1
|
Lafuente-Barquero J, Svejstrup JQ, Luna R, Aguilera A. Expression of human RECQL5 in Saccharomyces cerevisiae causes transcription defects and transcription-associated genome instability. Mol Genet Genomics 2024; 299:59. [PMID: 38796829 PMCID: PMC11128410 DOI: 10.1007/s00438-024-02152-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
RECQL5 is a member of the conserved RecQ family of DNA helicases involved in the maintenance of genome stability that is specifically found in higher eukaryotes and associates with the elongating RNA polymerase II. To expand our understanding of its function we expressed human RECQL5 in the yeast Saccharomyces cerevisiae, which does not have a RECQL5 ortholog. We found that RECQL5 expression leads to cell growth inhibition, increased genotoxic sensitivity and transcription-associated hyperrecombination. Chromatin immunoprecipitation and transcriptomic analysis of yeast cells expressing human RECQL5 shows that this is recruited to transcribed genes and although it causes only a weak impact on gene expression, in particular at G + C-rich genes, it leads to a transcription termination defect detected as readthrough transcription. The data indicate that the interaction between RNAPII and RECQL5 is conserved from yeast to humans. Unexpectedly, however, the RECQL5-ID mutant, previously shown to have reduced the association with RNAPII in vitro, associates with the transcribing polymerase in cells. As a result, expression of RECQL5-ID leads to similar although weaker phenotypes than wild-type RECQL5 that could be transcription-mediated. Altogether, the data suggests that RECQL5 has the intrinsic ability to function in transcription-dependent and independent genome dynamics in S. cerevisiae.
Collapse
Affiliation(s)
- Juan Lafuente-Barquero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain
| | - Jesper Q Svejstrup
- University of Copenhagen, Copenhagen, Denmark
- Francis Crick Institute, London, UK
| | - Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain.
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain
| |
Collapse
|
2
|
Herr LM, Schaffer ED, Fuchs KF, Datta A, Brosh RM. Replication stress as a driver of cellular senescence and aging. Commun Biol 2024; 7:616. [PMID: 38777831 PMCID: PMC11111458 DOI: 10.1038/s42003-024-06263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying of the genome. While long considered a nexus for DNA damage, the role of replication stress in aging is under-appreciated. The consequential role of replication stress in promotion of organismal aging phenotypes is evidenced by an extensive list of hereditary accelerated aging disorders marked by molecular defects in factors that promote replication fork progression and operate uniquely in the replication stress response. Additionally, recent studies have revealed cellular pathways and phenotypes elicited by replication stress that align with designated hallmarks of aging. Here we review recent advances demonstrating the role of replication stress as an ultimate driver of cellular senescence and aging. We discuss clinical implications of the intriguing links between cellular senescence and aging including application of senotherapeutic approaches in the context of replication stress.
Collapse
Affiliation(s)
- Lauren M Herr
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ethan D Schaffer
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
| |
Collapse
|
3
|
Bereda CC, Dewey EB, Nasr MA, Sekelsky J. Functions of the Bloom Syndrome Helicase N-terminal Intrinsically Disordered Region. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589165. [PMID: 38659896 PMCID: PMC11042211 DOI: 10.1101/2024.04.12.589165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bloom Syndrome helicase (Blm) is a RecQ family helicase involved in DNA repair, cell-cycle progression, and development. Pathogenic variants in human BLM cause the autosomal recessive disorder Bloom Syndrome, characterized by predisposition to numerous types of cancer. Prior studies of Drosophila Blm mutants lacking helicase activity or protein have shown sensitivity to DNA damaging agents, defects in repairing DNA double-strand breaks (DSBs), female sterility, and improper segregation of chromosomes in meiosis. Blm orthologs have a well conserved and highly structured RecQ helicase domain, but more than half of the protein, particularly in the N-terminus, is predicted to be unstructured. Because this region is poorly conserved across multicellular organisms, we compared closely related species to identify regions of conservation, potentially indicating important functions. We deleted two of these Drosophila-conserved regions in D. melanogaster using CRISPR/Cas9 gene editing and assessed the effects on different Blm functions. Each deletion had distinct effects on different Blm activities. Deletion of either conserved region 1 (CR1) or conserved region 2 (CR2) compromised DSB repair through synthesis-dependent strand annealing and resulted in increased mitotic crossovers. In contrast, CR2 is critical for embryonic development but CR1 is not as important. CR1 deletion allows for proficient meiotic chromosome segregation but does lead to defects in meiotic crossover designation and patterning. Finally, deletion of CR2 does not lead to significant meiotic defects, indicating that while each region has overlapping functions, there are discreet roles facilitated by each. These results provide novel insights into functions of the N-terminal disordered region of Blm.
Collapse
Affiliation(s)
- Colleen C. Bereda
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Evan B. Dewey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Mohamed A. Nasr
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jeff Sekelsky
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| |
Collapse
|
4
|
An D, Chen X, Li Z, Dai L, Huang J, Xiao M, Liu H, Xu J, Ruan Y. Genetic variation in the BLM gene and its expression in the ovaries is closely related to kidding number in goats. Theriogenology 2024; 218:254-266. [PMID: 38367334 DOI: 10.1016/j.theriogenology.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Bloom (BLM) helicase plays an important role in DNA replication and the maintenance of genome integrity. BLM protein deficiency, which plays a vital role in the sperm-egg union and germ-cell development during reproduction, can lead to severe DNA damage in goats. However, the effect of BLM protein deficiency on goat litter size has not been reported. Herein, we studied the association between the genetic variation in the BLM gene and the number of kids per litter in Guizhou white goats. We explored differences in the expression of the BLM protein in the follicles of single and multi-kid nanny goats. We also analyzed the effects of dysregulated BLM gene expression on the proliferation and apoptosis of ovarian granulosa cells and the expression of genes related to follicle development in goats. Five single nucleotide polymorphism (SNP) loci, including the non-synonymous mutations g.38179 A > G, g.40626 G > C and g.89621 T > G; the intron synonymous mutation g.56961 G > A and the exon synonymous mutation g.65796 C > T were found in the BLM gene. All SNPs loci were in Hardy-Weinberg equilibrium, and correlation analysis showed that the g.65796 C > T and g.89621 T > G loci polymorphism was strongly associated with litter size in the first three litters (P < 0.05). The diplogenotype Hap 2/2 (AAGGAACCTT) showed no significant difference in litter size between different births, indicating that the diploid genotype is stable in different litter sizes. Bioinformatics analysis showed that three non-synonymous mutation loci (p.T488A, p.A662S, and p.S1373A) could affect BLM protein stability, and mutations in p.T488A and p.S1373A led to changes in amino acid polarity and associated interactions. qPCR results showed that the expression level of the BLM gene in the uterus and ovaries of TT genotype nanny goats was significantly higher than that of GG genotype nanny goats. Indirect immunofluorescence assay (IF) showed that the BLM protein was significantly overexpressed in both the primordial and growing follicles of nanny goats with multiple kids (P < 0.01). Disrupting BLM gene expression in the ovarian granulosa cells down-regulated the expression of the Cyp19A1 gene. It also significantly inhibited the proliferation of follicles and induces early apoptosis of the granulosa cells. These findings confirm that polymorphism in the BLM gene is closely related to the littering traits of Guizhou white goats, and it affects the reproductive performance of nanny goats by regulating the development of the oocytes and granulosa cells. This work provides new evidence on the regulatory effect of the BLM gene on the litter size of nanny goats.
Collapse
Affiliation(s)
- Dongwei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Ziyang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Lingang Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Jiajin Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Meimei Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Huan Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Jiali Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China
| | - Yong Ruan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, 550025, PR China; Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, Guizhou University, Guiyang, 550025, PR China; College of Animal Science, Guizhou University, Guiyang, 550025, PR China.
| |
Collapse
|
5
|
Richl T, Kuper J, Kisker C. G-quadruplex-mediated genomic instability drives SNVs in cancer. Nucleic Acids Res 2024; 52:2198-2211. [PMID: 38407356 PMCID: PMC10954472 DOI: 10.1093/nar/gkae098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/13/2023] [Accepted: 02/21/2024] [Indexed: 02/27/2024] Open
Abstract
G-quadruplex (G4s) DNA structures have been implicated in inducing genomic instability and contributing to cancer development. However, the relationship between G4s and cancer-related single nucleotide variants (cSNVs) in clinical settings remains unclear. In this large-scale study, we integrated experimentally validated G4s with genomic cSNVs from 13480 cancer patients to investigate the spatial association of G4s with the cellular cSNV landscape. Our findings demonstrate an increase in local genomic instability with increasing local G4 content in cancer patients, suggesting a potential role for G4s in driving cSNVs. Notably, we observed distinct spatial patterns of cSNVs and common single nucleotide variants (dbSNVs) in relation to G4s, implying different mechanisms for their generation and accumulation. We further demonstrate large, cancer-specific differences in the relationship of G4s and cSNVs, which could have important implications for a new class of G4-stabilizing cancer therapeutics. Moreover, we show that high G4-content can serve as a prognostic marker for local cSNV density and patient survival rates. Our findings underscore the importance of considering G4s in cancer research and highlight the need for further investigation into the underlying molecular mechanisms of G4-mediated genomic instability, especially in the context of cancer.
Collapse
Affiliation(s)
- Tilmann Richl
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg 97080, Germany
| | - Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg 97080, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg 97080, Germany
| |
Collapse
|
6
|
Flynn JM, Yamashita YM. The implications of satellite DNA instability on cellular function and evolution. Semin Cell Dev Biol 2024; 156:152-159. [PMID: 37852904 DOI: 10.1016/j.semcdb.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Abundant tandemly repeated satellite DNA is present in most eukaryotic genomes. Previous limitations including a pervasive view that it was uninteresting junk DNA, combined with challenges in studying it, are starting to dissolve - and recent studies have found important functions for satellite DNAs. The observed rapid evolution and implied instability of satellite DNA now has important significance for their functions and maintenance within the genome. In this review, we discuss the processes that lead to satellite DNA copy number instability, and the importance of mechanisms to manage the potential negative effects of instability. Satellite DNA is vulnerable to challenges during replication and repair, since it forms difficult-to-process secondary structures and its homology within tandem arrays can result in various types of recombination. Satellite DNA instability may be managed by DNA or chromatin-binding proteins ensuring proper nuclear localization and repair, or by proteins that process aberrant structures that satellite DNAs tend to form. We also discuss the pattern of satellite DNA mutations from recent mutation accumulation (MA) studies that have tracked changes in satellite DNA for up to 1000 generations with minimal selection. Finally, we highlight examples of satellite evolution from studies that have characterized satellites across millions of years of Drosophila fruit fly evolution, and discuss possible ways that selection might act on the satellite DNA composition.
