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Functional analysis of helicase and three tandem HRDC domains of RecQ in Deinococcus radiodurans.

RecQ is a highly conserved helicase necessary for maintaining genome stability in all organisms. Genome comparison showed that a homologue of RecQ in Deinococcus radiodurans designated as DR1289 is a member of RecQ family with unusual domain arrangement: a helicase domain, an RecQ C-terminal domain, and surprisingly three HRDC domain repeats, whose function, however, remains obscure currently. Using an insertion deletion, we discovered that the DRRecQ mutation causes an increase in gamma radiation, hydroxyurea and mitomycine C and UV sensitivity. Using the shuttle plasmid pRADK, we complemented various domains of the D. radiodurans RecQ (DRRecQ) to the mutant in vivo. Results suggested that both the helicase and helicase-and-RNase-D-C-terminal (HRDC) domains are essential for complementing several phenotypes. The complementation and biochemical function of DRRecQ variants with different domains truncated in vitro suggested that both the helicase and three HRDC domains are necessary for RecQ functions in D. radiodurans, while three HRDC domains have a synergistic effect on the whole function. Our finding leads to the hypothesis that the RecF recombination pathway is likely a primary path of double strand break repair in this well-known radioresistant organism.

Amino Acid Sequence↗

[Transgenerational transmission of radiation induced genomic instability].

Stability of genome is one of the evolutionary important trait of cells. Various mutations (gene, chromosomal, genomic) as well as artificial manipulations with genomes (inbreeding, DNA transfection, introduction of Br-DU in DNA) cause the genetic instability. Ionizing radiation is known as the factor which induced instability of genome in late mitotic descendants of cells after in vitro and in vivo exposure. Radiation induced genetic instability can be transmitted through germline cells. On the cell level both types of radiation induced genomic instability are manifested in elevated frequency of mutations, chromosome aberrations, micronuclei, increased radiosensitivity, disappearance of adaptive response, changes in gene expression. In studies of 1970-1980 years clear evidences on the different morphological and functional injuries in tissues of irradiated organisms as well as in tissues of the progeny of exposed parents were obtained. On the organism level the instability of mitotic and of meiotic progeny of irradiated cells is resulted in increased risk of cancer and of other somatic diseases. It seems to be useful to review the earlier radiobiology literature where delayed and transgenerational effects of ionizing radiation on tissues and on organisms level were clearly shown in animals. For the estimation of pathogenic role of radiation induced genomic instability in humans, particularly in children of exposed parents the parallel study of the same human cohorts using clinical parameters and various characteristic of genomic instability seems to be very important.

Child, Preschool↗

Cohesin reshapes replication fork contacts to aid fork slowing and reversal.

DNA replication forks can be challenged by cancer chemotherapeutic treatments, leading to accumulation of single-stranded DNA and slowdown of DNA synthesis. The marked plasticity of replication forks under replication stress ensures fork stability, damage tolerance and complete genome duplication1. Initiation and progression of replication forks occur in a three-dimensionally organized genome. DNA loop extrusion by the cohesin complex organizes the genome2 and regulates the initiation and positioning of DNA replication origins3,4. Although transient interaction of sister forks was recently reported during unperturbed replication5, the functional relevance of fork contacts during replication stress and the role of cohesin in this context remain unknown. Here we show that cohesin-mediated loop extrusion rearranges nascent DNA contacts at stressed replication forks to promote genome stability. Using auxin-inducible degron6, separation-of-function mutants7-9 and a newly developed Micro-C-based technique to capture chromatin contacts at nascent DNA (Repli-C), we found that loop-extruding cohesin accumulates at stalled replication forks, limiting sister-fork coupling in favour of inter-replicon contacts. This process promotes active fork slowing and reversal by preventing PRIMPOL action on single-stranded DNA1. These findings show that the replication stress response is not merely an accumulation of individual regulatory events, but is topologically integrated across the genome through cohesin loop extrusion. While providing a new function for loop-extruding cohesin, our results indicate the potential impact on cancer therapy of frequent cohesin mutations in tumours10.

Journal Article↗

Decreased expression of topoisomerase IIbeta in poly(ADP-ribose) polymerase-deficient cells.

