links RAD52 to Protecting Common Fragile Sites. Cancers (Basel) 2019; 11:cancers11101467. [PMID: 31569559 PMCID: PMC6826974 DOI: 10.3390/cancers11101467] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022] Open
Abstract
Rad52 in yeast is a key player in homologous recombination (HR), but mammalian RAD52 is dispensable for HR as shown by the lack of a strong HR phenotype in RAD52-deficient cells and in RAD52 knockout mice. RAD52 function in mammalian cells first emerged with the discovery of its important backup role to BRCA (breast cancer genes) in HR. Recent new evidence further demonstrates that RAD52 possesses multiple activities to cope with replication stress. For example, replication stress-induced DNA repair synthesis in mitosis (MiDAS) and oncogene overexpression-induced DNA replication are dependent on RAD52. RAD52 becomes essential in HR to repair DSBs containing secondary structures, which often arise at collapsed replication forks. RAD52 is also implicated in break-induced replication (BIR) and is found to inhibit excessive fork reversal at stalled replication forks. These various functions of RAD52 to deal with replication stress have been linked to the protection of genome stability at common fragile sites, which are often associated with the DNA breakpoints in cancer. Therefore, RAD52 has important recombination roles under special stress conditions in mammalian cells, and presents as a promising anti-cancer therapy target.
Collapse
|
110
|
Gourzones C, Bret C, Moreaux J. Treatment May Be Harmful: Mechanisms/Prediction/Prevention of Drug-Induced DNA Damage and Repair in Multiple Myeloma. Front Genet 2019; 10:861. [PMID: 31620167 PMCID: PMC6759943 DOI: 10.3389/fgene.2019.00861] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/19/2019] [Indexed: 12/28/2022] Open
Abstract
Multiple myeloma (MM) is a malignancy characterized by accumulation of malignant plasma cells within the bone marrow (BM). MM is considered mostly without definitive treatment because of the inability of standard of care therapies to overcome drug-resistant relapse. Genotoxic agents are used in the treatment of MM and exploit the fact that DNA double-strand breaks are highly cytotoxic for cancer cells. However, their mutagenic effects are well-established and described. According to these effects, chemotherapy could cause harmful DNA damage associated with new driver genomic abnormalities providing selective advantage, drug resistance, and higher relapse risk. Several mechanisms associated with MM cell (MMC) resistance to genotoxic agents have been described, underlining MM heterogeneity. The understanding of these mechanisms provides several therapeutic strategies to overcome drug resistance and limit mutagenic effects of treatment in MM. According to this heterogeneity, adopting precision medicine into clinical practice, with the development of biomarkers, has the potential to improve MM disease management and treatment.
Collapse
Affiliation(s)
| | - Caroline Bret
- IGH, CNRS, Univ Montpellier, France.,Department of Biological Hematology, CHU Montpellier, Montpellier, France.,Univ Montpellier, UFR de Médecine, Montpellier, France
| | - Jerome Moreaux
- IGH, CNRS, Univ Montpellier, France.,Department of Biological Hematology, CHU Montpellier, Montpellier, France.,Univ Montpellier, UFR de Médecine, Montpellier, France.,Institut Universitaire de France, Paris, France
| |
Collapse
|
111
|
Erkilic N, Gatinois V, Torriano S, Bouret P, Sanjurjo-Soriano C, Luca VD, Damodar K, Cereso N, Puechberty J, Sanchez-Alcudia R, Hamel CP, Ayuso C, Meunier I, Pellestor F, Kalatzis V. A Novel Chromosomal Translocation Identified due to Complex Genetic Instability in iPSC Generated for Choroideremia. Cells 2019; 8:cells8091068. [PMID: 31514470 PMCID: PMC6770680 DOI: 10.3390/cells8091068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/28/2019] [Accepted: 09/07/2019] [Indexed: 12/19/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have revolutionized the study of human diseases as they can renew indefinitely, undergo multi-lineage differentiation, and generate disease-specific models. However, the difficulty of working with iPSCs is that they are prone to genetic instability. Furthermore, genetically unstable iPSCs are often discarded, as they can have unforeseen consequences on pathophysiological or therapeutic read-outs. We generated iPSCs from two brothers of a previously unstudied family affected with the inherited retinal dystrophy choroideremia. We detected complex rearrangements involving chromosomes 12, 20 and/or 5 in the generated iPSCs. Suspecting an underlying chromosomal aberration, we performed karyotype analysis of the original fibroblasts, and of blood cells from additional family members. We identified a novel chromosomal translocation t(12;20)(q24.3;q11.2) segregating in this family. We determined that the translocation was balanced and did not impact subsequent retinal differentiation. We show for the first time that an undetected genetic instability in somatic cells can breed further instability upon reprogramming. Therefore, the detection of chromosomal aberrations in iPSCs should not be disregarded, as they may reveal rearrangements segregating in families. Furthermore, as such rearrangements are often associated with reproductive failure or birth defects, this in turn has important consequences for genetic counseling of family members.
Collapse
Affiliation(s)
- Nejla Erkilic
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Vincent Gatinois
- Chromosomal Genetics Unit, Chromostem Platform, CHU, Montpellier, France
| | - Simona Torriano
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Pauline Bouret
- Chromosomal Genetics Unit, Chromostem Platform, CHU, Montpellier, France
| | - Carla Sanjurjo-Soriano
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Valerie De Luca
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Krishna Damodar
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Nicolas Cereso
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
| | - Jacques Puechberty
- Service of Clinical Genetics, Department of Medical Genetics, Rare Diseases and Personalized Medicine, CHU, Montpellier, France
| | - Rocio Sanchez-Alcudia
- Department of Genetics, Institute for Sanitary Investigation, Foundation Jimenez Diaz, 28040 Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Christian P Hamel
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, CHU, 34295 Montpellier, France
| | - Carmen Ayuso
- Department of Genetics, Institute for Sanitary Investigation, Foundation Jimenez Diaz, 28040 Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Isabelle Meunier
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France
- University of Montpellier, 34090 Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, CHU, 34295 Montpellier, France
| | - Franck Pellestor
- Chromosomal Genetics Unit, Chromostem Platform, CHU, Montpellier, France
| | - Vasiliki Kalatzis
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier CEDEX 5, France.
- University of Montpellier, 34090 Montpellier, France.
| |
Collapse
|
112
|
Shen L, Wang Q, Liu R, Chen Z, Zhang X, Zhou P, Wang Z. LncRNA lnc-RI regulates homologous recombination repair of DNA double-strand breaks by stabilizing RAD51 mRNA as a competitive endogenous RNA. Nucleic Acids Res 2019; 46:717-729. [PMID: 29216366 PMCID: PMC5778505 DOI: 10.1093/nar/gkx1224] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/25/2017] [Indexed: 12/11/2022] Open
Abstract
DNA double-strand break (DSB) repair is critical for the maintenance of genome stability. The current models of the mechanism of DSB repair are based on studies of DNA repair proteins. Long non-coding RNAs (lncRNAs) have recently emerged as new regulatory molecules, with diverse functions in biological processes. In the present study, we found that expression of the ionizing radiation-inducible lncRNA, lnc-RI, was correlate negatively with micronucleus frequencies in human peripheral blood lymphocytes. Knockdown of lnc-RI significantly increased spontaneous DSBs levels, which was confirmed to be associated with the decreased efficiency of homologous recombination (HR) repair of DSBs. The expression of RAD51, a key recombinase in the HR pathway, decreased sharply in lnc-RI-depressed cells. In a further investigation, we demonstrated that miR-193a-3p could bind with both lnc-RI and RAD51 mRNA and depressed the expression of lnc-RI and RAD51 mRNA. Lnc-RI acted as a competitive endogenous RNA (ceRNA) to stabilize RAD51 mRNA via competitive binding with miR-193a-3p and release of its inhibition of RAD51 expression. To our knowledge, this is the first study to demonstrate the role of lnc-RI in regulating HR repair of DSBs. The feedback loop established in the current study suggests that lnc-RI is critical for the maintenance of genomic stability.