Collapse
Affiliation(s)
- Jullien M Flynn
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
7
|
Wachter F, Pikman Y. Pathophysiology of Acute Myeloid Leukemia. Acta Haematol 2024; 147:229-246. [PMID: 38228114 DOI: 10.1159/000536152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is a biologically heterogenous disease arising in clonally proliferating hematopoietic stem cells. Sequential acquisition of mutations leads to expanded proliferation of clonal myeloid progenitors and failure of differentiation, leading to fulminant AML. SUMMARY Here, we review the pathophysiology of AML with a focus on factors predisposing to AML development, including prior chemo- and radiation therapy, environmental factors, and germline predisposition. KEY MESSAGE Increasing genomic characterization of AML and insight into mechanisms of its development will be critical to improvement in AML prognostication and therapy.
Collapse
Affiliation(s)
- Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
| |
Collapse
|
8
|
Tsukada K, Jones SE, Bannister J, Durin MA, Vendrell I, Fawkes M, Fischer R, Kessler BM, Chapman JR, Blackford AN. BLM and BRCA1-BARD1 coordinate complementary mechanisms of joint DNA molecule resolution. Mol Cell 2024; 84:640-658.e10. [PMID: 38266639 DOI: 10.1016/j.molcel.2023.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 10/10/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The Bloom syndrome helicase BLM interacts with topoisomerase IIIα (TOP3A), RMI1, and RMI2 to form the BTR complex, which dissolves double Holliday junctions and DNA replication intermediates to promote sister chromatid disjunction before cell division. In its absence, structure-specific nucleases like the SMX complex (comprising SLX1-SLX4, MUS81-EME1, and XPF-ERCC1) can cleave joint DNA molecules instead, but cells deficient in both BTR and SMX are not viable. Here, we identify a negative genetic interaction between BLM loss and deficiency in the BRCA1-BARD1 tumor suppressor complex. We show that this is due to a previously overlooked role for BARD1 in recruiting SLX4 to resolve DNA intermediates left unprocessed by BLM in the preceding interphase. Consequently, cells with defective BLM and BRCA1-BARD1 accumulate catastrophic levels of chromosome breakage and micronucleation, leading to cell death. Thus, we reveal mechanistic insights into SLX4 recruitment to DNA lesions, with potential clinical implications for treating BRCA1-deficient tumors.
Collapse
Affiliation(s)
- Kaima Tsukada
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Julius Bannister
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mary-Anne Durin
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - J Ross Chapman
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
| |
Collapse
|
9
|
Chen J, Wu M, Yang Y, Ruan C, Luo Y, Song L, Wu T, Huang J, Yang B, Liu T. TFIP11 promotes replication fork reversal to preserve genome stability. Nat Commun 2024; 15:1262. [PMID: 38341452 PMCID: PMC10858868 DOI: 10.1038/s41467-024-45684-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Replication fork reversal, a critical protective mechanism against replication stress in higher eukaryotic cells, is orchestrated via a series of coordinated enzymatic reactions. The Bloom syndrome gene product, BLM, a member of the highly conserved RecQ helicase family, is implicated in this process, yet its precise regulation and role remain poorly understood. In this study, we demonstrate that the GCFC domain-containing protein TFIP11 forms a complex with the BLM helicase. TFIP11 exhibits a preference for binding to DNA substrates that mimic the structure generated at stalled replication forks. Loss of either TFIP11 or BLM leads to the accumulation of the other protein at stalled forks. This abnormal accumulation, in turn, impairs RAD51-mediated fork reversal and slowing, sensitizes cells to replication stress-inducing agents, and enhances chromosomal instability. These findings reveal a previously unidentified regulatory mechanism that modulates the activities of BLM and RAD51 at stalled forks, thereby impacting genome integrity.
Collapse
Affiliation(s)
- Junliang Chen
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, China
| | - Mingjie Wu
- The Trauma Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yulan Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Chunyan Ruan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Yi Luo
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Lizhi Song
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Wu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Bing Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Liu
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Department of Cell Biology, Zhejiang University School of Medicine, 310058, Hangzhou, China.
| |
Collapse
|
10
|
Gombás BG, Villányi Z. 1,6-Hexanediol Is Inducing Homologous Recombination by Releasing BLM from Assemblysomes in Drosophila melanogaster. Int J Mol Sci 2024; 25:1611. [PMID: 38338890 PMCID: PMC10855627 DOI: 10.3390/ijms25031611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
We recently demonstrated that 1,6-hexanediol inhibits the formation of assemblysomes. These membraneless cell organelles have important roles in co-translational protein complex assembly and also store halfway translated DNA damage response proteins for a timely stress response. Recognizing the therapeutic potential of 1,6-hexanediol in dismantling assemblysomes likely to be involved in chemo- or radiotherapy resistance of tumor cells, we initiated an investigation into the properties of 1,6-hexanediol. Our particular interest was to determine if this compound induces DNA double-strand breaks by releasing the BLM helicase. Its yeast ortholog Sgs1 was confirmed to be a component of assemblysomes. The BLM helicase induces DNA damage when overexpressed due to the DNA double-strand breaks it generates during its normal function to repair DNA damage sites. It is evident that storing Sgs1 helicase in assemblysomes is crucial to express the full-length functional protein only in the event of DNA damage. Alternatively, if we dissolve assemblysomes using 1,6-hexanediol, ribosome-nascent chain complexes might become targets of ribosome quality control. We explored these possibilities and found, through the Drosophila wing-spot test assay, that 1,6-hexanediol induces DNA double-strand breaks. Lethality connected to recombination events following 1,6-hexanediol treatment can be mitigated by inducing DNA double-strand breaks with X-ray. Additionally, we confirmed that SMC5 recruits DmBLM to DNA damage sites, as knocking it down abolishes the rescue effect of DNA double-strand breaks on 1,6-hexanediol-induced lethality in Drosophila melanogaster.
Collapse
Affiliation(s)
| | - Zoltán Villányi
- Department of Biochemistry and Molecular Biology, University of Szeged, H-6720 Szeged, Hungary
| |
Collapse
|
11
|
Cui X, Hou J, Wang S, Yu J, Cheng S, Yu L, Song FJ, Luo H. Werner helicase mediates the senescence and cell cycle of leukemia cells by regulating DNA repair pathways. Int J Biol Macromol 2024; 255:128305. [PMID: 37992942 DOI: 10.1016/j.ijbiomac.2023.128305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/23/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023]
Abstract
Leukemia is a type of malignant hematological disease that is generally resistant to chemotherapy and has poor therapeutic outcomes. Werner (WRN) DNA helicase, an important member of the RecQ family of helicases, plays an important role in DNA repair and telomere stability maintenance. WRN gene dysfunction leads to premature aging and predisposes humans to various types of cancers. However, the biological function of WRN in cancer remains unknown. In this study, the expression of this RecQ family helicase was investigated in different types of leukemia cells, and the leukemia cell line K562 with high WRN expression was selected to construct a WRN knockdown cell line. The results showed that WRN knockdown inhibited leukemia occurrence and development by regulating the proliferation, cell cycle, differentiation, and aging of cells and other biological processes. The results of transcriptome sequencing revealed that WRN promoted the sensitivity of leukemia cells to the DNA damage inducer Etoposide by regulating cell cycle-related proteins, such as CDC2, cyclin B1, p16, and p21, as well as key proteins in DNA damage repair pathways, such as p53, RAD50, RAD51, and MER11. Our findings show that WRN helicase is a promising potential target for leukemia treatment, providing new ideas for the development of targeted drugs against leukemia.
Collapse
Affiliation(s)
- Xudong Cui
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China; Natural Products Research Center of Guizhou Province, Guiyang 550014, PR China; Department of Infectious Disease, The Fourth Hospital of Harbin Medical University, Harbin 150001, PR China
| | - Jing Hou
- Natural Products Research Center of Guizhou Province, Guiyang 550014, PR China; College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, PR China
| | - Shimei Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China; Natural Products Research Center of Guizhou Province, Guiyang 550014, PR China; Department of Infectious Disease, The Fourth Hospital of Harbin Medical University, Harbin 150001, PR China
| | - Jia Yu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China; Natural Products Research Center of Guizhou Province, Guiyang 550014, PR China
| | - Sha Cheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China; Natural Products Research Center of Guizhou Province, Guiyang 550014, PR China
| | - Lei Yu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China; Department of Infectious Disease, The Fourth Hospital of Harbin Medical University, Harbin 150001, PR China.
| | - Fa-Jun Song
- College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, PR China.
| | - Heng Luo
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, PR China; Natural Products Research Center of Guizhou Province, Guiyang 550014, PR China.
| |
Collapse
|
12
|
Bisoi A, Sarkar S, Singh PC. Hydrophobic Interaction-Induced Topology-Independent Destabilization of G-Quadruplex. Biochemistry 2023; 62:3430-3439. [PMID: 37971518 DOI: 10.1021/acs.biochem.3c00585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Since the inception of the G-quadruplex (G4), enormous attention has been devoted to designing small molecules which can stabilize the G-quadruplex. In contrast, the knowledge about the molecules and mechanisms involved in the destabilization of G4 is sparse, although it is well recognized that destabilization of G4 is important in neurobiology and age-related genetic issues. In this study, it has been shown that amphiphilic molecules having a long hydrocarbon chain can destabilize G4, regardless of its topology, using various biophysical and molecular dynamics simulation methods. It has been observed that the hydrophobic interaction induced by the long hydrocarbon chain of amphiphilic molecules is the main contributor in triggering the destabilization of G4, although hydrogen bonding by the polar part of the molecules also cooperates in the destabilization process. The experiment and simulation studies suggest that a long hydrocarbon chain containing amphiphilic molecules gets aggregated, and their hydrocarbon chain as well as the polar group intrude in the quartet region from the 5' side and interact with guanine bases as well as nearby loops through hydrophobic and electrostatic interactions, which trigger the destabilization of G4.
