Genome Integrity Research Articles

Effect of nicotinamide riboside on airway inflammation in COPD: a randomized, placebo-controlled trial.

Chronic obstructive pulmonary disease (COPD) is a progressive, incurable disease associated with smoking and advanced age, ranking as the third leading cause of death worldwide. DNA damage and loss of the central metabolite nicotinamide adenine dinucleotide (NAD+) may contribute to both aging and COPD, presenting a potential avenue for interventions. In this randomized, double-blind, placebo-controlled clinical trial, we treated patients with stable COPD (n = 40) with the NAD+ precursor nicotinamide riboside (NR) for 6 weeks and followed-up 12 weeks later. The primary outcome was change in sputum interleukin-8 (IL-8) from baseline to week 6. The estimated treatment difference between NR and placebo in IL-8 after 6 weeks was -52.6% (95% confidence interval (CI): -75.7% to -7.6%; P = 0.030). This effect persisted until the follow-up 12 weeks after the end of treatment (-63.7%: 95% CI -85.7% to -7.8%; P = 0.034). For secondary outcomes, NR treatment increased NAD+ levels by more than twofold in whole blood, whereas IL-6 levels in plasma remained unchanged. In exploratory analyses, treatment with NR showed indications of upregulated gene pathways related to genomic integrity in the airways and reduced epigenetic aging, possibly through a reduction in cellular senescence. These exploratory analyses need to be confirmed in future trials. ClinicalTrials.gov identifier: NCT04990869 .

Assessing the Impact of Bedaquiline, Clofazimine, and Linezolid on Mycobacterial Genome Integrity

Tuberculosis (TB) presents significant medical challenges, largely due to the genetic diversity of Mycobacterium tuberculosis, which enhances the resilience and resistance of the pathogen to first-line treatments. In response to the global rise of drug-resistant TB, second-line antitubercular drugs like bedaquiline (BDQ), linezolid (LZD), and clofazimine (CFZ) have become critical treatment options. Understanding the molecular changes these drugs induce is essential for optimizing TB therapy. To contribute to this effort, we investigated their impact on genome maintenance and stability using Mycobacterium smegmatis as a model organism. Using mutation accumulation assays and whole-genome sequencing, we found that the second-line antibiotics did not significantly increase mutation rates, unlike the positive control UV treatment. However, upon BDQ treatment, we detected mutations in transporter proteins and transcription factors without any increase in the minimal inhibitory concentration. Additionally, BDQ and CFZ were found to alter DNA repair pathways and reduce cellular dNTP levels, particularly CFZ, which depleted dGTP, impacting DNA synthesis. CFZ also upregulated DNA repair enzymes, enhancing error-free repairs. Despite minimal mutagenic effects, both drugs displayed distinct impacts on cellular mechanisms, suggesting additional modes of action.

The chromosome-level genome assembly and annotation of an invasive forest pest Obolodiplosis robiniae.

Biological invasion is a major global problem, leading to the loss of biodiversity and species extinction, and causing huge economic losses to countries. Obolodiplosis robiniae is a major invasive forest pest that has caused economic losses in Asia and Europe. Here, the chromosome- level genome of O. robiniae was assembled using the PacBio platform and Hi-C technology. A contig-level genome with a length of 199.49 Mb and a contig N50 of 4.66 Mb was assembled. Approximately 98.05% of contigs were successfully anchored to four chromosomes using Hi-C assisted genome assembly. The genome integrity was assessed to be 90.3% based on BUSCOs analysis. The high-quality genome provides valuable data for the study of invasive species, and a foundation for the understanding the biology and ecology of O. robiniae.

A Rapidly Inducible DNA Double-Strand Break to Monitor Telomere Formation, DNA Repair, and Checkpoint Activation.

The study of processes that govern genome integrity has been augmented by the ability to create a precise DNA double-strand break (DSB) in a short period of time that allows the kinetics of DNA metabolism and protein recruitment to be followed. Defined DSBs are made by expressing endonucleases with long recognition sites that are rare or absent in the genome, and require that the endonuclease is only active when induced. Research in this area in Schizosaccharomyces pombe was limited because rapidly inducible promoters were not available until around 2005, and several rapidly inducible DSB systems are now available. Here, we describe a system to rapidly induce a modified I-SceI endonuclease that can generate a DSB 20min after induction. I-SceI has no recognition sites in the S. pombe genome, allowing the introduction of complex substrates to monitor the effects of a new DSB in real time. This chapter describes how I-SceI can be most efficiently induced and a simple cell length measurement assay to monitor cell cycle checkpoint activation from a single DSB.