Collapse
Affiliation(s)
- Liping Shen
- School of Radiation Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, Jiangsu 215123, PR China.,Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Qi Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Ruixue Liu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Zhongmin Chen
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Xueqing Zhang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Pingkun Zhou
- School of Radiation Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, Jiangsu 215123, PR China.,Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| | - Zhidong Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, PR China
| |
Collapse
|
113
|
Deng Y, Luo S, Deng C, Luo T, Yin W, Zhang H, Zhang Y, Zhang X, Lan Y, Ping Y, Xiao Y, Li X. Identifying mutual exclusivity across cancer genomes: computational approaches to discover genetic interaction and reveal tumor vulnerability. Brief Bioinform 2019; 20:254-266. [PMID: 28968730 DOI: 10.1093/bib/bbx109] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Indexed: 02/06/2023] Open
Abstract
Systematic sequencing of cancer genomes has revealed prevalent heterogeneity, with patients harboring various combinatorial patterns of genetic alteration. In particular, a phenomenon that a group of genes exhibits mutually exclusive patterns has been widespread across cancers, covering a broad spectrum of crucial cancer pathways. Recently, there is considerable evidence showing that, mutual exclusivity reflects alternative functions in tumor initiation and progression, or suggests adverse effects of their concurrence. Given its importance, numerous computational approaches have been proposed to study mutual exclusivity using genomic profiles alone, or by integrating networks and phenotypes. Some of them have been routinely used to explore genetic associations, which lead to a deeper understanding of carcinogenic mechanisms and reveals unexpected tumor vulnerabilities. Here, we present an overview of mutual exclusivity from the perspective of cancer genome. We describe the common hypothesis underlying mutual exclusivity, summarize the strategies for the identification of significant mutually exclusive patterns, compare the performance of representative algorithms from simulated data sets and discuss their common confounders.
Collapse
Affiliation(s)
- Yulan Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shangyi Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Tao Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Wenkang Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongyi Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| |
Collapse
|
114
|
Kuhns KJ, Lopez-Bertoni H, Coulter JB, Bressler JP. TET1 regulates DNA repair in human glial cells. Toxicol Appl Pharmacol 2019; 380:114646. [PMID: 31278917 DOI: 10.1016/j.taap.2019.114646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 12/21/2022]
Abstract
Glioblastomas are the most aggressive of malignant brain cancers with a median patient survival of approximately 18 months. We recently demonstrated that Tet methylcytosine dioxygenase 1(TET1) is involved in cellular responses to ionizing radiation (IR) in glial-, glioblastoma-, and non-tumor-derived cells. This study used a lentiviral-mediated knockdown of TET1 to further dissect the contribution of TET1 to the DNA damage response in glial cell lines by evaluating its role in DNA repair. TET1-deficient glial cell lines displayed attenuated cytotoxicity compared to non-targeted knockdown after treatment with IR but these differences were not observed between control and TET1 deficient in response to inhibitors of Na+/K+-ATPase. Additionally, the percentage of glial cells displaying γH2A.x foci was greatly reduced in TET1-deficient glial cells compared to non-targeted knockdown conditions in response to IR and topoisomerase inhibitors. We also observed a lower percentage and a delay in 53BP1 foci formation, a marker of non-homologous end-joining, in response to IR and topoisomerase inhibitors in TET1-deficient glial cells. DNA-PK, another marker of non-homologous end-joining, was also lower in TET1-deficient glial cell lines. Interestingly, TET1-deficient glial cells displayed higher numbers of DNA strand breaks compared to control cells and repaired DNA breaks less efficiently in Comet assays. We suggest that attenuated DNA repair in TET1 deficient gliomas leads to genomic instability, which underlies poor patient survival.
Collapse
Affiliation(s)
- Katherine J Kuhns
- Environmental Health Sciences, The Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Hernando Lopez-Bertoni
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Jonathan B Coulter
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD 21205, USA; Environmental Health Sciences, The Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Joseph P Bressler
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 707 N. Broadway, Baltimore, MD 21205, USA; Environmental Health Sciences, The Johns Hopkins University Bloomberg School of Public Health, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD 21287, USA.
| |
Collapse
|
115
|
Yu R, Sun L, Sun Y, Han X, Qin L, Dang W. Cellular response to moderate chromatin architectural defects promotes longevity. SCIENCE ADVANCES 2019; 5:eaav1165. [PMID: 31309140 PMCID: PMC6620092 DOI: 10.1126/sciadv.aav1165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 05/30/2019] [Indexed: 05/05/2023]
Abstract
Changes in chromatin organization occur during aging. Overexpression of histones partially alleviates these changes and promotes longevity. We report that deletion of the histone H3-H4 minor locus HHT1-HHF1 extended the replicative life span of Saccharomyces cerevisiae. This longevity effect was mediated through TOR signaling inhibition. We present evidence for evolutionarily conserved transcriptional and phenotypic responses to defects in chromatin structure, collectively termed the chromatin architectural defect (CAD) response. Promoters of the CAD response genes were sensitive to histone dosage, with HHT1-HHF1 deletion, nucleosome occupancy was reduced at these promoters allowing transcriptional activation induced by stress response transcription factors Msn2 and Gis1, both of which were required for the life-span extension of hht1-hhf1Δ. Therefore, we conclude that the CAD response induced by moderate chromatin defects promotes longevity.
Collapse
Affiliation(s)
- Ruofan Yu
- Department of Molecular and Human Genetics, and Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luyang Sun
- Department of Molecular and Human Genetics, and Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yu Sun
- Department of Molecular and Human Genetics, and Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xin Han
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, and Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Corresponding author.
| |
Collapse
|
116
|
Elbadawy M, Usui T, Yamawaki H, Sasaki K. Emerging Roles of C-Myc in Cancer Stem Cell-Related Signaling and Resistance to Cancer Chemotherapy: A Potential Therapeutic Target Against Colorectal Cancer. Int J Mol Sci 2019; 20:E2340. [PMID: 31083525 PMCID: PMC6539579 DOI: 10.3390/ijms20092340] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 04/29/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022] Open
Abstract
Myc is a nuclear transcription factor that mainly regulates cell growth, cell cycle, metabolism, and survival. Myc family proteins contain c-Myc, n-Myc, and l-Myc. Among them, c-Myc can become a promising therapeutic target molecule in cancer. Cancer stem cells (CSCs) are known to be responsible for the therapeutic resistance. In the previous study, we demonstrated that c-Myc mediates drug resistance of colorectal CSCs using a patient-derived primary three-dimensional (3D) organoid culture. In this review, we mainly focus on the roles of c-Myc-related signaling in the regulation of CSCs, chemotherapy resistance, and colorectal cancer organoids. Finally, we introduce the various types of c-Myc inhibitors and propose the possibility of c-Myc as a therapeutic target against colorectal cancer.
Collapse
Affiliation(s)
- Mohamed Elbadawy
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
- Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya 13736, Egypt.
| | - Tatsuya Usui
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
| | - Hideyuki Yamawaki
- Laboratory of Veterinary Pharmacology, School of Veterinary Medicine, Kitasato University, Towada, Aomori 034-8628, Japan.
| | - Kazuaki Sasaki
- Laboratory of Veterinary Pharmacology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan.
| |
Collapse
|
117
|
Cheloshkina K, Poptsova M. Tissue-specific impact of stem-loops and quadruplexes on cancer breakpoints formation. BMC Cancer 2019; 19:434. [PMID: 31077166 PMCID: PMC6511154 DOI: 10.1186/s12885-019-5653-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/29/2019] [Indexed: 12/30/2022] Open
Abstract
Background Chromosomal rearrangements are the typical phenomena in cancer genomes causing gene disruptions and fusions, corruption of regulatory elements, damage to chromosome integrity. Among the factors contributing to genomic instability are non-B DNA structures with stem-loops and quadruplexes being the most prevalent. We aimed at investigating the impact of specifically these two classes of non-B DNA structures on cancer breakpoint hotspots using machine learning approach. Methods We developed procedure for machine learning model building and evaluation as the considered data are extremely imbalanced and it was required to get a reliable estimate of the prediction power. We built logistic regression models predicting cancer breakpoint hotspots based on the densities of stem-loops and quadruplexes, jointly and separately. We also tested Random Forest models varying different resampling schemes (leave-one-out cross validation, train-test split, 3-fold cross-validation) and class balancing techniques (oversampling, stratification, synthetic minority oversampling). Results We performed analysis of 487,425 breakpoints from 2234 samples covering 10 cancer types available from the International Cancer Genome Consortium. We showed that distribution of breakpoint hotspots in different types of cancer are not correlated, confirming the heterogeneous nature of cancer. It appeared that stem-loop-based model best explains the blood, brain, liver, and prostate cancer breakpoint hotspot profiles while quadruplex-based model has higher performance for the bone, breast, ovary, pancreatic, and skin cancer. For the overall cancer profile and uterus cancer the joint model shows the highest performance. For particular datasets the constructed models reach high predictive power using just one predictor, and in the majority of the cases, the model built on both predictors does not increase the model performance. Conclusion Despite the heterogeneity in breakpoint hotspots’ distribution across different cancer types, our results demonstrate an association between cancer breakpoint hotspots and stem-loops and quadruplexes. Approximately for half of the cancer types stem-loops are the most influential factors while for the others these are quadruplexes. This fact reflects the differences in regulatory potential of stem-loops and quadruplexes at the tissue-specific level, which yet to be discovered at the genome-wide scale. The performed analysis demonstrates that influence of stem-loops and quadruplexes on breakpoint hotspots formation is tissue-specific. Electronic supplementary material The online version of this article (10.1186/s12885-019-5653-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kseniia Cheloshkina
- Faculty of Computer Science, National Research University Higher School of Economics, 125319, Moscow, 3 Kochnovsky Proezd, Russia
| | - Maria Poptsova
- Faculty of Computer Science, National Research University Higher School of Economics, 125319, Moscow, 3 Kochnovsky Proezd, Russia.