Collapse
Affiliation(s)
- Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| |
Collapse
|
13
|
Wojtara MS, Kang J, Zaman M. Congenital Telangiectatic Erythema: Scoping Review. JMIR DERMATOLOGY 2023; 6:e48413. [PMID: 37796556 PMCID: PMC10587801 DOI: 10.2196/48413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/19/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Congenital telangiectatic erythema (CTE), also known as Bloom syndrome, is a rare autosomal recessive disorder characterized by below-average height, a narrow face, a red skin rash occurring on sun-exposed areas of the body, and an increased risk of cancer. CTE is one of many genodermatoses and photodermatoses associated with defects in DNA repair. CTE is caused by a mutation occurring in the BLM gene, which causes abnormal breaks in chromosomes. OBJECTIVE We aimed to analyze the existing literature on CTE to provide additional insight into its heredity, the spectrum of clinical presentations, and the management of this disorder. In addition, the gaps in current research and the use of artificial intelligence to streamline clinical diagnosis and the management of CTE are outlined. METHODS A literature search was conducted on PubMed, DOAJ, and Scopus using search terms such as "congenital telangiectatic erythema," "bloom syndrome," and "bloom-torre-machacek." Due to limited current literature, studies published from January 2000 to January 2023 were considered for this review. A total of 49 sources from the literature were analyzed. RESULTS Through this scoping review, the researchers were able to identify several publications focusing on Bloom syndrome. Some common subject areas included the heredity of CTE, clinical presentations of CTE, and management of CTE. In addition, the literature on rare diseases shows the potential advancements in understanding and treatment with artificial intelligence. Future studies should address the causes of heterogeneity in presentation and examine potential therapeutic candidates for CTE and similarly presenting syndromes. CONCLUSIONS This review illuminated current advances in potential molecular targets or causative pathways in the development of CTE as well as clinical features including erythema, increased cancer risk, and growth abnormalities. Future studies should continue to explore innovations in this space, especially in regard to the use of artificial intelligence, including machine learning and deep learning, for the diagnosis and clinical management of rare diseases such as CTE.
Collapse
Affiliation(s)
- Magda Sara Wojtara
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jayne Kang
- Department of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Mohammed Zaman
- Department of Biology, Stony Brook University, Stony Brook, NY, United States
| |
Collapse
|
14
|
Gupta SV, Campos L, Schmidt KH. Mitochondrial superoxide dismutase Sod2 suppresses nuclear genome instability during oxidative stress. Genetics 2023; 225:iyad147. [PMID: 37638880 PMCID: PMC10550321 DOI: 10.1093/genetics/iyad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023] Open
Abstract
Oxidative stress can damage DNA and thereby contribute to genome instability. To avoid an imbalance or overaccumulation of reactive oxygen species (ROS), cells are equipped with antioxidant enzymes that scavenge excess ROS. Cells lacking the RecQ-family DNA helicase Sgs1, which contributes to homology-dependent DNA break repair and chromosome stability, are known to accumulate ROS, but the origin and consequences of this oxidative stress phenotype are not fully understood. Here, we show that the sgs1 mutant exhibits elevated mitochondrial superoxide, increased mitochondrial mass, and accumulation of recombinogenic DNA lesions that can be suppressed by antioxidants. Increased mitochondrial mass in the sgs1Δ mutant is accompanied by increased mitochondrial branching, which was also inducible in wildtype cells by replication stress. Superoxide dismutase Sod2 genetically interacts with Sgs1 in the suppression of nuclear chromosomal rearrangements under paraquat (PQ)-induced oxidative stress. PQ-induced chromosome rearrangements in the absence of Sod2 are promoted by Rad51 recombinase and the polymerase subunit Pol32. Finally, the dependence of chromosomal rearrangements on the Rev1/Pol ζ mutasome suggests that under oxidative stress successful DNA synthesis during DNA break repair depends on translesion DNA synthesis.
Collapse
Affiliation(s)
- Sonia Vidushi Gupta
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Lillian Campos
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
| | - Kristina Hildegard Schmidt
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA
- Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA
| |
Collapse
|
15
|
Danino YM, Molitor L, Rosenbaum-Cohen T, Kaiser S, Cohen Y, Porat Z, Marmor-Kollet H, Katina C, Savidor A, Rotkopf R, Ben-Isaac E, Golani O, Levin Y, Monchaud D, Hickson I, Hornstein E. BLM helicase protein negatively regulates stress granule formation through unwinding RNA G-quadruplex structures. Nucleic Acids Res 2023; 51:9369-9384. [PMID: 37503837 PMCID: PMC10516661 DOI: 10.1093/nar/gkad613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023] Open
Abstract
Bloom's syndrome (BLM) protein is a known nuclear helicase that is able to unwind DNA secondary structures such as G-quadruplexes (G4s). However, its role in the regulation of cytoplasmic processes that involve RNA G-quadruplexes (rG4s) has not been previously studied. Here, we demonstrate that BLM is recruited to stress granules (SGs), which are cytoplasmic biomolecular condensates composed of RNAs and RNA-binding proteins. BLM is enriched in SGs upon different stress conditions and in an rG4-dependent manner. Also, we show that BLM unwinds rG4s and acts as a negative regulator of SG formation. Altogether, our data expand the cellular activity of BLM and shed light on the function that helicases play in the dynamics of biomolecular condensates.
Collapse
Affiliation(s)
- Yehuda M Danino
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lena Molitor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Rosenbaum-Cohen
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Brain science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sebastian Kaiser
- Center for Chromosome Stability, Dept. of Cellular and Molecular Medicine, Panum Institute, Copenhagen Univ, 2200 København N., Denmark
| | - Yahel Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hagai Marmor-Kollet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- 1E therapeutics, Rehovot, Israel
| | - Corine Katina
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Rotkopf
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal Ben-Isaac
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ofra Golani
- MICC Cell Observatory Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB CNRS UMR 6302, uB Dijon, France
| | - Ian D Hickson
- Center for Chromosome Stability, Dept. of Cellular and Molecular Medicine, Panum Institute, Copenhagen Univ, 2200 København N., Denmark
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 7610001, Israel
| |
Collapse
|
16
|
Mo C, Shiozaki Y, Omabe K, Liu Y. Understanding the Human RECQ5 Helicase-Connecting the Dots from DNA to Clinics. Cells 2023; 12:2037. [PMID: 37626846 PMCID: PMC10453775 DOI: 10.3390/cells12162037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
RECQ5, a member of the conserved RECQ helicase family, is the sole human RECQ homolog that has not been linked to a hereditary developmental syndrome. Nonetheless, dysregulation of RECQ5 has emerged as a significant clinical concern, being linked to cancer predisposition, cardiovascular disease, and inflammation. In cells, RECQ5 assumes a crucial role in the regulation of DNA repair pathways, particularly in the repair of DNA double-strand breaks and inter-strand DNA crosslinks. Moreover, RECQ5 exhibits a capacity to modulate gene expression by interacting with transcription machineries and their co-regulatory proteins, thus safeguarding against transcription-induced DNA damage. This review aims to provide an overview of the multifaceted functions of RECQ5 and its implications in maintaining genomic stability. We will discuss the potential effects of clinical variants of RECQ5 on its cellular functions and their underlying mechanisms in the pathogenesis of cancer and cardiovascular disease. We will review the impact of RECQ5 variants in the field of pharmacogenomics, specifically their influence on drug responses, which may pave the way for novel therapeutic interventions targeting RECQ5 in human diseases.
Collapse
Affiliation(s)
| | | | | | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| |
Collapse
|
17
|
Tsui V, Lyu R, Novakovic S, Stringer JM, Dunleavy JE, Granger E, Semple T, Leichter A, Martelotto LG, Merriner DJ, Liu R, McNeill L, Zerafa N, Hoffmann ER, O’Bryan MK, Hutt K, Deans AJ, Heierhorst J, McCarthy DJ, Crismani W. Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals. CELL GENOMICS 2023; 3:100349. [PMID: 37601968 PMCID: PMC10435384 DOI: 10.1016/j.xgen.2023.100349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/30/2023] [Accepted: 06/02/2023] [Indexed: 08/22/2023]
Abstract
Meiotic crossovers are required for accurate chromosome segregation and producing new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. Here, we reveal the tumor suppressor FANCM as a meiotic anti-crossover factor in mammals. We use unique large-scale crossover analyses with both single-gamete sequencing and pedigree-based bulk-sequencing datasets to identify a genome-wide increase in crossover frequencies in Fancm-deficient mice. Gametogenesis is heavily perturbed in Fancm loss-of-function mice, which is consistent with the reproductive defects reported in humans with biallelic FANCM mutations. A portion of the gametogenesis defects can be attributed to the cGAS-STING pathway after birth. Despite the gametogenesis phenotypes in Fancm mutants, both sexes are capable of producing offspring. We propose that the anti-crossover function and role in gametogenesis of Fancm are separable and will inform diagnostic pathways for human genomic instability disorders.
Collapse
Affiliation(s)
- Vanessa Tsui
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Stevan Novakovic
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jessica M. Stringer
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Jessica E.M. Dunleavy
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Elissah Granger
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Tim Semple
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Anna Leichter
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Luciano G. Martelotto
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - D. Jo Merriner
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruijie Liu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Lucy McNeill
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Nadeen Zerafa
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Eva R. Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Moira K. O’Bryan
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Karla Hutt
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Andrew J. Deans
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Genome Stability Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jörg Heierhorst
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Molecular Genetics Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
18
|
Becker RA, Hub JS. Molecular simulations of DEAH-box helicases reveal control of domain flexibility by ligands: RNA, ATP, ADP, and G-patch proteins. Biol Chem 2023; 404:867-879. [PMID: 37253384 DOI: 10.1515/hsz-2023-0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
DEAH-box helicases use the energy from ATP hydrolysis to translocate along RNA strands. They are composed of tandem RecA-like domains and a C-terminal domain connected by flexible linkers, and the activity of several DEAH-box helicases is regulated by cofactors called G-patch proteins. We used all-atom molecular dynamics simulations of the helicases Prp43, Prp22, and DHX15 in various liganded states to investigate how RNA, ADP, ATP, or G-patch proteins influence their conformational dynamics. The simulations suggest that apo helicases are highly flexible, whereas binding of RNA renders the helicases more rigid. ATP and ADP control the stability of the RecA1-RecA2 interface, but they have only a smaller effect on domain flexibility in absence of a RecA1-RecA2 interface. Binding of a G-patch protein to DHX15 imposes a more structured conformational ensemble, characterized by more defined relative domain arrangements and by an increased conformational stability of the RNA tunnel. However, the effect of the G-patch protein on domain dynamics is far more subtle as compared to the effects of RNA or ATP/ADP. The simulations characterize DEAH-box helicase as dynamic machines whose conformational ensembles are strongly defined by the presence of RNA, ATP, or ADP and only fine-tuned by the presence of G-patch proteins.