CNSC-49. ELUCIDATING THERAPEUTIC POTENTIAL OF USP1 INHIBITION IN DIFFUSE MIDLINE GLIOMAS

Abstract Diffuse midline gliomas (DMGs) are aggressive childhood brain tumors with the H3K27M mutation in the H3F3A or H3C2 gene. Despite treatment advances, radiotherapy is the only viable option, but 99% of patients die within 1.5-2 years. Therefore, there is an urgent need to identify potential novel therapeutic targets for the treatment of DMGs. Ubiquitin-specific protease 1 (USP1) is a key deubiquitinating enzyme involved in genome integrity, cell cycle regulation, and cell homeostasis. USP1 is overexpressed in various cancers, including gliomas, is linked to poor prognosis. It promotes glioma stem cell (GSC) self-renewal and radio-resistance by regulating ID1 and CHEK1. Our recent findings show that ID1 is crucial for DMG invasion and migration. Inhibiting USP1 suppresses malignant growth, enhances radiation sensitivity, and improves chemotherapy response, highlighting its potential for combined therapies. However, USP1’s role in DMGs and its feasibility as a therapeutic target remain poorly understood. In this study, we investigated USP1 in DMGs for the first time. RNA sequencing revealed high USP1 expression in DMG patient samples and cell lines, directly linked to the H3K27M mutation. Correcting this mutation reduced USP1 expression in DMG cell lines. Pharmacologic inhibition of USP1 with the specific inhibitor SJB3-019A significantly reduced DMG cell proliferation, triggered apoptosis, and altered cell cycle profile. SJB3-019A-mediated USP1 inhibition decreases migration and invasion in multiple patient-derived DMG cell lines. Additional in vitro experiments revealed that USP1 inhibition leads to a significant decrease in the expression of ID1 and pAKT, suggesting the ID1/AKT pathway as a potential mechanism underlying the observed effects. H3K27M-mediated activation of USP1 in DMG is a promising therapeutic target, with inhibition by SJB3-019A reducing tumor aggressiveness by inhibiting invasion and migration. We will next assess SJB3-019A’s efficacy in vivo using genetically engineered isogenic mouse models (GEMM) with DNp53/PDGFRA/H3.3K27M (PPK) alterations and evaluate USP1 inhibition combined with radiation therapy as a potential radiosensitizer in DMGs.

Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases.

DNA methylation is an important epigenetic mechanism essential for transposon silencing and genome integrity. Across evolution, the substrates of DNA methylation have diversified between kingdoms. In plants, chromomethylase3 (CMT3) and CMT2 mediate CHG and CHH methylation, respectively. However, how these two methyltransferases diverge on substrate specificities during evolution remains unknown. Here, we reveal that CMT2 originates from a duplication of an evolutionarily ancient CMT3 in flowering plants. Lacking a key arginine residue recognizing CHG in CMT2 impairs its CHG methylation activity in most flowering plants. An engineered V1200R mutation empowers CMT2 to restore CHG and CHH methylations in Arabidopsis cmt2cmt3 mutant, testifying a loss-of-function effect for CMT2 during evolution. CMT2 has evolved a long and unstructured amino terminus critical for protein stability, especially under heat stress, and is plastic to tolerate various natural mutations. Together, this study reveals the mechanism of chromomethylase divergence for context-specific DNA methylation in plants and sheds important lights on DNA methylation evolution and function.

Scoping the requirements for a genomic competency framework to inform the integration of genomics into pharmacy undergraduate curricula