| |
Collapse
|
118
|
Pellestor F, Gatinois V. Chromoanasynthesis: another way for the formation of complex chromosomal abnormalities in human reproduction. Hum Reprod 2019; 33:1381-1387. [PMID: 30325427 DOI: 10.1093/humrep/dey231] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Indexed: 12/24/2022] Open
Abstract
Chromoanasynthesis has been described as a novel cause of massive constitutional chromosomal rearrangements. Based on DNA replication machinery defects, chromoanasynthesis is characterized by the presence of chromosomal duplications and triplications locally clustered on one single chromosome, or a few chromosomes, associated with various other types of structural rearrangements. Two distinct mechanisms have been described for the formation of these chaotic genomic disorders, i.e. the fork stalling and template switching and the microhomology-mediated break-induced replication. Micronucleus-based processes have been evidenced as a causative mechanism, thus, highlighting the close connection between segregation errors and structural rearrangements. Accumulating data indicate that chromoanasynthesis is operating in human germline cells and during early embryonic development. The development of new tools for quantifying chromoanasynthesis events should provide further insight into the impact of this catastrophic cellular phenomenon in human reproduction.
Collapse
Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
| | - Vincent Gatinois
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, Montpellier, France
| |
Collapse
|
119
|
Kumar R, Nagpal G, Kumar V, Usmani SS, Agrawal P, Raghava GPS. HumCFS: a database of fragile sites in human chromosomes. BMC Genomics 2019; 19:985. [PMID: 30999860 PMCID: PMC7402404 DOI: 10.1186/s12864-018-5330-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/29/2018] [Indexed: 11/25/2022] Open
Abstract
Background Fragile sites are the chromosomal regions that are susceptible to breakage, and their frequency varies among the human population. Based on the frequency of fragile site induction, they are categorized as common and rare fragile sites. Common fragile sites are sensitive to replication stress and often rearranged in cancer. Rare fragile sites are the archetypal trinucleotide repeats. Fragile sites are known to be involved in chromosomal rearrangements in tumors. Human miRNA genes are also present at fragile sites. A better understanding of genes and miRNAs lying in the fragile site regions and their association with disease progression is required. Result HumCFS is a manually curated database of human chromosomal fragile sites. HumCFS provides useful information on fragile sites such as coordinates on the chromosome, cytoband, their chemical inducers and frequency of fragile site (rare or common), genes and miRNAs lying in fragile sites. Protein coding genes in the fragile sites were identified by mapping the coordinates of fragile sites with human genome Ensembl (GRCh38/hg38). Genes present in fragile sites were further mapped to DisGenNET database, to understand their possible link with human diseases. Human miRNAs from miRBase was also mapped on fragile site coordinates. In brief, HumCFS provides useful information about 125 human chromosomal fragile sites and their association with 4921 human protein-coding genes and 917 human miRNA’s. Conclusion User-friendly web-interface of HumCFS and hyper-linking with other resources will help researchers to search for genes, miRNAs efficiently and to intersect the relationship among them. For easy data retrieval and analysis, we have integrated standard web-based tools, such as JBrowse, BLAST etc. Also, the user can download the data in various file formats such as text files, gff3 files and Bed-format files which can be used on UCSC browser. Database URL:http://webs.iiitd.edu.in/raghava/humcfs/ Electronic supplementary material The online version of this article (10.1186/s12864-018-5330-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rajesh Kumar
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, 110020, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Gandharva Nagpal
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Vinod Kumar
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, 110020, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Salman Sadullah Usmani
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, 110020, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Piyush Agrawal
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, 110020, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Gajendra P S Raghava
- Center for Computational Biology, Indraprastha Institute of Information Technology, New Delhi, 110020, India.
| |
Collapse
|
120
|
Dukić M, Berner D, Haag CR, Ebert D. How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna. J Evol Biol 2019; 32:619-628. [PMID: 30888725 PMCID: PMC6850383 DOI: 10.1111/jeb.13443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 03/04/2019] [Indexed: 12/25/2022]
Abstract
Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within‐individual allelic divergence (heterozygosity); however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high‐throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by restriction site‐associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re‐sequenced the top 17 candidate RAD‐loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.
Collapse
Affiliation(s)
- Marinela Dukić
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive-CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, campus CNRS, Montpellier, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Dieter Ebert
- Zoological Institute, University of Basel, Basel, Switzerland
| |
Collapse
|
121
|
Reilly NM, Novara L, Di Nicolantonio F, Bardelli A. Exploiting DNA repair defects in colorectal cancer. Mol Oncol 2019; 13:681-700. [PMID: 30714316 PMCID: PMC6441925 DOI: 10.1002/1878-0261.12467] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/11/2019] [Accepted: 01/19/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third leading cause of cancer-related deaths worldwide. Therapies that take advantage of defects in DNA repair pathways have been explored in the context of breast, ovarian, and other tumor types, but not yet systematically in CRC. At present, only immune checkpoint blockade therapies have been FDA approved for use in mismatch repair-deficient colorectal tumors. Here, we discuss how systematic identification of alterations in DNA repair genes could provide new therapeutic opportunities for CRCs. Analysis of The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) and Rectal Adenocarcinoma (TCGA-READ) PanCancer Atlas datasets identified 141 (out of 528) cases with putative driver mutations in 29 genes associated with DNA damage response and repair, including the mismatch repair and homologous recombination pathways. Genetic defects in these pathways might confer repair-deficient characteristics, such as genomic instability in the absence of homologous recombination, which can be exploited. For example, inhibitors of poly(ADP)-ribose polymerase are effectively used to treat cancers that carry mutations in BRCA1 and/or BRCA2 and have shown promising results in CRC preclinical studies. HR deficiency can also occur in cells with no detectable BRCA1/BRCA2 mutations but exhibiting BRCA-like phenotypes. DNA repair-targeting therapies, such as ATR and CHK1 inhibitors (which are most effective against cancers carrying ATM mutations), can be used in combination with current genotoxic chemotherapies in CRCs to further improve therapy response. Finally, therapies that target alternative DNA repair mechanisms, such as thiopurines, also have the potential to confer increased sensitivity to current chemotherapy regimens, thus expanding the spectrum of therapy options and potentially improving clinical outcomes for CRC patients.
Collapse
Affiliation(s)
- Nicole M. Reilly
- Fondazione Piemontese per la Ricerca sul Cancro ONLUSCandioloItaly
| | - Luca Novara
- Candiolo Cancer InstituteFPO‐IRCCSCandioloItaly
| | - Federica Di Nicolantonio
- Candiolo Cancer InstituteFPO‐IRCCSCandioloItaly
- Department of OncologyUniversity of TorinoCandioloItaly
| | - Alberto Bardelli
- Candiolo Cancer InstituteFPO‐IRCCSCandioloItaly
- Department of OncologyUniversity of TorinoCandioloItaly
| |
Collapse
|
122
|
Abstract
Green tea polyphenols may protect cells from UV damage through antioxidant activities and by stimulating the removal of damaged or cross-linked DNA. Recently, DNA repair pathways have been predicted as possible targets of epigallocatechin gallate (EGCG)-initiated signaling. However, whether and how green tea polyphenols can promote nucleotide excision repair and homologous recombination in diverse organisms requires further investigation. In this report, we used the budding yeast, Saccharomyces cerevisiae, as a model to investigate the effects of green tea extract on DNA repair pathways. We first showed that green tea extract increased the survival rate and decreased the frequency of mutations in yeast exposed to UVB-irradiation. Furthermore, green tea extract increased the expression of homologous recombination genes, RFA1, RAD51 and RAD52, and nucleotide excision repair genes, RAD4 and RAD14. Importantly, we further used a specific strand invasion assay to show that green tea extract promotes homologous recombination at double-strand breaks. Thus, green tea extract acts to preserve genome stability by activating DNA repair pathways in yeast. Because homologous recombination repair is highly conserved in yeast and humans, this study demonstrates yeast may be a useful platform for future research to investigate the underlying mechanisms of the bioactive compounds in DNA repair.