Collapse
Affiliation(s)
- Robert A Becker
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
| |
Collapse
|
19
|
Farcy S, Hachour H, Bahi-Buisson N, Passemard S. Genetic Primary Microcephalies: When Centrosome Dysfunction Dictates Brain and Body Size. Cells 2023; 12:1807. [PMID: 37443841 PMCID: PMC10340463 DOI: 10.3390/cells12131807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Primary microcephalies (PMs) are defects in brain growth that are detectable at or before birth and are responsible for neurodevelopmental disorders. Most are caused by biallelic or, more rarely, dominant mutations in one of the likely hundreds of genes encoding PM proteins, i.e., ubiquitous centrosome or microtubule-associated proteins required for the division of neural progenitor cells in the embryonic brain. Here, we provide an overview of the different types of PMs, i.e., isolated PMs with or without malformations of cortical development and PMs associated with short stature (microcephalic dwarfism) or sensorineural disorders. We present an overview of the genetic, developmental, neurological, and cognitive aspects characterizing the most representative PMs. The analysis of phenotypic similarities and differences among patients has led scientists to elucidate the roles of these PM proteins in humans. Phenotypic similarities indicate possible redundant functions of a few of these proteins, such as ASPM and WDR62, which play roles only in determining brain size and structure. However, the protein pericentrin (PCNT) is equally required for determining brain and body size. Other PM proteins perform both functions, albeit to different degrees. Finally, by comparing phenotypes, we considered the interrelationships among these proteins.
Collapse
Affiliation(s)
- Sarah Farcy
- UMR144, Institut Curie, 75005 Paris, France;
- Inserm UMR-S 1163, Institut Imagine, 75015 Paris, France
| | - Hassina Hachour
- Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, 75019 Paris, France;
| | - Nadia Bahi-Buisson
- Service de Neurologie Pédiatrique, DMU MICADO, APHP, Hôpital Necker Enfants Malades, 75015 Paris, France;
- Université Paris Cité, Inserm UMR-S 1163, Institut Imagine, 75015 Paris, France
| | - Sandrine Passemard
- Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, 75019 Paris, France;
- Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France
| |
Collapse
|
20
|
Erdinc D, Rodríguez‐Luis A, Fassad MR, Mackenzie S, Watson CM, Valenzuela S, Xie X, Menger KE, Sergeant K, Craig K, Hopton S, Falkous G, Poulton J, Garcia‐Moreno H, Giunti P, de Moura Aschoff CA, Morales Saute JA, Kirby AJ, Toro C, Wolfe L, Novacic D, Greenbaum L, Eliyahu A, Barel O, Anikster Y, McFarland R, Gorman GS, Schaefer AM, Gustafsson CM, Taylor RW, Falkenberg M, Nicholls TJ. Pathological variants in TOP3A cause distinct disorders of mitochondrial and nuclear genome stability. EMBO Mol Med 2023; 15:e16775. [PMID: 37013609 PMCID: PMC10165364 DOI: 10.15252/emmm.202216775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
Topoisomerase 3α (TOP3A) is an enzyme that removes torsional strain and interlinks between DNA molecules. TOP3A localises to both the nucleus and mitochondria, with the two isoforms playing specialised roles in DNA recombination and replication respectively. Pathogenic variants in TOP3A can cause a disorder similar to Bloom syndrome, which results from bi-allelic pathogenic variants in BLM, encoding a nuclear-binding partner of TOP3A. In this work, we describe 11 individuals from 9 families with an adult-onset mitochondrial disease resulting from bi-allelic TOP3A gene variants. The majority of patients have a consistent clinical phenotype characterised by bilateral ptosis, ophthalmoplegia, myopathy and axonal sensory-motor neuropathy. We present a comprehensive characterisation of the effect of TOP3A variants, from individuals with mitochondrial disease and Bloom-like syndrome, upon mtDNA maintenance and different aspects of enzyme function. Based on these results, we suggest a model whereby the overall severity of the TOP3A catalytic defect determines the clinical outcome, with milder variants causing adult-onset mitochondrial disease and more severe variants causing a Bloom-like syndrome with mitochondrial dysfunction in childhood.
Collapse
Affiliation(s)
- Direnis Erdinc
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
| | - Alejandro Rodríguez‐Luis
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Mahmoud R Fassad
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Sarah Mackenzie
- The Newcastle Upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Christopher M Watson
- North East and Yorkshire Genomic Laboratory Hub, Central LabSt. James's University HospitalLeedsUK
- Leeds Institute of Medical ResearchUniversity of Leeds, St. James's University HospitalLeedsUK
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Kate Sergeant
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Kate Craig
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Sila Hopton
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | | | - Joanna Poulton
- Nuffield Department of Women's & Reproductive Health, The Women's CentreUniversity of OxfordOxfordUK
| | - Hector Garcia‐Moreno
- Department of Clinical and Movement Neurosciences, Ataxia CentreUCL Queen Square Institute of NeurologyLondonUK
| | - Paola Giunti
- Department of Clinical and Movement Neurosciences, Ataxia CentreUCL Queen Square Institute of NeurologyLondonUK
| | | | - Jonas A Morales Saute
- Medical Genetics ServiceHospital de Clínicas de Porto Alegre (HCPA)Porto AlegreBrazil
- Department of Internal MedicineUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Graduate Program in Medicine: Medical SciencesUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | - Amelia J Kirby
- Department of PediatricsWake Forest School of MedicineWinston‐SalemNCUSA
| | - Camilo Toro
- Undiagnosed Diseases ProgramNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Lynne Wolfe
- Undiagnosed Diseases ProgramNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Danica Novacic
- Undiagnosed Diseases ProgramNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Lior Greenbaum
- The Danek Gertner Institute of Human GeneticsSheba Medical CenterTel HashomerIsrael
- The Joseph Sagol Neuroscience Center, Sheba Medical CenterTel HashomerIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Aviva Eliyahu
- The Danek Gertner Institute of Human GeneticsSheba Medical CenterTel HashomerIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Ortal Barel
- Genomics UnitThe Center for Cancer Research, Sheba Medical CenterTel HashomerIsrael
| | - Yair Anikster
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Metabolic Disease UnitEdmond and Lily Safra Children's Hospital, Sheba Medical CenterTel HashomerIsrael
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Gráinne S Gorman
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew M Schaefer
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| |
Collapse
|
21
|
Sharin F, Pai A, Mair M. Management of osteosarcoma of the head and neck. Curr Opin Otolaryngol Head Neck Surg 2023:00020840-990000000-00066. [PMID: 37144500 DOI: 10.1097/moo.0000000000000900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
PURPOSE OF REVIEW There is no clear consensus guideline that specifies the optimum course of treatment for adult head and neck osteosarcoma (HNO) because of its rarity. The review's goal is to examine the most recent research on the presentation, diagnosis, prognosis, and therapy of head and neck osteosarcoma. RECENT FINDINGS Due to overlapping symptoms with various benign disorders of the lower jaw and midface bone, these patients present with a noticeable delay. The greatest results for these malignancies can be achieved with surgery with sufficient margins. However, it may not be able to achieve sufficient margins in tumours of the midface and skull base, and the significance of adjuvant radiation/chemotherapy needs to be investigated. The use of adjuvant radiation in instances with an advanced stage, poor prognostic indicators, and inadequate resection is supported by evidence. Nonetheless, there are divergent opinions regarding the advantages of chemotherapy in adjuvant and neoadjuvant conditions, and further multicentric randomized control trials are required to provide robust evidence. SUMMARY Multimodality treatments seem to yield better results for advanced HNO with adverse features and incomplete resections.
Collapse
Affiliation(s)
| | | | - Manish Mair
- University hospital of Leicester, Leicester, UK
| |
Collapse
|
22
|
Becker RA, Hub JS. Continuous millisecond conformational cycle of a DEAH box helicase reveals control of domain motions by atomic-scale transitions. Commun Biol 2023; 6:379. [PMID: 37029280 PMCID: PMC10082070 DOI: 10.1038/s42003-023-04751-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
Helicases are motor enzymes found in every living organism and viruses, where they maintain the stability of the genome and control against false recombination. The DEAH-box helicase Prp43 plays a crucial role in pre-mRNA splicing in unicellular organisms by translocating single-stranded RNA. The molecular mechanisms and conformational transitions of helicases are not understood at the atomic level. We present a complete conformational cycle of RNA translocation by Prp43 in atomic detail based on molecular dynamics simulations. To enable the sampling of such complex transition on the millisecond timescale, we combined two enhanced sampling techniques, namely simulated tempering and adaptive sampling guided by crystallographic data. During RNA translocation, the center-of-mass motions of the RecA-like domains followed the established inchworm model, whereas the domains crawled along the RNA in a caterpillar-like movement, suggesting an inchworm/caterpillar model. However, this crawling required a complex sequence of atomic-scale transitions involving the release of an arginine finger from the ATP pocket, stepping of the hook-loop and hook-turn motifs along the RNA backbone, and several others. These findings highlight that large-scale domain dynamics may be controlled by complex sequences of atomic-scale transitions.