Recent studies with poly(ADP-ribose) polymerase (PARP)-deficient mice have highlighted the role of this enzyme in genomic stability and response to various genomic insults. In the absence of DNA damaging treatment, we report here that a PARP-deficient cell line (PARP-/-) established from knockout mice displays a decrease in topoisomerase II (topo II) activity as measured by decatenation of kinetoplast DNA. Immunoblotting of whole and nuclear cell extracts showed that reduced activity was associated with decreased amount of the 180 kDa topo IIbeta protein but not of the 170 kDa topo IIalpha. The decreased topo IIbeta expression did not stem from transcriptional regulation of gene expression since levels of topo IIbeta mRNA were similar in PARP (-/-) compared with the parental PARP (+/+) cells. The decreased topo II activity was associated with cell resistance to VP16, a topo II inhibitor. These observations indicate that PARP may play a role in the stabilization and/or distribution of topo IIbeta.

Animals↗

Personalized medicine strategy for MPNSTs: using precision oncology on PDOX models to inform tumor boards.

BACKGROUND: Malignant peripheral nerve sheath tumors (MPNSTs) are a heterogeneous group of aggressive soft tissue sarcomas with poor prognosis. Currently there is a lack of effective treatments for MPNSTs. Here, we propose a personalized medicine approach that integrates a precision oncology strategy guided by MPNST genomic analysis, with a functional validation of treatment response in an orthotopic xenograft model (PDOX) derived from the same MPNST. METHODS: Comprehensive whole genome sequencing analysis was performed in primary MPNSTs, relapses and (in one case) metastases, following disease progression in two independent individuals. Matched MPNST PDOX models were generated by orthotopically implanting tumor fragments near the sciatic nerve of immunodeficient mice. Candidate targeted combination therapies were prioritized based on genomic alterations and tested in vivo in the PDOX models. RESULTS: The feasibility of the developed strategy is illustrated for two MPNST patients, one Neurofibromatosis type 1 (NF1) individual that developed two independent MPNSTs and another sporadic MPNST case with multiple metastatic relapses. Genomic analysis revealed a remarkable degree of genomic stability across primary MPNSTs and their successive relapses in each patient, and even metastases in one individual. While based on a small number of cases requiring additional analyses, this finding aligns with previous evidence suggesting a fair genomic conservation throughout tumor evolution. This stability supports the identification of consistent therapeutic vulnerabilities throughout disease progression. Among the therapies tested, co-treatment of MEK inhibitor (MEKi) plus bromodomain inhibitor (BETi) elicited the highest antitumor activity, resulting in approximately 60% tumor volume reduction in the sporadic MPNST PDX model, whose patient has been receiving this therapy for eight months with sustained remission. CONCLUSIONS: This study demonstrates the feasibility and clinical utility of integrating genomic-driven precision oncology with PDOX-based functional testing for MPNSTs. This strategy may support molecular tumor boards (MTBs) in their treatment decisions. The observed genomic stability supports the use of longitudinal tumor profiling to guide treatment, and the success of MEKi+BETi highlights its potential as a combination therapy for MPNSTs.

Precision Medicine↗

Pathogenic variants in MAEA disrupt DNA replication fork stability and are associated with developmental abnormalities in humans.

Replication stress (RS) poses a threat to genome stability and drives genomic rearrangements. The homologous recombination (HR) pathway repairs stalled replication forks (RFs) and prevents such instability. Through an E3 ubiquitin ligase screen aimed at identifying regulators of RAD51, we identified macrophage erythroblast attacher (MAEA), a core component of C-terminal to Lish (CTLH) E3 ubiquitin ligase complex, as a regulator of the HR pathway. Loss of MAEA impairs RAD51 recruitment at stalled RFs, leading to increased sensitivity to RS-inducing agents and excessive degradation of nascent DNA strands. Mechanistically, MAEA associates with and mediates the ubiquitylation of Ku80, enabling its removal from RF ends and facilitating the loading of RAD51. Notably, MAEA deficiency is associated with a developmental disorder involving microcephaly, craniofacial abnormalities, ocular defects, and heart malformations. Functional assays show that disease-linked MAEA variants (R34C, E349G, Y394D, and M396R) are defective in RS response. These findings establish MAEA as an essential factor in RF protection and genome integrity.

Humans↗

Chromosomal stability and the DNA double-stranded break connection.

Genome stability is of primary importance for the survival and proper functioning of all organisms. Double-stranded breaks in DNA are important threats to genome integrity because they can result in chromosomal aberrations that can affect, simultaneously, many genes, and lead to cell malfunctioning and cell death. These detrimental consequences are counteracted by two mechanistically distinct pathways of double-stranded break repair: homologous recombination and non-homologous end-joining. Recently, unexpected links between these double-stranded break-repair systems, and several human genome instability and cancer predisposition syndromes, have emerged. Now, interactions between both double-stranded break-repair pathways and other cellular processes, such as cell-cycle regulation and replication, are being unveiled.