Collapse
|
123
|
Downregulation of c-Myc and p21 expression and induction of S phase arrest by naphthalene diimide derivative in gastric adenocarcinoma cells. Chem Biol Interact 2019; 304:106-123. [PMID: 30840857 DOI: 10.1016/j.cbi.2019.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/23/2019] [Accepted: 02/14/2019] [Indexed: 12/13/2022]
Abstract
Naphthalene diimide (NDI) derivatives have been shown to exhibit promising antineoplastic properties. In the current study, we assessed the anticancer and anti-bacterial properties of di-substituted NDI derivative. The naphthalene-bis-hydrazimide, 1, negatively affected the cell viability of three cancer cell lines (AGS, HeLa and PC3) and induced S phase cell cycle arrest along with SubG0/G1 accumulation. Amongst three cell lines, gastric cancer cell line, AGS, showed the highest sensitivity towards the NDI derivative 1. Compound 1 induced extensive DNA double strand breaks causing p53 activation leading to transcription of p53 target gene p21 in AGS cells. Reduction in protein levels of p21 and BRCA1 suggested that 1 treated AGS cells underwent cell death due to accumulation of DNA damage as a result of impaired DNA damage repair. β-catenin downregulation and consequently decrease in levels of c-Myc may have led to 1 induced AGS cell proliferation inhibition.1 induced AGS cell S phase arrest was mediated through CylinA/CDK2 downregulation. The possible mechanisms involved in anticancer activity of 1 includes ROS upregulation, induction of DNA damage, disruption of mitochondrial membrane potential causing ATP depletion, inhibition of cell proliferation and downregulation of antiapoptotic factors ultimately leading to mitochondria mediated apoptosis. Further compound 1 also inhibited H. pylori proliferation as well as H. pylori induced morphological changes in AGS cells. These findings suggest that NDI derivative 1 exhibits two-pronged anticancer activity, one by directly inhibiting cancer cell growth and inducing apoptosis and the other by inhibiting H. pylori.
Collapse
|
124
|
Pellestor F. Chromoanagenesis: cataclysms behind complex chromosomal rearrangements. Mol Cytogenet 2019; 12:6. [PMID: 30805029 PMCID: PMC6371609 DOI: 10.1186/s13039-019-0415-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background During the last decade, genome sequencing projects in cancer genomes as well as in patients with congenital diseases and healthy individuals have led to the identification of new types of massive chromosomal rearrangements arising during single chaotic cellular events. These unanticipated catastrophic phenomenon are termed chromothripsis, chromoanasynthesis and chromoplexis., and are grouped under the name of “chromoanagenesis”. Results For each process, several specific features have been described, allowing each phenomenon to be distinguished from each other and to understand its mechanism of formation and to better understand its aetiology. Thus, chromothripsis derives from chromosome shattering followed by the random restitching of chromosomal fragments with low copy-number change whereas chromoanasynthesis results from erroneous DNA replication of a chromosome through serial fork stalling and template switching with variable copy-number gains, and chromoplexy refers to the occurrence of multiple inter-and intra-chromosomal translocations and deletions with little or no copy-number alterations in prostate cancer. Cumulating data and experimental models have shown that chromothripsis and chromoanasynthesis may essentially result from lagging chromosome encapsulated in micronuclei or telomere attrition and end-to-end telomere fusion. Conclusion The concept of chromanagenesis has provided new insight into the aetiology of complex structural rearrangements, the connection between defective cell cycle progression and genomic instability, and the complexity of cancer evolution. Increasing reported chromoanagenesis events suggest that these chaotic mechanisms are probably much more frequent than anticipated.
Collapse
Affiliation(s)
- Franck Pellestor
- Unit of Chromosomal Genetics, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHRU, 371, avenue du Doyen Gaston Giraud, 34295 Montpellier cedex 5, France.,INSERM 1183 Unit «Genome and Stem Cell Plasticity in Development and Aging », Institute of Regenerative Medicine and Biotherapies, St Eloi Hospital, Montpellier, France
| |
Collapse
|
125
|
van Gijn SE, Wierenga E, van den Tempel N, Kok YP, Heijink AM, Spierings DCJ, Foijer F, van Vugt MATM, Fehrmann RSN. TPX2/Aurora kinase A signaling as a potential therapeutic target in genomically unstable cancer cells. Oncogene 2019; 38:852-867. [PMID: 30177840 PMCID: PMC6367211 DOI: 10.1038/s41388-018-0470-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/30/2018] [Accepted: 07/30/2018] [Indexed: 12/17/2022]
Abstract
Genomic instability is a hallmark feature of cancer cells, and can be caused by defective DNA repair, for instance due to inactivation of BRCA2. Paradoxically, loss of Brca2 in mice results in embryonic lethality, whereas cancer cells can tolerate BRCA2 loss. This holds true for multiple DNA repair genes, and suggests that cancer cells are molecularly "rewired" to cope with defective DNA repair and the resulting high levels of genomic instability. In this study, we aim to identify genes that genomically unstable cancer cells rely on for their survival. Using functional genomic mRNA (FGmRNA) profiling, 16,172 cancer samples were previously ranked based on their degree of genomic instability. We analyzed the top 250 genes that showed a positive correlation between FGmRNA levels and the degree of genomic instability, in a co-functionality network. Within this co-functionality network, a strong cluster of 11 cell cycle-related genes was identified, including TPX2. We then assessed the dependency on these 11 genes in the context of survival of genomically unstable cancer cells, induced by BRCA2 inactivation. Depletion of TPX2 or its associated kinase Aurora-A preferentially reduced cell viability in a panel of BRCA2-deficient cancer cells. In line with these findings, BRCA2-depleted and BRCA2-mutant human cell lines, or tumor cell lines derived from Brca2-/-;p53-/- mice showed increased sensitivity to the Aurora-A kinase inhibitor alisertib, with delayed mitotic progression and frequent mitotic failure. Our findings reveal that BRCA2-deficient cancer cells show enhanced sensitivity to inactivation of TPX2 or its partner Aurora-A, which points at an actionable dependency of genomically unstable cancers.
Collapse
Affiliation(s)
- Stephanie E van Gijn
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elles Wierenga
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Nathalie van den Tempel
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anne Margriet Heijink
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Rudolf S N Fehrmann
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| |
Collapse
|
126
|
Abstract
A tumor is made up of a heterogeneous collection of cell types, all competing on a fitness landscape mediated by microenvironmental conditions that dictate their interactions. Despite the fact that much is known about cell signaling, cellular cooperation, and the functional constraints that affect cellular behavior, the specifics of how these constraints (and the range over which they act) affect the macroscopic tumor growth laws that govern total volume, mass, and carrying capacity remain poorly understood. We develop a statistical mechanics approach that focuses on the total number of possible states each cell can occupy and show how different assumptions on correlations of these states give rise to the many different macroscopic tumor growth laws used in the literature. Although it is widely understood that molecular and cellular heterogeneity within a tumor is a driver of growth, here we emphasize that focusing on the functional coupling of states at the cellular level is what determines macroscopic growth characteristics.
Collapse
|
127
|
A new role for Drosophila Aurora-A in maintaining chromosome integrity. Chromosoma 2019; 128:41-52. [PMID: 30612150 DOI: 10.1007/s00412-018-00687-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023]
Abstract
Aurora-A is a conserved mitotic kinase overexpressed in many types of cancer. Growing evidence shows that Aurora-A plays a crucial role in DNA damage response (DDR) although this aspect has been less characterized. We isolated a new aur-A mutation, named aur-A949, in Drosophila, and we showed that it causes chromosome aberrations (CABs). In addition, aur-A949 mutants were sensitive to X-ray treatment and showed impaired γ-H2Av foci dissolution kinetics. To identify the pathway in which Aur-A works, we conducted an epistasis analysis by evaluating CAB frequencies in double mutants carrying aur-A949 mutation combined to mutations in genes related to DNA damage response (DDR). We found that mutations in tefu (ATM) and in the histone variant H2Av were epistatic over aur-A949 indicating that Aur-A works in DDR and that it is required for γ-H2Av foci dissolution. More interestingly, we found that a mutation in lig4, a gene belonging to the non-homologous end joining (NHEJ) repair pathway, was epistatic over aur-A949. Based on studies in other systems, which show that phosphorylation is important to target Lig4 for degradation, we hypothesized that in aur-A949 mutant cells, there is a persistence of Lig4 that could be, in the end, responsible for CABs. Finally, we observed a synergistic interaction between Aur-A and the homologous recombination (HR) repair system component Rad 51 in the process that converts chromatid deletions into isochromatid deletions. Altogether, these data indicate that Aur-A depletion can elicit chromosome damage. This conclusion should be taken into consideration, since some anticancer therapies are aimed at reducing Aurora-A expression.
Collapse
|
128
|
Warmerdam DO, Wolthuis RMF. Keeping ribosomal DNA intact: a repeating challenge. Chromosome Res 2018; 27:57-72. [PMID: 30556094 PMCID: PMC6394564 DOI: 10.1007/s10577-018-9594-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/20/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
More than half of the human genome consists of repetitive sequences, with the ribosomal DNA (rDNA) representing two of the largest repeats. Repetitive rDNA sequences may form a threat to genomic integrity and cellular homeostasis due to the challenging aspects of their transcription, replication, and repair. Predisposition to cancer, premature aging, and neurological impairment in ataxia-telangiectasia and Bloom syndrome, for instance, coincide with increased cellular rDNA repeat instability. However, the mechanisms by which rDNA instability contributes to these hereditary syndromes and tumorigenesis remain unknown. Here, we review how cells govern rDNA stability and how rDNA break repair influences expansion and contraction of repeat length, a process likely associated with human disease. Recent advancements in CRISPR-based genome engineering may help to explain how cells keep their rDNA intact in the near future.