Collapse
Affiliation(s)
- Robert A Becker
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
| |
Collapse
|
23
|
Datta A, Sommers JA, Jhujh SS, Harel T, Stewart GS, Brosh RM. Discovery of a new hereditary RECQ helicase disorder RECON syndrome positions the replication stress response and genome homeostasis as centrally important processes in aging and age-related disease. Ageing Res Rev 2023; 86:101887. [PMID: 36805074 PMCID: PMC10018417 DOI: 10.1016/j.arr.2023.101887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
Characterizing the molecular deficiencies underlying human aging has been a formidable challenge as it is clear that a complex myriad of factors including genetic mutations, environmental influences, and lifestyle choices influence the deterioration responsible for human pathologies. In addition, the common denominators of human aging, exemplified by the newly updated hallmarks of aging (López-Otín et al., 2023), suggest multiple avenues and layers of crosstalk between pathways important for genome and cellular homeostasis, both of which are major determinants of both good health and lifespan. In this regard, we postulate that hereditary disorders characterized by chromosomal instability offer a unique window of insight into aging and age-related disease processes. Recently, we discovered a new RECQ helicase disorder, designated RECON syndrome attributed to bi-allelic mutations in the RECQL1 gene (Abu-Libdeh et al., 2022). Cells deficient in RECQL1 exhibit genomic instability and a compromised response to replication stress, providing further evidence for the significance of genome homeostasis to suppress disease phenotypes. Here we provide a perspective on the pathology of RECON syndrome to inform the reader as to how molecular defects in the RECQL1 gene contribute to underlying deficiencies in nucleic acid metabolism often seen in certain aging or age-related diseases.
Collapse
Affiliation(s)
- Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Joshua A Sommers
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Satpal S Jhujh
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tamar Harel
- Department of Genetics, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Grant S Stewart
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA.
| |
Collapse
|
24
|
Yilmaz Demirdag Y, Gupta S. Infections in DNA Repair Defects. Pathogens 2023; 12:pathogens12030440. [PMID: 36986362 PMCID: PMC10054915 DOI: 10.3390/pathogens12030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
DNA repair defects are heterogenous conditions characterized by a wide spectrum of clinical phenotypes. The common presentations of DNA repair defects include increased risk of cancer, accelerated aging, and defects in the development of various organs and systems. The immune system can be affected in a subset of these disorders leading to susceptibility to infections and autoimmunity. Infections in DNA repair defects may occur due to primary defects in T, B, or NK cells and other factors such as anatomic defects, neurologic disorders, or during chemotherapy. Consequently, the characteristics of the infections may vary from mild upper respiratory tract infections to severe, opportunistic, and even fatal infections with bacteria, viruses, or fungi. Here, infections in 15 rare and sporadic DNA repair defects that are associated with immunodeficiencies are discussed. Because of the rarity of some of these conditions, limited information is available regarding infectious complications.
Collapse
|
25
|
Intellectual disability and abnormal cortical neuron phenotypes in patients with Bloom syndrome. J Hum Genet 2023; 68:321-327. [PMID: 36646944 DOI: 10.1038/s10038-023-01121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/17/2022] [Accepted: 01/08/2023] [Indexed: 01/18/2023]
Abstract
Bloom syndrome (BS) is a rare autosomal recessive disorder characterized by genomic instability that leads to various complications, including cancer. Given the low prevalence of BS in Japan, we conducted a nationwide survey. We recruited eight patients with BS, three of whom exhibited intellectual disability. The 631delCAA mutation in the BLM gene was detected in 9 out of 16 alleles. To investigate neuronal development in patients with BS, we generated induced pluripotent stem cells derived from one of these patients (BS-iPSCs). We examined the phenotypes of the induced cortical neurons derived from the generated BS-iPSCs using a previously reported protocol; the generated BS-iPSCs showed an approximately 10-times higher frequency of sister-chromatid exchange (SCE) than the control iPSCs. Immunocytochemistry revealed shorter axons and higher proliferative potential in BS-iPSC-derived cortical neurons compared with control iPSCs. To our knowledge, our study is the first to clarify the abnormality of the cortical neuron phenotypes derived from patients with BS. Our findings may help identify the pathogenesis of neuronal differentiation in BS and aid in the development of novel therapeutic agents.
Collapse
|
26
|
Shin S, Hyun K, Lee J, Joo D, Kulikowicz T, Bohr V, Kim J, Hohng S. Werner syndrome protein works as a dimer for unwinding and replication fork regression. Nucleic Acids Res 2022; 51:337-348. [PMID: 36583333 PMCID: PMC9841404 DOI: 10.1093/nar/gkac1200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/31/2022] Open
Abstract
The determination of the oligomeric state of functional enzymes is essential for the mechanistic understanding of their catalytic activities. RecQ helicases have diverse biochemical activities, but it is still unclear how their activities are related to their oligomeric states. We use single-molecule multi-color fluorescence imaging to determine the oligomeric states of Werner syndrome protein (WRN) during its unwinding and replication fork regression activities. We reveal that WRN binds to a forked DNA as a dimer, and unwinds it without any change of its oligomeric state. In contrast, WRN binds to a replication fork as a tetramer, and is dimerized during activation of replication fork regression. By selectively inhibiting the helicase activity of WRN on specific strands, we reveal how the active dimers of WRN distinctly use the energy of ATP hydrolysis for repetitive unwinding and replication fork regression.
Collapse
Affiliation(s)
| | | | - Jinwoo Lee
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
| | - Dongwon Joo
- Department of Physics and Astronomy, Institute of Applied Physics, Seoul National University, Seoul, Republic of Korea
| | - Tomasz Kulikowicz
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vilhelm A Bohr
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sungchul Hohng
- To whom correspondence should be addressed. Tel: +82 2 880 6593;
| |
Collapse
|
27
|
Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
Collapse
Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| |
Collapse
|
28
|
Marchena-Perea EM, Salazar-Hidalgo ME, Gómez-Sanz A, Arranz-Ledo M, Barroso A, Fernández V, Tejera-Pérez H, Pita G, Núñez-Torres R, Pombo L, Morales-Chamorro R, Cano-Cano JM, Soriano MDC, Garre P, Durán M, Currás-Freixes M, de la Hoya M, Osorio A. A Large Case-Control Study Performed in Spanish Population Suggests That RECQL5 Is the Only RECQ Helicase Involved in Breast Cancer Susceptibility. Cancers (Basel) 2022; 14:cancers14194738. [PMID: 36230663 PMCID: PMC9563930 DOI: 10.3390/cancers14194738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Around 50% of the familial breast cancer (BC) cases are estimated to be caused by variants in low-, moderate-, and high-risk susceptibility genes; however, the other half is of unknown origin. The finding of new susceptibility genes is key to improve diagnosis, take preventive measures, and identify new therapies. In this context, previous studies have discussed whether the genes encoding for the RECQ helicase family could play a role in BC susceptibility, without very conclusive results. To clarify this, in this study, we sequenced the whole coding sequence of the RECQL1, BLM, WRN, RECQL4, and RECQL5 genes in 1993 Spanish BC familial cases and compared it with controls from gnomAD. No association was found for RECQL1, BLM, WRN, and RECQL4; however, we did find an association between RECQL5 and breast cancer as a moderate-risk gene, making it a perfect candidate for further studies. Abstract Around 50% of the familial breast cancer (BC) cases are estimated to be caused by germline variants in known low-, moderate-, and high-risk susceptibility genes, while the other half is of unknown genetic origin. In the present study, we wanted to evaluate the role of the RECQ helicases, some of which have been studied in the past as candidates, with unclear results about their role in the disease. Using next-generation sequencing (NGS) technology, we analyzed the whole coding sequence of BLM, RECQL1, RECQL4, RECQL5, and WRN in almost 2000 index cases from BC Spanish families that had previously tested negative for the known BC susceptibility genes (BRCAX) and compared the results with the controls extracted from gnomAD. Our results suggest that BLM, RECQL1, RECQL4, and WRN do not play a major role in BC susceptibility. However, in the combined analysis, joining the present results with those previously reported in a series of 1334 BC Spanish patients and controls, we found a statistically significant association between Loss of Function (LoF) variants in RECQL5 and BC risk, with an OR of 2.56 (p = 0.009; 95% CI, 1.18–4.98). Our findings support our previous work and places the RECQL5 gene as a new moderate-risk BC gene.
Collapse
Affiliation(s)
- Erik Michel Marchena-Perea
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Milton Eduardo Salazar-Hidalgo
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Alicia Gómez-Sanz
- Molecular Oncology Laboratory (CIBERONC), Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Mónica Arranz-Ledo
- Cancer Genetics Group, Unidad de Excelencia Instituto de Biología y Genética Molecular, Universidad de Valladolid-Consejo Superior de Investigaciones Científicas (IBGM, UVa-CSIC), 47003 Valladolid, Spain
| | - Alicia Barroso
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Victoria Fernández
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Hugo Tejera-Pérez
- Human Cancer Genetics Programme, Human Genotyping Unit (CEGEN), Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Guillermo Pita
- Human Cancer Genetics Programme, Human Genotyping Unit (CEGEN), Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Rocío Núñez-Torres
- Human Cancer Genetics Programme, Human Genotyping Unit (CEGEN), Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Luz Pombo
- Medical Oncology Section, Universitary Hospital Complex of Albacete, 02006 Albacete, Spain
| | - Rafael Morales-Chamorro
- Medical Oncology Section, Hospitalary Compex La Mancha Centro, 13600 Alcázar de San Juan, Spain
| | - Juana María Cano-Cano
- Medical Oncology Service, Universitary General Hospital of Ciudad Real, 13005 Ciudad Real, Spain
| | | | - Pilar Garre
- Molecular Oncology Laboratory (CIBERONC), Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Mercedes Durán
- Cancer Genetics Group, Unidad de Excelencia Instituto de Biología y Genética Molecular, Universidad de Valladolid-Consejo Superior de Investigaciones Científicas (IBGM, UVa-CSIC), 47003 Valladolid, Spain
| | - María Currás-Freixes
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory (CIBERONC), Hospital Clínico San Carlos, IdISSC, 28040 Madrid, Spain
| | - Ana Osorio
- Human Cancer Genetics Programme, Familial Cancer Clinical Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
- Spanish Network on Rare Diseases (CIBERER), 28029 Madrid, Spain
- Genetics Service, Fundación Jiménez Díaz, 28043 Madrid, Spain
- Correspondence: ; Tel.: +34-917-328-002
| |
Collapse
|
29
|
Usami M, Ikawa Y, Sakai Y, Fujiki T, Wada T. Refractory gastroduodenal ulcers: A rare complication with Bloom syndrome. Clin Case Rep 2022; 10:CCR36141. [PMID: 36110332 PMCID: PMC9465695 DOI: 10.1002/ccr3.6141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/23/2022] [Accepted: 07/04/2022] [Indexed: 11/08/2022] Open
Abstract
Bloom syndrome patients often develop severe gastrointestinal symptoms mainly caused by gastric tumors due to DNA repair disorder. Here, we report 31‐year‐old Bloom syndrome patient suffering persistent abdominal pain due to refractory gastroduodenal ulcers which required gastroduodenectomy. Various causes should be considered, and the accumulation of their reports is warranted.