Animals↗

Defective DNA repair genes in a primary culture of human renal cell carcinoma.

PURPOSE: Genomic stability is maintained by error-free DNA replication, repair, and recombination. To determine if repair genes contribute to genomic instability, we used a newly established cell line RCC-AJR (from clear-cell renal cell carcinoma) to examine hMSH2 (a mismatch-repair gene) and the gene encoding DNA beta polymerase (polbeta; a known contributor to base-excision repair). METHODS: Coding sequences of hMSH2 and polbeta were amplified by the polymerase chain reaction (PCR) using RNA from RCC-AJR cells and matched normal kidney (NK) cells from the same patient. Nucleotide sequences of the PCR products were determined by the dideoxy-DNA method and direct sequencing. Expressions of repair genes were assayed by Western blotting. Microsatellite stability in RCC-AJR cells was assayed by alteration in (CA)n repeats. RESULTS: In the RCC-AJR cells, we detected (a) a deletion of 1476 bp encoding 492 amino acids of hMSH2 cDNA, (b) an 87-bp deletion in the polbeta coding sequence, (c) truncated forms of hMSH2 and polbeta proteins, and (d) microsatellite instability. CONCLUSIONS: This study provides evidence of alterations in hMSH2 and polbeta in the homogeneous cell population of an RCC-AJR tumor culture. The data indicate that repair genes may help preserve genomic stability in this cell line. We believe that this new primary RCC-AJR cell line will prove a useful model for investigating the cascade of genetic events in renal cells that leads to renal carcinogenesis.

Carcinoma, Renal Cell↗

Base excision repair capacity in mitochondria and nuclei: tissue-specific variations.

Base excision repair is the main pathway for repair of oxidative base lesions in DNA. Mammalian cells must maintain genomic stability in their nuclear and mitochondrial genomes, which have different degrees of vulnerability to DNA damage. This study quantifies DNA glycosylase activity in mitochondria and nucleus from C57/BL 6 mouse tissues including brain, liver, heart, muscle, kidney, and testis. The activities of oxoguanine DNA glycosylase (OGG1), uracil DNA glycosylase, and endonuclease III homologue 1 (NTH1) were measured using oligonucleotide substrates with DNA lesions specific for each glycosylase. Mitochondrial content was normalized to citrate synthase activity and mitochondrial function was assessed by measuring cytochrome c oxidase (COX) activity. In nuclear and mitochondrial extracts, the highest DNA glycosylase activities were in testis. Brain and heart, tissues with the highest oxidative load, did not have higher levels of OGG1 or NTH1 activity than muscle or kidney, which are more glycolytic tissues. In general, mitochondrial extracts have lower DNA glycosylase activity than nuclear extracts. There was no correlation between glycosylase activities in the mitochondrial extracts and COX activity, suggesting that DNA repair enzymes may be regulated by a mechanism different from this mitochondrial enzyme.

Animals↗

Connecting chromosomes, crisis, and cancer.

Cancer is a disease of impaired genome stability. The molecular forces that maintain genome integrity and sense altered chromosome structure are invariably subverted in cancer cells. Here, we explore the contrasting contributions of telomeres in the initiation and suppression of cancer and review the evidence supporting a role for telomere dysfunction as a mechanism driving the radical chromosomal aberrations that typify cancer genomes. Recent work suggests that passage of cells through crisis in the setting of deactivated DNA damage checkpoints provides a mutational mechanism that can generate the diverse genetic alterations required for cancer initiation. A greater understanding of telomere-induced crisis and the cell's crisis management mechanisms should guide the rational development of new therapeutics for cancer and other disorders.

Animals↗

Homologous recombination and RecA protein: towards a new generation of tools for genome manipulations.

Homologous recombination (HR) is one of the central processes of DNA metabolism, combining roles in both cell housekeeping and the evolution of genomes. In eukaryotes, HR underlies meiosis and ensures genome stability. The complete sequencing of numerous bacterial genomes has shown that HR has a substantial role in the evolution of microorganisms, especially pathogens. HR systems from different species and their isolated components are finding an expanding field of applications in modern genetic engineering and bio- and nanotechnologies. Recently, much progress has been made in our understanding of HR mechanisms in eukaryotes and the practical applications of HR systems.

Animals↗

RecQ helicases: lessons from model organisms.