Collapse
Affiliation(s)
- Daniël O Warmerdam
- CRISPR Platform, University of Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105 AZ, Amsterdam, the Netherlands.
| | - Rob M F Wolthuis
- Section of Oncogenetics, Department of Clinical Genetics, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, de Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| |
Collapse
|
129
|
Bouwman BAM, Crosetto N. Endogenous DNA Double-Strand Breaks during DNA Transactions: Emerging Insights and Methods for Genome-Wide Profiling. Genes (Basel) 2018; 9:E632. [PMID: 30558210 PMCID: PMC6316733 DOI: 10.3390/genes9120632] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 02/07/2023] Open
Abstract
DNA double-strand breaks (DSBs) jeopardize genome integrity and can-when repaired unfaithfully-give rise to structural rearrangements associated with cancer. Exogenous agents such as ionizing radiation or chemotherapy can invoke DSBs, but a vast amount of breakage arises during vital endogenous DNA transactions, such as replication and transcription. Additionally, chromatin looping involved in 3D genome organization and gene regulation is increasingly recognized as a possible contributor to DSB events. In this review, we first discuss insights into the mechanisms of endogenous DSB formation, showcasing the trade-off between essential DNA transactions and the intrinsic challenges that these processes impose on genomic integrity. In the second part, we highlight emerging methods for genome-wide profiling of DSBs, and discuss future directions of research that will help advance our understanding of genome-wide DSB formation and repair.
Collapse
Affiliation(s)
- Britta A M Bouwman
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165 Stockholm, Sweden.
| | - Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17165 Stockholm, Sweden.
| |
Collapse
|
130
|
Bianchi FT, Berto GE, Di Cunto F. Impact of DNA repair and stability defects on cortical development. Cell Mol Life Sci 2018; 75:3963-3976. [PMID: 30116853 PMCID: PMC11105354 DOI: 10.1007/s00018-018-2900-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/16/2018] [Accepted: 08/08/2018] [Indexed: 02/07/2023]
Abstract
Maintenance of genome stability is a crucial cellular function for normal mammalian development and physiology. However, despite the general relevance of this process, genome stability alteration due to genetic or non-genetic conditions has a particularly profound impact on the developing cerebral cortex. In this review, we will analyze the main pathways involved in maintenance of genome stability, the consequences of their alterations with regard to central nervous system development, as well as the possible molecular and cellular basis of this specificity.
Collapse
Affiliation(s)
- Federico T Bianchi
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy.
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.
| | - Gaia E Berto
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Ferdinando Di Cunto
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Department of Neuroscience, University of Turin, Turin, Italy
| |
Collapse
|
131
|
A Zebrafish Acromegaly Model Elevates DNA Damage and Impairs DNA Repair Pathways. BIOLOGY 2018; 7:biology7040047. [PMID: 30336646 PMCID: PMC6315448 DOI: 10.3390/biology7040047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 01/09/2023]
Abstract
Acromegaly is a pathological condition due to excess growth hormone (GH) secretion. Acromegaly patients exhibit a deterioration of health and many associated complications, such as cardiovascular issues, arthritis, kidney diseases, muscular weakness, and colon cancer. Since these complications are generalized throughout the body, we investigated the effect of GH excess on cellular integrity. Here, we established stable acromegaly model zebrafish lines that overexpress tilapia GH and the red fluorescence protein (RFP) reporter gene for tracking GH gene expression throughout generations, and performed RNA-Seq data analysis from different organs. Intriguingly, heatmap and Expression2Kinases (X2K) analysis revealed the enrichment of DNA damage markers in various organs. Moreover, H2A.X immunostaining analysis in acromegaly zebrafish larvae and the adult acromegaly model brain and muscle showed a robust increase in the number of DNA-damaged cells. Using Gene Set Enrichment Analysis (GSEA), we found that the acromegaly zebrafish model had impaired DNA repair pathways in the liver, such as double-strand break (DSB), homologous recombination repair (HRR), non-homologous end joining (NHEJ), nucleotide excision repair (NER), and translesion synthesis (TLS). Interestingly, the impairment of DNA repair was even more prominent in acromegaly model than in aged zebrafish (three years old). Thus, our study demonstrates that affection of cellular integrity is characteristic of acromegaly.
Collapse
|
132
|
Nandi B, Talluri S, Kumar S, Yenumula C, Gold JS, Prabhala R, Munshi NC, Shammas MA. The roles of homologous recombination and the immune system in the genomic evolution of cancer. ACTA ACUST UNITED AC 2018; 5. [PMID: 30873294 PMCID: PMC6411307 DOI: 10.15761/jts.1000282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A variety of factors, whether extracellular (mutagens/carcinogens and viruses in the environment, chronic inflammation and radiation associated with the environment and/or electronic devices/machines) and/or intracellular (oxidative metabolites of food, oxidative stress due to inflammation, acid production, replication stress, DNA replication/repair errors, and certain hormones, cytokines, growth factors), pose a constant threat to the genomic integrity of a living cell. However, in the normal cellular environment multiple biological pathways including DNA repair, cell cycle, apoptosis and the immune system work in a precise, regulated (tightly controlled), timely and concerted manner to ensure genomic integrity, stability and proper functioning of a cell. If damage to DNA takes place, it is efficiently and accurately repaired by the DNA repair systems. Homologous recombination (HR) which utilizes either a homologous chromosome (in G1 phase) or a sister chromatid (in G2) as a template to repair the damage, is known to be the most precise repair system. HR in G2 which utilizes a sister chromatid as a template is also called an error free repair system. If DNA damage in a cell is so extensive that it overwhelms the repair system/s, the cell is eliminated by apoptosis. Thus, multiple pathways ensure that genome of a cell is intact and stable. However, constant exposure to DNA damage and/or dysregulation of DNA repair mechanism/s poses a risk of mutation and cancer. Oncogenesis, which seems to be a multistep process, is associated with acquisition of a number of genomic changes that enable a normal cell to progress from benign to malignant transformation. Transformed/cancer cells are recognized and killed by the immune system. However, the ongoing acquisition of new genomic changes enables cancer cells to survive/escape immune attack, evolve into a more aggressive phenotype, and eventually develop resistance to therapy. Although DNA repair (especially the HR) and the immune system play unique roles in preserving genomic integrity of a cell, they can also contribute to DNA damage, genomic instability and oncogenesis. The purpose of this article is to highlight the roles of DNA repair (especially HR) and the immune system in genomic evolution, with special focus on gastrointestinal cancer.
Collapse
Affiliation(s)
- B Nandi
- Harvard Medical School and Brigham and Women's Hospital, USA.,Researh Services, VA Healthcare System, West Roxbury, MA, USA
| | - S Talluri
- Harvard (Dana Farber) Cancer Institute, Boston, MA, USA.,Researh Services, VA Healthcare System, West Roxbury, MA, USA
| | - S Kumar
- Harvard (Dana Farber) Cancer Institute, Boston, MA, USA.,Harvard Medical School and Brigham and Women's Hospital, USA
| | - C Yenumula
- Harvard Medical School and Brigham and Women's Hospital, USA.,Researh Services, VA Healthcare System, West Roxbury, MA, USA
| | - J S Gold
- Harvard Medical School and Brigham and Women's Hospital, USA.,Surgery Services, VA Healthcare System, West Roxbury, MA, USA
| | - R Prabhala
- Harvard (Dana Farber) Cancer Institute, Boston, MA, USA.,Researh Services, VA Healthcare System, West Roxbury, MA, USA
| | - N C Munshi
- Harvard (Dana Farber) Cancer Institute, Boston, MA, USA.,Harvard Medical School and Brigham and Women's Hospital, USA.,Researh Services, VA Healthcare System, West Roxbury, MA, USA
| | - M A Shammas
- Harvard (Dana Farber) Cancer Institute, Boston, MA, USA.,Researh Services, VA Healthcare System, West Roxbury, MA, USA
| |
Collapse
|
133
|
Aung HM, Huangteerakul C, Panvongsa W, Jensen AN, Chairoungdua A, Sukrong S, Jensen LT. Interrogation of ethnomedicinal plants for synthetic lethality effects in combination with deficiency in the DNA repair endonuclease RAD1 using a yeast cell-based assay. JOURNAL OF ETHNOPHARMACOLOGY 2018; 223:10-21. [PMID: 29777901 DOI: 10.1016/j.jep.2018.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Plant materials used in this study were selected based on the ethnobotanical literature. Plants have either been utilized by Thai practitioners as alternative treatments for cancer or identified to exhibit anti-cancer properties. AIM OF THE STUDY To screen ethnomedicinal plants using a yeast cell-based assay for synthetic lethal interactions with cells deleted for RAD1, the yeast homologue of human ERCC4 (XPF) MATERIALS AND METHODS: Ethanolic extracts from thirty-two species of medicinal plants utilized in Thai traditional medicine were screened for synthetic lethal/sick interactions using a yeast cell-based assay. Cell growth was compared between the parental strain and rad1∆ yeast following exposure to select for specific toxicity of plant extracts. Candidate extracts were further examined for the mode of action using genetic and biochemical approaches. RESULTS Screening a library of ethanolic extracts from medicinal plants identified Bacopa monnieri and Colubrina asiatica as having synthetic lethal effects in the rad1∆ cells but not the parental strain. Synthetic lethal effects for B. monneiri extracts were more apparent and this plant was examined further. Genetic analysis indicates that pro-oxidant activities and defective excision repair pathways do not significantly contribute to enhanced sensitivity to B. monneiri extracts. Exposure to B. monneiri extracts resulted in nuclear fragmentation and elevated levels of ethidium bromide staining in rad1∆ yeast suggesting promotion of an apoptosis-like event. Growth inhibition also observed in the human Caco-2 cell line suggesting the effects of B. monnieri extracts on both yeast and human cells may be similar. CONCLUSIONS B. monneiri extracts may have utility in treatment of colorectal cancers that exhibit deficiency in ERCC4 (XPF).