Abstract Introduction The application of genomics is due to have a significant impact on the role of pharmacy within future healthcare systems. Since 2021, the updated GPhC education standards have included a requirement to apply the principles of genomics,1 but a lack of consistency across UK pharmacy programmes has led to inequity of genomics literacy for pharmacy students.1 National UK genomic workforce strategies include a pharmacy undergraduate indicative syllabus focussing on upskilling the NHS workforce in readiness for the wider implementation of genomics.2,3 There is a lack of UK research exploring the undergraduate genomic education requirements of pharmacy professionals. Aim Scope the requirements of a genomic competency framework for undergraduate pharmacy curricula. Methods Ethics approval was obtained from Swansea University ethics committee in July 2023. Fifteen multi-professional stakeholders from across the UK, perceived as genomic experts and/or pharmacy educationalists from each devolved nation, were selected using purposive sampling and all were invited to participate within a virtual semi-structured interview (SSI) and a consecutive focus group. SSIs and the focus group were facilitated and recorded using Microsoft® Teams and pre-designed open question topic frameworks were used. All data was anonymously transcribed verbatim and analysed using thematic analysis. Results Twelve participants consented and SSIs were held between September/October 2023. Five participants attended the consecutive focus group in December 2023. Five SSI themes were identified: Competency development - where the need for pharmacists to have comprehensive knowledge of the aspects and factors affecting the use of genomic testing within clinical practice (e.g. research and consent) was identified, whilst others described the need for pharmacists to focus on pharmacogenomics only; Curriculum approach – where there were variations in the depth of general genomic training and appropriate topics needed by pharmacists and the requirement for genomics to be scattered throughout undergraduate programmes; Future practice roles - the current postgraduate pharmacogenomic module could be used to establish the future undergraduate requirements and the need for pharmacy curricula to focus on the application of genomics to medicines rather than as a diagnostic tool; Genomic topics - participants acknowledged the complex nature of determining the genomic undergraduate curricula requirements without routine mainstream use of genomics within clinical practice but suggested pharmacy genomic competencies needing further refinement; Level of knowledge - participants highlighted the need for overall genomic pharmacy knowledge but a deeper level of pharmacogenomic knowledge and recommended that the competency framework should be relevant and achievable across healthcare sectors. Discussion and conclusion Genomic competencies should be established for pharmacy professionals as appropriate to their job roles. Once genomics is widely implemented, clarity around genomic competence requirements will develop, following workforce upskilling. The varied backgrounds of study participants impacted their opinions which were potentially influenced by their knowledge of the pharmacist role across sectors and their lack of familiarity with current pharmacy training. Study limitations are small participant numbers and low data generalisability. A genomic competency framework is needed to standardise pharmacy training and study findings will be used to develop a UK consensus for UK genomic undergraduate pharmacy training.

HnRNPA2B1 deacetylation by SIRT6 restrains local transcription and safeguards genome stability.

Repair of double strand breaks (DSBs) by RNA-binding proteins (RBPs) is vital for ensuring genome integrity. DSB repair is accompanied by local transcriptional repression in the vicinity of transcriptionally active genes, but the mechanism by which RBPs regulate transcriptional regulation is unclear. Here, we demonstrated that RBP hnRNPA2B1 functions as a RNA polymerase-associated factor that stabilizes the transcription complex under physiological conditions. Following a DSB, hnRNPA2B1 is released from damaged chromatin, reducing the efficiency of RNAPII complex assembly, leading to local transcriptional repression. Mechanistically, SIRT6 deacetylates hnRNPA2B1 at K113/173 residues, enforcing its rapid detachment from DSBs. This process disrupts the integrity of the RNAPII complex on active chromatin, which is a pre-requisite for transient but complete repression of local transcription. Functionally, the overexpression of an acetylation mimic stabilizes the transcription complex and facilitates the functioning of the transcription machinery. hnRNPA2B1 acetylation status was negatively correlated with SIRT6 expression, and acetylation mimic enhanced radio-sensitivity in vivo. Our findings demonstrate that hnRNPA2B1 is crucial for transcriptional repression. We have uncovered the missing link between DSB repair and transcriptional regulation in genome stability maintenance, highlighting the potential of hnRNPA2B1 as a therapeutic target.

Unusual modes of cell and nuclear divisions characterise Drosophila development.

The growth and development of metazoan organisms is dependent upon a co-ordinated programme of cellular proliferation and differentiation, from the initial formation of the zygote through to maintenance of mature organs in adult organisms. Early studies of proliferation of ex vivo cultures and unicellular eukaryotes described a cyclic nature of cell division characterised by periods of DNA synthesis (S-phase) and segregation of newly synthesized chromosomes (M-phase) interspersed by seeming inactivity, the gap phases, G1 and G2. We now know that G1 and G2 play critical roles in regulating the cell cycle, including monitoring of favourable environmental conditions to facilitate cell division, and ensuring genomic integrity prior to DNA replication and nuclear division. M-phase is usually followed by the physical separation of nascent daughters, termed cytokinesis. These phases where G1 leads to S phase, followed by G2 prior to M phase and the subsequent cytokinesis to produce two daughters, both identical in genomic composition and cellular morphology are what might be termed an archetypal cell division. Studies of development of many different organs in different species have demonstrated that this stereotypical cell cycle is often subverted to produce specific developmental outcomes, and examples from over 100 years of analysis of the development of Drosophila melanogaster have uncovered many different modes of cell division within this one species.