Collapse
Affiliation(s)
- Masaaki Usami
- Department of Pediatrics School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University Kanazawa Japan
| | - Yasuhiro Ikawa
- Department of Pediatrics School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University Kanazawa Japan
| | - Yuta Sakai
- Department of Pediatrics School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University Kanazawa Japan
| | - Toshihiro Fujiki
- Department of Pediatrics School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University Kanazawa Japan
| | - Taizo Wada
- Department of Pediatrics School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University Kanazawa Japan
| |
Collapse
|
30
|
Kohzaki M. Mammalian Resilience Revealed by a Comparison of Human Diseases and Mouse Models Associated With DNA Helicase Deficiencies. Front Mol Biosci 2022; 9:934042. [PMID: 36032672 PMCID: PMC9403131 DOI: 10.3389/fmolb.2022.934042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 12/01/2022] Open
Abstract
Maintaining genomic integrity is critical for sustaining individual animals and passing on the genome to subsequent generations. Several enzymes, such as DNA helicases and DNA polymerases, are involved in maintaining genomic integrity by unwinding and synthesizing the genome, respectively. Indeed, several human diseases that arise caused by deficiencies in these enzymes have long been known. In this review, the author presents the DNA helicases associated with human diseases discovered to date using recent analyses, including exome sequences. Since several mouse models that reflect these human diseases have been developed and reported, this study also summarizes the current knowledge regarding the outcomes of DNA helicase deficiencies in humans and mice and discusses possible mechanisms by which DNA helicases maintain genomic integrity in mammals. It also highlights specific diseases that demonstrate mammalian resilience, in which, despite the presence of genomic instability, patients and mouse models have lifespans comparable to those of the general population if they do not develop cancers; finally, this study discusses future directions for therapeutic applications in humans that can be explored using these mouse models.
Collapse
|
31
|
James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
Collapse
Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
Collapse
Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
| |
Collapse
|
32
|
Barmettler S, Sharapova SO, Milota T, Greif PA, Magg T, Hauck F. Genomics Driving Diagnosis and Treatment of Inborn Errors of Immunity With Cancer Predisposition. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:1725-1736.e2. [PMID: 35364342 DOI: 10.1016/j.jaip.2022.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
Abstract
Inborn errors of immunity (IEI) are genetically and clinically heterogeneous disorders that, in addition to infection susceptibility and immune dysregulation, can have an enhanced cancer predisposition. The increasing availability of upfront next-generation sequencing diagnostics in immunology and oncology have uncovered substantial overlap of germline and somatic genetic conditions that can result in immunodeficiency and cancer. However, broad application of unbiased genetics in these neighboring disciplines still needs to be deployed, and joined therapeutic strategies guided by germline and somatic genetic risk factors are lacking. We illustrate the current difficulties encountered in clinical practice, summarize the historical development of pathophysiological concepts of cancer predisposition, and review select genetic, molecular, and cellular mechanisms of well-defined and illustrative disease entities such as DNA repair defects, combined immunodeficiencies with Epstein-Barr virus susceptibility, autoimmune lymphoproliferative syndromes, regulatory T-cell disorders, and defects in cell intrinsic immunity. We review genetic variants that, when present in the germline, cause IEI with cancer predisposition but, when arising as somatic variants, behave as oncogenes and cause specific cancer entities. We finally give examples of small molecular compounds that are developed and studied to target genetically defined cancers but might also proof useful to treat IEI.
Collapse
Affiliation(s)
- Sara Barmettler
- Allergy and Clinical Immunology Unit, Division of Rheumatology, Allergy, & Immunology, Massachusetts General Hospital, Boston, Mass
| | - Svetlana O Sharapova
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Tomas Milota
- Department of Immunology, Second Faculty of Medicine, Charles University Hospital and Motol University Hospital, Prague, Czechia
| | - Philipp A Greif
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, 81377 Munich, Germany; German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Thomas Magg
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Hauck
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.
| |
Collapse
|
33
|
Thakkar MK, Lee J, Meyer S, Chang VY. RecQ Helicase Somatic Alterations in Cancer. Front Mol Biosci 2022; 9:887758. [PMID: 35782872 PMCID: PMC9240438 DOI: 10.3389/fmolb.2022.887758] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Named the “caretakers” of the genome, RecQ helicases function in several pathways to maintain genomic stability and repair DNA. This highly conserved family of enzymes consist of five different proteins in humans: RECQL1, BLM, WRN, RECQL4, and RECQL5. Biallelic germline mutations in BLM, WRN, and RECQL4 have been linked to rare cancer-predisposing syndromes. Emerging research has also implicated somatic alterations in RecQ helicases in a variety of cancers, including hematological malignancies, breast cancer, osteosarcoma, amongst others. These alterations in RecQ helicases, particularly overexpression, may lead to increased resistance of cancer cells to conventional chemotherapy. Downregulation of these proteins may allow for increased sensitivity to chemotherapy, and, therefore, may be important therapeutic targets. Here we provide a comprehensive review of our current understanding of the role of RecQ DNA helicases in cancer and discuss the potential therapeutic opportunities in targeting these helicases.
Collapse
Affiliation(s)
- Megha K. Thakkar
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jamie Lee
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Stefan Meyer
- Division of Cancer Studies, University of Manchester, Manchester, United Kingdom
- Department of Pediatric Hematology Oncology, Royal Manchester Children’s Hospital and Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Vivian Y. Chang
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, University of California, Los Angeles, Los Angeles, CA, United States
- Childrens Discovery and Innovation Institute, UCLA, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, United States
- *Correspondence: Vivian Y. Chang,
| |
Collapse
|
34
|
Samir P, Kanneganti TD. DEAD/H-Box Helicases in Immunity, Inflammation, Cell Differentiation, and Cell Death and Disease. Cells 2022; 11:1608. [PMID: 35626643 PMCID: PMC9139286 DOI: 10.3390/cells11101608] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 12/21/2022] Open
Abstract
DEAD/H-box proteins are the largest family of RNA helicases in mammalian genomes, and they are present in all kingdoms of life. Since their discovery in the late 1980s, DEAD/H-box family proteins have been a major focus of study. They have been found to play central roles in RNA metabolism, gene expression, signal transduction, programmed cell death, and the immune response to bacterial and viral infections. Aberrant functions of DEAD/H-box proteins have been implicated in a wide range of human diseases that include cancer, neurodegeneration, and inherited genetic disorders. In this review, we provide a historical context and discuss the molecular functions of DEAD/H-box proteins, highlighting the recent discoveries linking their dysregulation to human diseases. We will also discuss the state of knowledge regarding two specific DEAD/H-box proteins that have critical roles in immune responses and programmed cell death, DDX3X and DDX58, also known as RIG-I. Given their importance in homeostasis and disease, an improved understanding of DEAD/H-box protein biology and protein-protein interactions will be critical for informing strategies to counteract the pathogenesis associated with several human diseases.
Collapse
|
35
|
Georgakopoulos-Soares I, Parada GE, Hemberg M. Secondary structures in RNA synthesis, splicing and translation. Comput Struct Biotechnol J 2022; 20:2871-2884. [PMID: 35765654 PMCID: PMC9198270 DOI: 10.1016/j.csbj.2022.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
Even though the functional role of mRNA molecules is primarily decided by the nucleotide sequence, several properties are determined by secondary structure conformations. Examples of secondary structures include long range interactions, hairpins, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. Here, we discuss advances in our understanding of how secondary structures can impact RNA synthesis, splicing, translation and mRNA half-life. During RNA synthesis, secondary structures determine RNA polymerase II (RNAPII) speed, thereby influencing splicing. Splicing is also determined by RNA binding proteins and their binding rates are modulated by secondary structures. For the initiation of translation, secondary structures can control the choice of translation start site. Here, we highlight the mechanisms by which secondary structures modulate these processes, discuss advances in technologies to detect and study them systematically, and consider the roles of RNA secondary structures in disease.
Collapse
|
36
|
Xue C, Salunkhe SJ, Tomimatsu N, Kawale AS, Kwon Y, Burma S, Sung P, Greene EC. Bloom helicase mediates formation of large single-stranded DNA loops during DNA end processing. Nat Commun 2022; 13:2248. [PMID: 35473934 PMCID: PMC9042962 DOI: 10.1038/s41467-022-29937-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
Bloom syndrome (BS) is associated with a profoundly increased cancer risk and is caused by mutations in the Bloom helicase (BLM). BLM is involved in the nucleolytic processing of the ends of DNA double-strand breaks (DSBs), to yield long 3' ssDNA tails that serve as the substrate for break repair by homologous recombination (HR). Here, we use single-molecule imaging to demonstrate that BLM mediates formation of large ssDNA loops during DNA end processing. A BLM mutant lacking the N-terminal domain (NTD) retains vigorous in vitro end processing activity but fails to generate ssDNA loops. This same mutant supports DSB end processing in cells, however, these cells do not form RAD51 DNA repair foci and the processed DSBs are channeled into synthesis-dependent strand annealing (SSA) instead of HR-mediated repair, consistent with a defect in RAD51 filament formation. Together, our results provide insights into BLM functions during homologous recombination.
Collapse
Affiliation(s)
- Chaoyou Xue
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Sameer J Salunkhe
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Nozomi Tomimatsu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ajinkya S Kawale
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
- The Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
| |
Collapse
|
37
|
Bloom syndrome helicase contributes to germ line development and longevity in zebrafish. Cell Death Dis 2022; 13:363. [PMID: 35436990 PMCID: PMC9016072 DOI: 10.1038/s41419-022-04815-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 03/18/2022] [Accepted: 03/31/2022] [Indexed: 11/08/2022]
Abstract
RecQ helicases—also known as the “guardians of the genome”—play crucial roles in genome integrity maintenance through their involvement in various DNA metabolic pathways. Aside from being conserved from bacteria to vertebrates, their importance is also reflected in the fact that in humans impaired function of multiple RecQ helicase orthologs are known to cause severe sets of problems, including Bloom, Werner, or Rothmund-Thomson syndromes. Our aim was to create and characterize a zebrafish (Danio rerio) disease model for Bloom syndrome, a recessive autosomal disorder. In humans, this syndrome is characterized by short stature, skin rashes, reduced fertility, increased risk of carcinogenesis, and shortened life expectancy brought on by genomic instability. We show that zebrafish blm mutants recapitulate major hallmarks of the human disease, such as shortened lifespan and reduced fertility. Moreover, similarly to other factors involved in DNA repair, some functions of zebrafish Blm bear additional importance in germ line development, and consequently in sex differentiation. Unlike fanc genes and rad51, however, blm appears to affect its function independent of tp53. Therefore, our model will be a valuable tool for further understanding the developmental and molecular attributes of this rare disease, along with providing novel insights into the role of genome maintenance proteins in somatic DNA repair and fertility.