Collapse
Affiliation(s)
- Hsu Mon Aung
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok Thailand
| | | | - Wittaya Panvongsa
- Toxicology Graduate Program, Faculty of Science, Mahidol University, Bangkok, Thailand; Excellent Center for Drug Discovery (ECDD), Mahidol University, Bangkok, Thailand
| | - Amornrat N Jensen
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Arthit Chairoungdua
- Toxicology Graduate Program, Faculty of Science, Mahidol University, Bangkok, Thailand; Excellent Center for Drug Discovery (ECDD), Mahidol University, Bangkok, Thailand; Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand.
| | - Suchada Sukrong
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Laran T Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok Thailand.
| |
Collapse
|
134
|
Merigliano C, Mascolo E, Burla R, Saggio I, Vernì F. The Relationship Between Vitamin B6, Diabetes and Cancer. Front Genet 2018; 9:388. [PMID: 30271425 PMCID: PMC6146109 DOI: 10.3389/fgene.2018.00388] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/29/2018] [Indexed: 11/15/2022] Open
Abstract
Pyridoxal 5′-phosphate (PLP), the active form of vitamin B6, works as cofactor in numerous enzymatic reactions and it behaves as antioxidant molecule. PLP deficiency has been associated to many human pathologies including cancer and diabetes and the mechanism behind this connection is now becoming clearer. Inadequate intake of this vitamin increases the risk of many cancers; furthermore, PLP deprivation impairs insulin secretion in rats, whereas PLP supplementation prevents diabetic complications and improves gestational diabetes. Growing evidence shows that diabetes and cancer are correlated not only because they share same risk factors but also because diabetic patients have a higher risk of developing tumors, although the underlying mechanisms remain elusive. In this review, we will explore data obtained in Drosophila revealing the existence of a connection between vitamin B6, DNA damage and diabetes, as flies in the past decade turned out to be a promising model also for metabolic diseases including diabetes. We will focus on recent studies that revealed a specific role for PLP in maintaining chromosome integrity and glucose homeostasis, and we will show that these aspects are correlated. In addition, we will discuss recent data identifying PLP as a putative linking factor between diabetes and cancer.
Collapse
Affiliation(s)
- Chiara Merigliano
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Rome, Italy
| | - Elisa Mascolo
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Rome, Italy
| | - Romina Burla
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Rome, Italy
| | - Isabella Saggio
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Rome, Italy.,Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Fiammetta Vernì
- Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza Università di Roma, Rome, Italy
| |
Collapse
|
135
|
Su D, Ma S, Shan L, Wang Y, Wang Y, Cao C, Liu B, Yang C, Wang L, Tian S, Ding X, Liu X, Yu N, Song N, Liu L, Yang S, Zhang Q, Yang F, Zhang K, Shi L. Ubiquitin-specific protease 7 sustains DNA damage response and promotes cervical carcinogenesis. J Clin Invest 2018; 128:4280-4296. [PMID: 30179224 DOI: 10.1172/jci120518] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/24/2018] [Indexed: 12/24/2022] Open
Abstract
Central to the recognition, signaling, and repair of DNA double-strand breaks (DSBs) are the MRE11-RAD50-NBS1 (MRN) complex and mediator of DNA damage checkpoint protein 1 (MDC1), the interplay of which is essential for initiation and amplification of the DNA damage response (DDR). The intrinsic rule governing the regulation of the function of this molecular machinery remains to be investigated. We report here that the ubiquitin-specific protease USP7 was physically associated with the MRN-MDC1 complex and that the MRN-MDC1 complex acted as a platform for USP7 to efficiently deubiquitinate and stabilize MDC1, thereby sustaining the DDR. Accordingly, depletion of USP7 impaired the engagement of the MRN-MDC1 complex and the consequent recruitment of the downstream factors p53-binding protein 1 (53BP1) and breast cancer protein 1 (BRCA1) at DNA lesions. Significantly, USP7 was overexpressed in cervical cancer, and the level of its expression positively correlated with that of MDC1 and worse survival rates for patients with cervical cancer. We demonstrate that USP7-mediated MDC1 stabilization promoted cervical cancer cell survival and conferred cellular resistance to genotoxic insults. Together, our study reveals a role for USP7 in regulating the function of the MRN-MDC1 complex and activity of the DDR, supporting the pursuit of USP7 as a potential therapeutic target for MDC1-proficient cancers.
Collapse
Affiliation(s)
- Dongxue Su
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shuai Ma
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yuejiao Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Cheng Cao
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Beibei Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Chao Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Liyong Wang
- Core Facilities for Molecular Biology, Capital Medical University, Beijing, China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiang Ding
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xinhua Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Na Yu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Nan Song
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ling Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shangda Yang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Qi Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lei Shi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| |
Collapse
|
136
|
Li XQ, Ren J, Chen P, Chen YJ, Wu M, Wu Y, Chen K, Li J. Co-inhibition of Pol η and ATR sensitizes cisplatin-resistant non-small cell lung cancer cells to cisplatin by impeding DNA damage repair. Acta Pharmacol Sin 2018; 39:1359-1372. [PMID: 29849128 DOI: 10.1038/aps.2017.187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 12/14/2017] [Indexed: 02/08/2023] Open
Abstract
For the majority of patients with advanced non-small cell lung cancer (NSCLC), the standard of care remains platinum-based chemotherapy. However, cisplatin resistance is a big obstacle to the treatment, and elucidation of its mechanism is warranted. In this study, we showed that there was no difference in intracellular uptake of cisplatin or the removal of platinum-DNA adducts between a cisplatin-resistant NSCLC cell line (A549/DR) and a cisplatin-sensitive NSCLC cell line (A549). However, the capacity to repair DNA interstrand crosslinks (ICLs) and double-strand breaks (DSBs) was significantly enhanced in the A549/DR cell line compared to 3 cisplatin-sensitive cell lines. We found that the protein and mRNA expression levels of Pol η, a Y-family translesion synthesis (TLS) polymerase, were markedly increased upon cisplatin exposure in A549/DR cells compared with A549 cells. Furthermore, intracellular co-localization of Pol η and proliferation cell nuclear antigen (PCNA) induced by cisplatin or cisplatin plus gemcitabine treatment was inhibited by depleting ataxia telangiectasia mutated and Rad-3-related (ATR). Pol η depletion by siRNA sensitized A549/DR cells to cisplatin; co-depletion of Pol η and ATR further increased A549/DR cell death induced by cisplatin or cisplatin plus gemcitabine compared to depletion of Pol η or ATR alone, concomitant with inhibition of DNA ICL and DSB repair and accumulation of DNA damage. No additional sensitization effect of co-depleting Pol η and ATR was observed in A549 cells. These results demonstrate that co-inhibition of Pol η and ATR reverses the drug resistance of cisplatin-resistant NSCLC cells by blocking the repair of DNA ICLs and DSBs induced by cisplatin or cisplatin plus gemcitabine.