RecQ DNA helicases function during DNA replication and are essential for the maintenance of genome stability. There is increasing evidence that spontaneous genomic instability occurs primarily during DNA replication, and that proteins involved in the S-phase checkpoint are a principal defence against such instability. Cells that lack functional RecQ helicases exhibit phenotypes consistent with an inability to fully resume replication fork progress after encountering DNA damage or fork arrest. In this review we will concentrate on the various functions of RecQ helicases during S phase in model organisms.

Adenosine Triphosphatases↗

The sources of variation in the human genome and genome instability in human cancers.

The human genome is viewed as a stable collection of about 60,000-70,000 genes--a minority of protein--coding DNA sequences--dispersed in a large majority of noncoding DNA sequences--more than 90 per cent of the entire genome sequences. Some of these ubiquitous noncoding DNA sequences, metonymically called "parasitic DNA," "ballast DNA," "selfish DNA" or "extra DNA," especially, the repeated sequences tandemly organized, are not stable but vary with considerable frequency. Recently, the confused or inadequately known origin of native of pathological variations of these DNA sequences appears to be unravelled, with great implications in genome stability. The human chromosomes, the bearer of genome, store and carry it. Their structure is qualified to perform its fastidious functions. The chromosomal conformation, "with variable geometry," exposed to genetoxic action of different damaging factors and to torsional stress after their fast and repeated changes during mitosis. The exaggerate exceeding of the native variation of human genome in disease states, probably, generates genome instability. The chromosome fragility--the cellular phenotypic expression of these molecular instability--reflects the closely relations between the genome and its carrier. The pattern of DNA replication with asynchrony of different domains of "parcelled" genome and the results of replication, susceptible to be corrected by the action of DNA repair genes, render certain limited regions of genome more vulnerable to damaging. These "target" regions focused damaging effects and exhibit an increased susceptibility to breakage and recombination, often with chromosomal expression. The coincidence of these regions, frequently, with locations of many protooncogenes and sometimes, antioncogenes could be subsequently, starting points for a genuine chain of genomic events related to growth cell and cell division. Cancer multistage accumulation of various genomic disorders in a single cell tends to take advantage of discriminating situations of these regions, which themselves can generate other genetic disorders, involving its in carcinogenesis. The gene expression disorders or the genuine mutations of dominant protooncogenes and the recessive behaviour of antioncogenes explain the nature of human cancers--a mixture of inherited and somatically acquired gene disorders. They attest the recessive characteristic of human cell malignancy and emphasize the decisive role of cancer predisposition which operates in interaction with damaging environmental factors. Seemingly, the pivotal causes of genome instability originate from strange behaviour of certain repeated DNA sequences dispersed throughout the human genome. Perhaps they hold the key to the puzzle of cancer processes.

Chromosome Aberrations↗

[A possible molecular mechanism of the impairment of the stability of the genome in cells capable of replicating DNA in acute and chronic forms of radiation sickness].

On the basis of the experimentally grounded concept concerning the functional antagonism of various domains of chromosomal SSB-proteins, that play a major role in the implementation of the contrary processes which either provide stability of DNA macromolecules or bear the responsibility for their degradation, a possible molecular mechanism of the disturbance of cell genome stability upon acute and chronic radiation sickness is discussed.

Acute Disease↗

G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration.

MOTIVATION: G-quadruplexes (G4s) are non-canonical nucleic acid structures formed in guanine-rich regions that modulate gene regulation and genomic stability. The thermodynamic stability of G4s directly influences their biological functions and potential as therapeutic targets. However, current quantitative frameworks for predicting G4 stability rely on predetermined structural features, limiting their effectiveness for diverse G4 topologies, and fail to account for environmental factors such as ion concentration and pH that significantly modulate G4 stability in cellular contexts. RESULTS: We present G4STAB, a multi-input deep learning neural network that accurately predicts DNA G4 melting temperatures based on sequence features, salt concentration, and pH. Trained on 2382 diverse DNA G4 sequences, our model achieves high accuracy (R 2=0.8) without relying on predetermined G4 structural features. G4STAB successfully captures established G4 stability determinants and proposes previously unobserved sequence-stability relationships. Analysis of 391 502 experimentally validated G4s reveals that cancer-like ionic environments alter G4 stability profiles, with a 13.5-fold increase in the number of structures exhibiting physiological melting temperatures (36-42°C). These findings suggest systematic genomic patterns in G4 stability responses across chromosomes and gene types. AVAILABILITY AND IMPLEMENTATION: G4STAB is available at https://github.com/donn-liew/G4STAB; G4STAB web database interface is available at https://donn-liew.github.io/g4stab-web-database/.

G-Quadruplexes↗

Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae.