Collapse
|
38
|
Courcelle J, Worley TK, Courcelle CT. Recombination Mediator Proteins: Misnomers That Are Key to Understanding the Genomic Instabilities in Cancer. Genes (Basel) 2022; 13:genes13030437. [PMID: 35327990 PMCID: PMC8950967 DOI: 10.3390/genes13030437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
Recombination mediator proteins have come into focus as promising targets for cancer therapy, with synthetic lethal approaches now clinically validated by the efficacy of PARP inhibitors in treating BRCA2 cancers and RECQ inhibitors in treating cancers with microsatellite instabilities. Thus, understanding the cellular role of recombination mediators is critically important, both to improve current therapies and develop new ones that target these pathways. Our mechanistic understanding of BRCA2 and RECQ began in Escherichia coli. Here, we review the cellular roles of RecF and RecQ, often considered functional homologs of these proteins in bacteria. Although these proteins were originally isolated as genes that were required during replication in sexual cell cycles that produce recombinant products, we now know that their function is similarly required during replication in asexual or mitotic-like cell cycles, where recombination is detrimental and generally not observed. Cells mutated in these gene products are unable to protect and process replication forks blocked at DNA damage, resulting in high rates of cell lethality and recombination events that compromise genome integrity during replication.
Collapse
|
39
|
Maity J, Horibata S, Zurcher G, Lee JM. Targeting of RecQ Helicases as a Novel Therapeutic Strategy for Ovarian Cancer. Cancers (Basel) 2022; 14:cancers14051219. [PMID: 35267530 PMCID: PMC8909030 DOI: 10.3390/cancers14051219] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022] Open
Abstract
RecQ helicases are essential for DNA replication, recombination, DNA damage repair, and other nucleic acid metabolic pathways required for normal cell growth, survival, and genome stability. More recently, RecQ helicases have been shown to be important for replication fork stabilization, one of the major mechanisms of PARP inhibitor resistance. Cancer cells often have upregulated helicases and depend on these enzymes to repair rapid growth-promoted DNA lesions. Several studies are now evaluating the use of RecQ helicases as potential biomarkers of breast and gynecologic cancers. Furthermore, RecQ helicases have attracted interest as possible targets for cancer treatment. In this review, we discuss the characteristics of RecQ helicases and their interacting partners that may be utilized for effective treatment strategies (as cancers depend on helicases for survival). We also discuss how targeting helicase in combination with DNA repair inhibitors (i.e., PARP and ATR inhibitors) can be used as novel approaches for cancer treatment to increase sensitivity to current treatment to prevent rise of treatment resistance.
Collapse
Affiliation(s)
- Jyotirindra Maity
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (J.M.); (G.Z.)
| | - Sachi Horibata
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
- Department of Pharmacology and Toxicology, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (S.H.); (J.M.L.)
| | - Grant Zurcher
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (J.M.); (G.Z.)
| | - Jung-Min Lee
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (J.M.); (G.Z.)
- Correspondence: (S.H.); (J.M.L.)
| |
Collapse
|
40
|
Bando H, Urai S, Kanie K, Sasaki Y, Yamamoto M, Fukuoka H, Iguchi G, Camper SA. Novel genes and variants associated with congenital pituitary hormone deficiency in the era of next-generation sequencing. Front Endocrinol (Lausanne) 2022; 13:1008306. [PMID: 36237189 PMCID: PMC9551393 DOI: 10.3389/fendo.2022.1008306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/09/2022] [Indexed: 01/07/2023] Open
Abstract
Combined pituitary hormone deficiency (CPHD) is not a rare disorder, with a frequency of approximately 1 case per 4,000 live births. However, in most cases, a genetic diagnosis is not available. Furthermore, the diagnosis is challenging because no clear correlation exists between the pituitary hormones affected and the gene(s) responsible for the disorder. Next-generation sequencing (NGS) has recently been widely used to identify novel genes that cause (or putatively cause) CPHD. This review outlines causative genes for CPHD that have been newly reported in recent years. Moreover, novel variants of known CPHD-related genes (POU1F1 and GH1 genes) that contribute to CPHD through unique mechanisms are also discussed in this review. From a clinical perspective, variants in some of the recently identified causative genes result in extra-pituitary phenotypes. Clinical research on the related symptoms and basic research on pituitary formation may help in inferring the causative gene(s) of CPHD. Future NGS analysis of a large number of CPHD cases may reveal new genes related to pituitary development. Clarifying the causative genes of CPHD may help to understand the process of pituitary development. We hope that future innovations will lead to the identification of genes responsible for CPHD and pituitary development.
Collapse
Affiliation(s)
- Hironori Bando
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- *Correspondence: Hironori Bando,
| | - Shin Urai
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University School of Medicine, Kobe, Japan
| | - Keitaro Kanie
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Yuriko Sasaki
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University School of Medicine, Kobe, Japan
| | - Masaaki Yamamoto
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Hidenori Fukuoka
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
| | - Genzo Iguchi
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Hospital, Kobe, Japan
- Division of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan
- Medical Center for Student Health, Kobe University, Kobe, Japan
| | - Sally A. Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
| |
Collapse
|
41
|
de Renty C, Pond KW, Yagle MK, Ellis NA. BLM Sumoylation Is Required for Replication Stability and Normal Fork Velocity During DNA Replication. Front Mol Biosci 2022; 9:875102. [PMID: 35847987 PMCID: PMC9284272 DOI: 10.3389/fmolb.2022.875102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
BLM is sumoylated in response to replication stress. We have studied the role of BLM sumoylation in physiologically normal and replication-stressed conditions by expressing in BLM-deficient cells a BLM with SUMO acceptor-site mutations, which we refer to as SUMO-mutant BLM cells. SUMO-mutant BLM cells exhibited multiple defects in both stressed and unstressed DNA replication conditions, including, in hydroxyurea-treated cells, reduced fork restart and increased fork collapse and, in untreated cells, slower fork velocity and increased fork instability as assayed by track-length asymmetry. We further showed by fluorescence recovery after photobleaching that SUMO-mutant BLM protein was less dynamic than normal BLM and comprised a higher immobile fraction at collapsed replication forks. BLM sumoylation has previously been linked to the recruitment of RAD51 to stressed forks in hydroxyurea-treated cells. An important unresolved question is whether the failure to efficiently recruit RAD51 is the explanation for replication stress in untreated SUMO-mutant BLM cells.
Collapse
Affiliation(s)
- Christelle de Renty
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Kelvin W Pond
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Mary K Yagle
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States
| | - Nathan A Ellis
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, United States.,Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, United States
| |
Collapse
|
42
|
Yoshida M, Tomobe Y, Tomotaki S, Niwa F, Kawai M. Bloom syndrome for which second chromosomal analysis led to early diagnosis. Pediatr Int 2022; 64:e15020. [PMID: 35278254 DOI: 10.1111/ped.15020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/06/2021] [Accepted: 09/30/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Mai Yoshida
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yutaro Tomobe
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seiichi Tomotaki
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fusako Niwa
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Kawai
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| |
Collapse
|
43
|
Hua LL, Casas C, Mikawa T. Mitotic Antipairing of Homologous Chromosomes. Results Probl Cell Differ 2022; 70:191-220. [PMID: 36348108 PMCID: PMC9731508 DOI: 10.1007/978-3-031-06573-6_6] [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: 11/09/2022]
Abstract
Chromosome organization is highly dynamic and plays an essential role during cell function. It was recently found that pairs of the homologous chromosomes are continuously separated at mitosis and display a haploid (1n) chromosome set, or "antipairing," organization in human cells. Here, we provide an introduction to the current knowledge of homologous antipairing in humans and its implications in human disease.
Collapse
Affiliation(s)
- Lisa L. Hua
- Department of Biology, Sonoma State University, San Francisco
| | - Christian Casas
- Department of Biology, Sonoma State University, San Francisco
| | - Takashi Mikawa
- Department of Anatomy, Cardiovascular Research Institute, University of California, San Francisco,Corresponding author:
| |
Collapse
|
44
|
Suszynska M, Ratajska M, Galka-Marciniak P, Ryszkowska A, Wydra D, Debniak J, Jasiak A, Wasag B, Cybulski C, Kozlowski P. Variant identification in BARD1, PRDM9, RCC1, and RECQL in patients with ovarian cancer by targeted next-generation sequencing of DNA pools. Cancer Prev Res (Phila) 2021; 15:151-160. [PMID: 34906988 DOI: 10.1158/1940-6207.capr-21-0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/27/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022]
Abstract
Several ovarian cancer susceptibility genes have been discovered, but more are likely to exist. In this study, we aimed to analyze knowledge-based selected genes, i.e., BARD1, PRDM9, RCC1, and RECQL, in which pathogenic germline variants have been reported in patients with breast and/or ovarian cancer. As deep sequencing of DNA samples remains costly, targeted next-generation sequencing of DNA pools was utilized to screen the exons of BARD1, PRDM9, RCC1, and RECQL in ~400 Polish ovarian cancer cases. 25 pools of 16 samples (including several duplicated samples with known variants) were sequenced on the NovaSeq6000 and analyzed with SureCall (Agilent) application. The set of variants was filtrated to exclude spurious variants, and, subsequently, the identified rare genetic variants were validated using Sanger sequencing. No pathogenic mutation was found within the analyzed cohort of ovarian cancer patients. Validation genotyping of filtered rare silent and missense variants revealed that the majority of them were true alterations, especially those with a higher mutation quality value. The high concordance (R2=0.95) of population allele frequency for 44 common SNPs in the European control population (gnomAD) and our experiment confirmed the reliability of pooled sequencing. Mutations in BARD1, PRDM9, RCC1, and RECQL do not contribute substantially to the risk of ovarian cancer. Pooled DNA sequencing is a cost-effective and reliable method for the initial screening of candidate genes; however, it still requires validation of identified rare variants.