Collapse
|
137
|
Turner I, Garimella KV, Iqbal Z, McVean G. Integrating long-range connectivity information into de Bruijn graphs. Bioinformatics 2018; 34:2556-2565. [PMID: 29554215 PMCID: PMC6061703 DOI: 10.1093/bioinformatics/bty157] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/25/2017] [Accepted: 03/14/2018] [Indexed: 12/27/2022] Open
Abstract
Motivation The de Bruijn graph is a simple and efficient data structure that is used in many areas of sequence analysis including genome assembly, read error correction and variant calling. The data structure has a single parameter k, is straightforward to implement and is tractable for large genomes with high sequencing depth. It also enables representation of multiple samples simultaneously to facilitate comparison. However, unlike the string graph, a de Bruijn graph does not retain long range information that is inherent in the read data. For this reason, applications that rely on de Bruijn graphs can produce sub-optimal results given their input data. Results We present a novel assembly graph data structure: the Linked de Bruijn Graph (LdBG). Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph. We show that with error-free data it is possible to losslessly store and recover sequence from a Linked de Bruijn graph. With assembly simulations we demonstrate that the LdBG data structure outperforms both our de Bruijn graph and the String Graph Assembler (SGA). Finally we apply the LdBG to Klebsiella pneumoniae short read data to make large (12 kbp) variant calls, which we validate using PacBio sequencing data, and to characterize the genomic context of drug-resistance genes. Availability and implementation Linked de Bruijn Graphs and associated algorithms are implemented as part of McCortex, which is available under the MIT license at https://github.com/mcveanlab/mccortex. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Isaac Turner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kiran V Garimella
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| |
Collapse
|
138
|
Protective role of vitamin B6 (PLP) against DNA damage in Drosophila models of type 2 diabetes. Sci Rep 2018; 8:11432. [PMID: 30061626 PMCID: PMC6065437 DOI: 10.1038/s41598-018-29801-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/19/2018] [Indexed: 12/24/2022] Open
Abstract
Growing evidence shows that improper intake of vitamin B6 increases cancer risk and several studies indicate that diabetic patients have a higher risk of developing tumors. We previously demonstrated that in Drosophila the deficiency of Pyridoxal 5′ phosphate (PLP), the active form of vitamin B6, causes chromosome aberrations (CABs), one of cancer prerequisites, and increases hemolymph glucose content. Starting from these data we asked if it was possible to provide a link between the aforementioned studies. Thus, we tested the effect of low PLP levels on DNA integrity in diabetic cells. To this aim we generated two Drosophila models of type 2 diabetes, the first by impairing insulin signaling and the second by rearing flies in high sugar diet. We showed that glucose treatment induced CABs in diabetic individuals but not in controls. More interestingly, PLP deficiency caused high frequencies of CABs in both diabetic models demonstrating that hyperglycemia, combined to reduced PLP level, impairs DNA integrity. PLP-depleted diabetic cells accumulated Advanced Glycation End products (AGEs) that largely contribute to CABs as α-lipoic acid, an AGE inhibitor, rescued not only AGEs but also CABs. These data, extrapolated to humans, indicate that low PLP levels, impacting on DNA integrity, may be considered one of the possible links between diabetes and cancer.
Collapse
|
139
|
de Cárcer G, Huertas P, López-Contreras AJ. Chromosome instability: From molecular mechanisms to disease. DNA Repair (Amst) 2018. [DOI: 10.1016/j.dnarep.2018.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
140
|
Cheung SW, Bi W. Novel applications of array comparative genomic hybridization in molecular diagnostics. Expert Rev Mol Diagn 2018; 18:531-542. [PMID: 29848116 DOI: 10.1080/14737159.2018.1479253] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.
Collapse
Affiliation(s)
- Sau W Cheung
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA
| | - Weimin Bi
- a Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , TX , USA.,b Baylor Genetics , Houston , TX , USA
| |
Collapse
|
141
|
Zhu Q, Hoong N, Aslanian A, Hara T, Benner C, Heinz S, Miga KH, Ke E, Verma S, Soroczynski J, Yates JR, Hunter T, Verma IM. Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer. Mol Cell 2018; 70:842-853.e7. [PMID: 29861157 DOI: 10.1016/j.molcel.2018.04.023] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 02/22/2018] [Accepted: 04/26/2018] [Indexed: 12/19/2022]
Abstract
Heterochromatic repetitive satellite RNAs are extensively transcribed in a variety of human cancers, including BRCA1 mutant breast cancer. Aberrant expression of satellite RNAs in cultured cells induces the DNA damage response, activates cell cycle checkpoints, and causes defects in chromosome segregation. However, the mechanism by which satellite RNA expression leads to genomic instability is not well understood. Here we provide evidence that increased levels of satellite RNAs in mammary glands induce tumor formation in mice. Using mass spectrometry, we further show that genomic instability induced by satellite RNAs occurs through interactions with BRCA1-associated protein networks required for the stabilization of DNA replication forks. Additionally, de-stabilized replication forks likely promote the formation of RNA-DNA hybrids in cells expressing satellite RNAs. These studies lay the foundation for developing novel therapeutic strategies that block the effects of non-coding satellite RNAs in cancer cells.
Collapse
Affiliation(s)
- Quan Zhu
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nien Hoong
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Aaron Aslanian
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Toshiro Hara
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Christopher Benner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sven Heinz
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karen H Miga
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eugene Ke
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sachin Verma
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jan Soroczynski
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Inder M Verma
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| |
Collapse
|
142
|
Prakash A, Garcia-Moreno JF, Brown JAL, Bourke E. Clinically Applicable Inhibitors Impacting Genome Stability. Molecules 2018; 23:E1166. [PMID: 29757235 PMCID: PMC6100577 DOI: 10.3390/molecules23051166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022] Open
Abstract
Advances in technology have facilitated the molecular profiling (genomic and transcriptomic) of tumours, and has led to improved stratification of patients and the individualisation of treatment regimes. To fully realize the potential of truly personalised treatment options, we need targeted therapies that precisely disrupt the compensatory pathways identified by profiling which allow tumours to survive or gain resistance to treatments. Here, we discuss recent advances in novel therapies that impact the genome (chromosomes and chromatin), pathways targeted and the stage of the pathways targeted. The current state of research will be discussed, with a focus on compounds that have advanced into trials (clinical and pre-clinical). We will discuss inhibitors of specific DNA damage responses and other genome stability pathways, including those in development, which are likely to synergistically combine with current therapeutic options. Tumour profiling data, combined with the knowledge of new treatments that affect the regulation of essential tumour signalling pathways, is revealing fundamental insights into cancer progression and resistance mechanisms. This is the forefront of the next evolution of advanced oncology medicine that will ultimately lead to improved survival and may, one day, result in many cancers becoming chronic conditions, rather than fatal diseases.
Collapse
Affiliation(s)
- Anu Prakash
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - Juan F Garcia-Moreno
- Discipline of Surgery, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - James A L Brown
- Discipline of Surgery, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - Emer Bourke
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| |
Collapse
|
143
|
Lindström MS, Jurada D, Bursac S, Orsolic I, Bartek J, Volarevic S. Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis. Oncogene 2018; 37:2351-2366. [PMID: 29429989 PMCID: PMC5931986 DOI: 10.1038/s41388-017-0121-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
Abstract
The nucleolus is the major site for synthesis of ribosomes, complex molecular machines that are responsible for protein synthesis. A wealth of research over the past 20 years has clearly indicated that both quantitative and qualitative alterations in ribosome biogenesis can drive the malignant phenotype via dysregulation of protein synthesis. However, numerous recent proteomic, genomic, and functional studies have implicated the nucleolus in the regulation of processes that are unrelated to ribosome biogenesis, including DNA-damage response, maintenance of genome stability and its spatial organization, epigenetic regulation, cell-cycle control, stress responses, senescence, global gene expression, as well as assembly or maturation of various ribonucleoprotein particles. In this review, the focus will be on features of rDNA genes, which make them highly vulnerable to DNA damage and intra- and interchromosomal recombination as well as built-in mechanisms that prevent and repair rDNA damage, and how dysregulation of this interplay affects genome-wide DNA stability, gene expression and the balance between euchromatin and heterochromatin. We will also present the most recent insights into how malfunction of these cellular processes may be a central driving force of human malignancies, and propose a promising new therapeutic approach for the treatment of cancer.
Collapse
Affiliation(s)
- Mikael S Lindström
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Deana Jurada
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Sladana Bursac
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Ines Orsolic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Jiri Bartek
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- The Danish Cancer Society Research Centre, Copenhagen, Denmark.
| | - Sinisa Volarevic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia.