Homologous recombination between dispersed repeated genetic elements is an important source of genetic variation. In this review, we discuss chromosome rearrangements that are a consequence of homologous recombination between transposable elements in the yeast Saccharomyces cerevisiae. The review will be divided into five sections: (1) Introduction (mechanisms of homologous recombination involving ectopic repeats), (2) Spontaneous chromosome rearrangements in wild-type yeast cells, (3) Chromosome rearrangements induced by low DNA polymerase, mutagenic agents or mutations in genes affecting genome stability, (4) Recombination between retrotransposons as a mechanism of genome evolution, and (5) Important unanswered questions about homologous recombination between retrotransposons. This review complements several others [S. Liebman, S. Picologlou, Recombination associated with yeast retrotransposons, in: Y. Koltin, M.J. Leibowitz (Eds.), Viruses of Fungi and Simple Eukaryotes, Marcel Dekker Inc., New York, 1988, pp. 63-89; P. Lesage, A.L. Todeschini, Happy together: the life and times of Ty retrotransposons and their hosts, Cytogenet. Genome Res. 110 (2005) 70-90; D.J. Garfinkel, Genome evolution mediated by Ty elements in Saccharomyces, Cytogenet. Genome Res. 110 (2005) 63-69] that discuss genomic rearrangements involving Ty elements.

Chromosomes, Fungal↗

Development of surrogate endpoint biomarkers for clinical trials of cancer chemopreventive agents: relationships to fundamental properties of preinvasive (intraepithelial) neoplasia.

The tissue changes offering the greatest immediate potential for development as surrogate endpoint biomarkers (SEBs) to be used in Phase II trials of cancer chemopreventive agents are those derived from the microscopic tissue changes pathologists use to make the diagnosis of preinvasive (intraepithelial) neoplasia. These changes comprise four categories: proliferative index, ploidy, nuclear morphometry (size, shape, texture, and pleomorphism), and nucleolar morphometry (number, size, shape, position, and pleomorphism). Computer-assisted image analysis (CIA) permits dozens of additional morphometric parameters to be developed. Other categories of candidate SEBs are: DNA and chromosomal structural changes associated with genomic instability, activation of oncogenes and inactivation of tumor suppressor genes, structural changes in differentiated molecules, and aberrations of growth factor/receptor structure and function. Self-perpetuating DNA breakage with secondary mutator mutations in genomic stability genes is a major mechanism by which the genomic instability characteristic of neoplasia occurs, and from which stem other basic neoplastic properties, including clonal evolution, along multiple pathways of genetic variation that are stochastically determined, continuously increasing proliferation, rate and extent of phenotypic heterogeneity. SEBs resulting from genomic instability include homogeneously staining regions, double minute chromosomes, micronuclei, dicentrics, gene amplification, loss of heterozygosity, and alterations in chromosome number. Newly developed assays for detecting genomic instability include comparative genomic hybridization using fluorescence in situ hybridization on > 20 micron-thick sections monitored by confocal laser scanning microscopy, assays for microsatellite instability, and restriction landmark genomic scanning. These assays offer promise for detecting the earliest molecular changes of neoplasia in normal-appearing epithelium prior to the onset of the dysplastic phase of intraepithelial neoplasia.

Anticarcinogenic Agents↗

L2DTL/CDT2 and PCNA interact with p53 and regulate p53 polyubiquitination and protein stability through MDM2 and CUL4A/DDB1 complexes.

The CUL4-ROC1 E3 ligase complex regulates genome stability, replication and cell cycle progression. A novel WD40 domain-containing protein, L2DTL/CDT2 and PCNA were identified as proteins associated with CUL4/DDB1 complexes. Inactivation of CUL4A, L2DTL, PCNA, DDB1 or ROC1 induced p53 stabilization and growth arrest. L2DTL, PCNA and DDB1/CUL4A complexes were found to physically interact with p53 tumor suppressor and its regulator MDM2/HDM2. The isolated CUL4A complexes display potent and robust polyubiquitination activity towards p53 and this activity is dependent on L2DTL, PCNA, DDB1, ROC1 and MDM2/HDM2. We also found that the interaction between p53 and CUL4 complex is regulated by DNA damage. Our data further showed that MDM2/HDM2 is rapidly proteolyzed in response to UV irradiation and this process is regulated by CUL4/DDB1 and PCNA. Our studies demonstrate that PCNA, L2DTL and the DDB1-CUL4A complex play critical and differential roles in regulating the protein stability of p53 and MDM2/HDM2 in unstressed and stressed cells.

Adaptor Proteins, Signal Transducing↗