Collapse
Affiliation(s)
- Malwina Suszynska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Ratajska
- Department of Pathology, Dunedin School of Medicine, University of Otago
| | - Paulina Galka-Marciniak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Aleksandra Ryszkowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dariusz Wydra
- Department of Gynaecology, Oncologic Gynaecology and Gynaecological Endocrinology, Medical University of Gdansk
| | - Jaroslaw Debniak
- Department of Gynaecology, Oncologic Gynaecology and Gynaecological Endocrinology, Medical University of Gdansk
| | - Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk
| | | | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
45
|
Xu X, Chang CW, Li M, Liu C, Liu Y. Molecular Mechanisms of the RECQ4 Pathogenic Mutations. Front Mol Biosci 2021; 8:791194. [PMID: 34869606 PMCID: PMC8637615 DOI: 10.3389/fmolb.2021.791194] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 12/03/2022] Open
Abstract
The human RECQ4 gene encodes an ATP-dependent DNA helicase that contains a conserved superfamily II helicase domain located at the center of the polypeptide. RECQ4 is one of the five RECQ homologs in human cells, and its helicase domain is flanked by the unique amino and carboxyl termini with sequences distinct from other members of the RECQ helicases. Since the identification of the RECQ4 gene in 1998, multiple RECQ4 mutations have been linked to the pathogenesis of three clinical diseases, which are Rothmund-Thomson syndrome, Baller-Gerold syndrome, and RAPADILINO. Patients with these diseases show various developmental abnormalities. In addition, a subset of RECQ4 mutations are associated with high cancer risks, especially for osteosarcoma and/or lymphoma at early ages. The discovery of clinically relevant RECQ4 mutations leads to intriguing questions: how is the RECQ4 helicase responsible for preventing multiple clinical syndromes? What are the mechanisms by which the RECQ4 disease mutations cause tissue abnormalities and drive cancer formation? Furthermore, RECQ4 is highly overexpressed in many cancer types, raising the question whether RECQ4 acts not only as a tumor suppressor but also an oncogene that can be a potential new therapeutic target. Defining the molecular dysfunctions of different RECQ4 disease mutations is imperative to improving our understanding of the complexity of RECQ4 clinical phenotypes and the dynamic roles of RECQ4 in cancer development and prevention. We will review recent progress in examining the molecular and biochemical properties of the different domains of the RECQ4 protein. We will shed light on how the dynamic roles of RECQ4 in human cells may contribute to the complexity of RECQ4 clinical phenotypes.
Collapse
Affiliation(s)
- Xiaohua Xu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Chou-Wei Chang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Chao Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, CA, United States
| |
Collapse
|
46
|
Abstract
Ring-shaped hexameric helicases are essential motor proteins that separate duplex nucleic acid strands for DNA replication, recombination, and transcriptional regulation. Two evolutionarily distinct lineages of these enzymes, predicated on RecA and AAA+ ATPase folds, have been identified and characterized to date. Hexameric helicases couple NTP hydrolysis with conformational changes that move nucleic acid substrates through a central pore in the enzyme. How hexameric helicases productively engage client DNA or RNA segments and use successive rounds of NTPase activity to power translocation and unwinding have been longstanding questions in the field. Recent structural and biophysical findings are beginning to reveal commonalities in NTP hydrolysis and substrate translocation by diverse hexameric helicase families. Here, we review these molecular mechanisms and highlight aspects of their function that are yet to be understood.
Collapse
|
47
|
Vu TV, Das S, Nguyen CC, Kim J, Kim JY. Single-strand annealing: Molecular mechanisms and potential applications in CRISPR-Cas-based precision genome editing. Biotechnol J 2021; 17:e2100413. [PMID: 34846104 DOI: 10.1002/biot.202100413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Spontaneous double-stranded DNA breaks (DSBs) frequently occur within the genome of all living organisms and must be well repaired for survival. Recently, more important roles of the DSB repair pathways that were previously thought to be minor pathways, such as single-strand annealing (SSA), have been shown. Nevertheless, the biochemical mechanisms and applications of the SSA pathway in genome editing have not been updated. PURPOSE AND SCOPE Understanding the molecular mechanism of SSA is important to design potential applications in gene editing. This review provides insights into the recent progress of SSA studies and establishes a model for their potential applications in precision genome editing. SUMMARY AND CONCLUSION The SSA mechanism involved in DNA DSB repair appears to be activated by a complex signaling cascade starting with broken end sensing and 5'-3' resection to reveal homologous repeats on the 3' ssDNA overhangs that flank the DSB. Annealing the repeats would help to amend the discontinuous ends and restore the intact genome, resulting in the missing of one repeat and the intervening sequence between the repeats. We proposed a model for CRISPR-Cas-based precision insertion or replacement of DNA fragments to take advantage of the characteristics. The proposed model can add a tool to extend the choice for precision gene editing. Nevertheless, the model needs to be experimentally validated and optimized with SSA-favorable conditions for practical applications.
Collapse
Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.,National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Bac Tu Liem, Hanoi, Vietnam
| | - Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Cam Chau Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.,Division of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| |
Collapse
|
48
|
Ruchert JM, Brady MM, McMahan S, Lacey KJ, Latta LC, Sekelsky J, Stoffregen EP. Blm helicase facilitates rapid replication of repetitive DNA sequences in early Drosophila development. Genetics 2021; 220:6407149. [PMID: 34849849 DOI: 10.1093/genetics/iyab169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/18/2021] [Indexed: 11/12/2022] Open
Abstract
The absence of functional BLM DNA helicase, a member of the RecQ family of helicases, is responsible for the rare human disorder Bloom Syndrome, which results in developmental abnormalities, DNA repair defects, genomic instability, and a predisposition to cancer. In Drosophila melanogaster, the orthologous Blm protein is essential during early development when the embryo is under the control of maternal gene products. We show that lack of functional maternal Blm during the syncytial cell cycles of Drosophila embryonic development results in severe nuclear defects and lethality. Amongst the small fraction of embryos from Blm mutant mothers that survive to adulthood, a prominent sex-bias favors the class that inherits less repetitive DNA content, which serves as an endogenous source of replication stress. This selection against repetitive DNA content reflects a role for Blm in facilitating replication through repetitive sequences during the rapid S-phases of syncytial cell cycles. During these syncytial cycles, Blm is not required for complex DNA double-strand break repair; however, the progeny sex-bias resulting from the absence of maternal Blm is exacerbated by repetitive DNA sequences and by the slowing of replication fork progression, suggesting that the essential role for Blm during this stage is to manage replication fork stress brought about by impediments to fork progression. Additionally, our data suggest that Blm is only required to manage this replication stress during embryonic development, and likely only during the early, rapid syncytial cell cycles, and not at later developmental stages. These results provide novel insights into Blm function throughout development.
Collapse
Affiliation(s)
- Jolee M Ruchert
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Morgan M Brady
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Susan McMahan
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karly J Lacey
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Leigh C Latta
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Jeff Sekelsky
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric P Stoffregen
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA.,SPIRE Postdoctoral Fellowship Program, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
49
|
Benitez EK, Lomova Kaufman A, Cervantes L, Clark DN, Ayoub PG, Senadheera S, Osborne K, Sanchez JM, Crisostomo RV, Wang X, Reuven N, Shaul Y, Hollis RP, Romero Z, Kohn DB. Global and Local Manipulation of DNA Repair Mechanisms to Alter Site-Specific Gene Editing Outcomes in Hematopoietic Stem Cells. Front Genome Ed 2021; 2:601541. [PMID: 34713224 PMCID: PMC8525354 DOI: 10.3389/fgeed.2020.601541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Monogenic disorders of the blood system have the potential to be treated by autologous stem cell transplantation of ex vivo genetically modified hematopoietic stem and progenitor cells (HSPCs). The sgRNA/Cas9 system allows for precise modification of the genome at single nucleotide resolution. However, the system is reliant on endogenous cellular DNA repair mechanisms to mend a Cas9-induced double stranded break (DSB), either by the non-homologous end joining (NHEJ) pathway or by the cell-cycle regulated homology-directed repair (HDR) pathway. Here, we describe a panel of ectopically expressed DNA repair factors and Cas9 variants assessed for their ability to promote gene correction by HDR or inhibit gene disruption by NHEJ at the HBB locus. Although transient global overexpression of DNA repair factors did not improve the frequency of gene correction in primary HSPCs, localization of factors to the DSB by fusion to the Cas9 protein did alter repair outcomes toward microhomology-mediated end joining (MMEJ) repair, an HDR event. This strategy may be useful when predictable gene editing outcomes are imperative for therapeutic success.
Collapse
Affiliation(s)
- Elizabeth K Benitez
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Anastasia Lomova Kaufman
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lilibeth Cervantes
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Danielle N Clark
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Paul G Ayoub
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Shantha Senadheera
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kyle Osborne
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Julie M Sanchez
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ralph Valentine Crisostomo
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xiaoyan Wang
- Department of General Internal Medicine and Health Services Research, University of California, Los Angeles, Los Angeles, CA, United States
| | - Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roger P Hollis
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Zulema Romero
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Donald B Kohn
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
50
|
Abstract
Innate immunity is regulated by a broad set of evolutionary conserved receptors to finely probe the local environment and maintain host integrity. Besides pathogen recognition through conserved motifs, several of these receptors also sense aberrant or misplaced self-molecules as a sign of perturbed homeostasis. Among them, self-nucleic acid sensing by the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING) pathway alerts on the presence of both exogenous and endogenous DNA in the cytoplasm. We review recent literature demonstrating that self-nucleic acid detection through the STING pathway is central to numerous processes, from cell physiology to sterile injury, auto-immunity and cancer. We address the role of STING in autoimmune diseases linked to dysfunctional DNAse or related to mutations in DNA sensing pathways. We expose the role of the cGAS/STING pathway in inflammatory diseases, neurodegenerative conditions and cancer. Connections between STING in various cell processes including autophagy and cell death are developed. Finally, we review proposed mechanisms to explain the sources of cytoplasmic DNA.
Collapse
Affiliation(s)
| | - Nicolas Riteau
- Experimental and Molecular Immunology and Neurogenetics Laboratory (INEM), Centre National de la Recherche Scientifique (CNRS), UMR7355 and University of Orleans, Orleans, France
| |
Collapse
|