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia.
| |
Collapse
|
144
|
Misino S, Bonetti D, Luke-Glaser S, Luke B. Increased TERRA levels and RNase H sensitivity are conserved hallmarks of post-senescent survivors in budding yeast. Differentiation 2018; 100:37-45. [DOI: 10.1016/j.diff.2018.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/08/2018] [Accepted: 02/14/2018] [Indexed: 01/17/2023]
|
145
|
Zavodna M, Bagshaw A, Brauning R, Gemmell NJ. The effects of transcription and recombination on mutational dynamics of short tandem repeats. Nucleic Acids Res 2018; 46:1321-1330. [PMID: 29300948 PMCID: PMC5814968 DOI: 10.1093/nar/gkx1253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 11/27/2017] [Accepted: 12/27/2017] [Indexed: 01/07/2023] Open
Abstract
Short tandem repeats (STR) are ubiquitous components of the genomic architecture of most living organisms. Recent work has highlighted the widespread functional significance of such repeats, particularly around gene regulation, but the mutational processes underlying the evolution of these highly abundant and highly variable sequences are not fully understood. Traditional models assume that strand misalignment during replication is the predominant mechanism, but empirical data suggest the involvement of other processes including recombination and transcription. Despite this evidence, the relative influences of these processes have not previously been tested experimentally on a genome-wide scale. Using deep sequencing, we identify mutations at >200 microsatellites, across 700 generations in replicated populations of two otherwise identical sexual and asexual Saccharomyces cerevisiae strains. Using generalized linear models, we investigate correlates of STR mutability including the nature of the mutation, STR composition and contextual factors including recombination, transcription and replication origins. Sexual capability was not a significant predictor of microsatellite mutability, but, intriguingly, we identify transcription as a significant positive predictor. We also find that STR density is substantially increased in regions neighboring, but not within, recombination hotspots.
Collapse
Affiliation(s)
- Monika Zavodna
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Andrew Bagshaw
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Rudiger Brauning
- AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin 9054, New Zealand
| |
Collapse
|
146
|
Carbonell A, Fueyo R, Izquierdo-Bouldstridge A, Moreta C, Jordan A. Epigenetic mechanisms in health and disease: BCEC 2017. Epigenetics 2018; 13:331-341. [PMID: 29384431 DOI: 10.1080/15592294.2018.1434391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled "Epigenetic Mechanisms in Health and Disease" was held in Barcelona, October 26-26, 2017. The 2017 BCEC was the fifth and last edition of a series of annual conferences organized as a joint effort of five leading Barcelona research institutes together with B-Debate. This edition was organized by Albert Jordan from the Molecular Biology Institute of Barcelona (IBMB-CSIC) and Marcus Bushbeck from the Josep Carreras Leukaemia Research Institute (IJC). Jordi Bernués, Marian Martínez-Balbás, and Ferran Azorín were also part of the scientific committee. In 22 talks and 51 posters, researchers presented their latest results in the fields of histone variants, epigenetic regulation, and chromatin 3D organization to an audience of around 250 participants from 16 countries. This year, a broad number of talks focused on the epigenetic causes and possible related treatments of complex diseases such as cancer. Participants at the 2017 BCEC elegantly closed the series, discussing progress made in the field of epigenetics and highlighting its role in human health and disease.
Collapse
Affiliation(s)
- Albert Carbonell
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain.,b Institute for Research in Biomedicine, IRB Barcelona , The Barcelona Institute for Science and Technology , Baldiri i Reixac, 10, 08028 Barcelona , Catalonia , Spain
| | - Raquel Fueyo
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
| | - Andrea Izquierdo-Bouldstridge
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
| | - Cristina Moreta
- c Germans Trias i Pujol Research Institute (IGTP) , Can Ruti Campus , 08916 , Badalona , Catalonia , Spain
| | - Albert Jordan
- a Department of Molecular Genomics , Molecular Biology Institute of Barcelona (IBMB-CSIC) , Baldiri i Reixac 4-8, 08028 Barcelona , Catalonia , Spain
| |
Collapse
|
147
|
Grunseich C, Wang IX, Watts JA, Burdick JT, Guber RD, Zhu Z, Bruzel A, Lanman T, Chen K, Schindler AB, Edwards N, Ray-Chaudhury A, Yao J, Lehky T, Piszczek G, Crain B, Fischbeck KH, Cheung VG. Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters. Mol Cell 2018; 69:426-437.e7. [PMID: 29395064 PMCID: PMC5815878 DOI: 10.1016/j.molcel.2017.12.030] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 12/11/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022]
Abstract
R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins.
Collapse
Affiliation(s)
- Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jason A Watts
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Joshua T Burdick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Robert D Guber
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Zhengwei Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tyler Lanman
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Kelian Chen
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Alice B Schindler
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Nancy Edwards
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Abhik Ray-Chaudhury
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Jianhua Yao
- Department of Radiology and Imaging Sciences, Clinical Center, NIH, Bethesda, MD, USA
| | - Tanya Lehky
- Electromyography Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Grzegorz Piszczek
- Biophysics Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Barbara Crain
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
148
|
Eldakhakhny S, Zhou Q, Crosbie EJ, Sayan BS. Human papillomavirus E7 induces p63 expression to modulate DNA damage response. Cell Death Dis 2018; 9:127. [PMID: 29374145 PMCID: PMC5833683 DOI: 10.1038/s41419-017-0149-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 12/19/2022]
Abstract
Cervical cancer is the third most common malignancy diagnosed in women worldwide. The major aetiological factor underlying the malignant transformation of cervical cells is the persistent infection with high-risk human papillomaviruses (HR-HPV), with more than 99% of cases expressing viral sequences. Here, we report a previously unknown mechanism driven by high-risk human papillomavirus E7 protein to modulate response to DNA damage in cervical cancer cells. Our data shows that HR-HPV E7 oncoprotein induces the transcription of the p53-family member p63, which modulates DNA damage response pathways, to facilitate repair of DNA damage. Based on our findings, we proposed a model, where HR-HPV could interfere with the sensitivity of transformed cells to radiation therapy by modulating DNA damage repair efficiency. Importantly, we have shown for the first time a critical role for p63 in response to DNA damage in cervical cancer cells.
Collapse
Affiliation(s)
- Sahar Eldakhakhny
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, Wilmslow Road, Manchester, M20 4QL, UK
| | - Qing Zhou
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, Wilmslow Road, Manchester, M20 4QL, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, Wilmslow Road, Manchester, M20 4QL, UK
| | - Berna S Sayan
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, Wilmslow Road, Manchester, M20 4QL, UK.
| |
Collapse
|
149
|
van Wietmarschen N, Merzouk S, Halsema N, Spierings DCJ, Guryev V, Lansdorp PM. BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes. Nat Commun 2018; 9:271. [PMID: 29348659 PMCID: PMC5773480 DOI: 10.1038/s41467-017-02760-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/21/2017] [Indexed: 11/16/2022] Open
Abstract
Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand sequencing (Strand-seq) to map the genomic locations of SCEs. Our results show that in the absence of BLM, SCEs in human and murine cells do not occur randomly throughout the genome but are strikingly enriched at coding regions, specifically at sites of guanine quadruplex (G4) motifs in transcribed genes. We propose that BLM protects against genome instability by suppressing recombination at sites of G4 structures, particularly in transcribed regions of the genome. Bloom syndrome is characterized by high levels of sister chromatid exchanges (SCEs). Here, the authors use single-cell DNA template strand-sequencing to map SCEs in patient cells, and propose that the BLM helicase protects the genome against unwanted recombination at sites of G-quadruplex structures.
Collapse
Affiliation(s)
- Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sarra Merzouk
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Nancy Halsema
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands. .,Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, V5Z 1L3, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| |
Collapse
|
150
|
Lee EJ, Hwang I, Lee JY, Park JN, Kim KC, Kim GH, Kang CM, Kim I, Lee SY, Kim HS. Hepatocyte Growth Factor Improves the Therapeutic Efficacy of Human Bone Marrow Mesenchymal Stem Cells via RAD51. Mol Ther 2017; 26:845-859. [PMID: 29398486 DOI: 10.1016/j.ymthe.2017.12.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/29/2017] [Accepted: 12/14/2017] [Indexed: 02/08/2023] Open
Abstract
Human embryonic stem cell-derived mesenchymal stem cells (hE-MSCs) have greater proliferative capacity than other human mesenchymal stem cells (hMSCs), suggesting that they may have wider applications in regenerative cellular therapy. In this study, to uncover the anti-senescence mechanism in hE-MSCs, we compared hE-MSCs with adult bone marrow (hBM-MSCs) and found that hepatocyte growth factor (HGF) was more abundantly expressed in hE-MSCs than in hBM-MSCs and that it induced the transcription of RAD51 and facilitated its SUMOylation at K70. RAD51 induction/modification by HGF not only increased telomere length but also increased mtDNA replication, leading to increased ATP generation. Moreover, HGF-treated hBM-MSCs showed significantly better therapeutic efficacy than naive hBM-MSCs. Together, the data suggest that the RAD51-mediated effects of HGF prevent hMSC senescence by promoting telomere lengthening and inducing mtDNA replication and function, which opens the prospect of developing novel therapies for liver disease.
Collapse
Affiliation(s)
- Eun Ju Lee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Injoo Hwang
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ji Yeon Lee
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong Nam Park
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Keun Cheon Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Gi-Hwan Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Chang-Mo Kang
- Korea Institute of Radiological & Medical Sciences, Seoul, Republic of Korea
| | - Irene Kim
- Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Seo-Yeon Lee
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyo-Soo Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Molecular Medicine & Biopharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
| |
Collapse
|