Advanced Disease Detection and Personalized Medicine: Integrated Data Approaches for Enhanced Parkinson's Disease and Breast Cancer Detection and Treatment in the USA

This present study focuses on integrating data-driven approaches into personalized medicine for better detection and treatment of Parkinson's disease and breast cancer through the US healthcare system. The deeper integration of genomics, clinical records, and patient self-reported data with machine learning algorithms will enhance early disease detection and optimization of treatment pathways. The results show that, more precisely, Random Forest and XGBoost machine learning models hold great promise for considerably improving diagnostic precision and predictive power. This realization opens a door for precision medicine-tailored health services according to the peculiarities of individual patients, which would improve treatment outcomes and encourage preventive healthcare. In addition, this approach aligns with the latest US efforts in precision medicine and contributes to evidence-based transformation in healthcare practice.

Profound synthetic lethality between SMARCAL1 and FANCM.

DNA replication stress is a threat to genome integrity. The large SNF2-family of ATPases participates in preventing and mitigating DNA replication stress by employing their ATP-driven motor to remodel DNA or DNA-bound proteins. To understand the contribution of these ATPases in genome maintenance, we undertook CRISPR-based synthetic lethality screens in human cells with three SNF2-type ATPases: SMARCAL1, ZRANB3, and HLTF. Here, we show that SMARCAL1 displays a profound synthetic-lethal interaction with FANCM, another ATP-dependent translocase involved in DNA replication and genome stability. Their combined loss causes severe genome instability that we link to chromosome breakage at loci enriched in simple repeats, which are known to challenge replication fork progression. Our findings illuminate a critical genetic buffering mechanism that provides an essential function for maintaining genome integrity.

Genomic integrity in Bordetella pertussis: avoiding contaminant-derived misinterpretations of acquired antimicrobial resistance

Genomic integrity in Bordetella pertussis: avoiding contaminant-derived misinterpretations of acquired antimicrobial resistance

Key insights into cannabis-cancer pathobiology and genotoxicity.

Whilst mitochondrial inhibition and micronuclear fragmentation are well established features of the cannabis literature mitochondrial stress and dysfunction has recently been shown to be a powerful and direct driver of micronucleus formation and chromosomal breakage by multiple mechanisms. In turn genotoxic damage can be expected to be expressed as increased rates of cancer, congenital anomalies and aging; pathologies which are increasingly observed in modern continent-wide studies. Whilst cannabinoid genotoxicity has long been essentially overlooked it may in fact be all around us through the rapid induction of aging of eggs, sperm, zygotes, foetus and adult organisms with many lines of evidence demonstrating transgenerational impacts. Indeed this multigenerational dimension of cannabinoid genotoxicity reframes the discussion of cannabis legalization within the absolute imperative to protect the genomic and epigenomic integrity of multiple generations to come.

Advances in PIWI-piRNA function in female reproduction in mammals.

PIWI-interacting RNAs (piRNAs), which associate with PIWI clade Argonaute proteins to form piRNA-induced silencing complexes (piRISCs) in germline cells, are responsible for maintaining genomic integrity and reproductive function through transcriptional or post-transcriptional suppression of transposable elements and regulation of protein-coding genes. Recent discoveries of crucial PIWI-piRNA functions in oogenesis and embryogenesis in golden hamsters suggest an indispensable role in female fertility that has been obscured in the predominant mouse model of PIWI-piRNA pathway regulation. In particular, studies of piRNA expression dynamics, functional redundancies, and compositional variations across mammal species have advanced our understanding of piRNA functions in male and, especially, female reproduction. These findings further support the use of hamsters as a more representative model of piRNA biology in mammals. In addition to discussing these new perspectives, the current review also covers emerging directions for piRNA research, its implications for female fertility, and our fundamental understanding of reproductive mechanisms.

Transient HR enhancement by RAD51-stimulatory compound confers protection on intestinal rather than hematopoietic tissue against irradiation in mice

DNA double-strand breaks (DSBs) are cytotoxic lesions that compromise genomic integrity and trigger cell death. Homologous recombination (HR) is a major pathway for repairing DSBs in cycling cells. However, it remains unclear whether transient modulation of HR could confer protection to adult stem cells against lethal irradiation exposure. In this study, we investigated the radio-protective effect of the RAD51-stimulatory compound RS-1 on adult stem cells and progenitor cells with varying cycling rates in intestinal and hematopoietic tissues. Treatment with RS-1 even at high doses did not induce noticeable cell death or proliferation of intestinal crypt cells in vivo. Pretreatment with RS-1 before irradiation significantly decreased mitotic death, promoted DNA repair and enhanced the survival of intestinal stem cells and progenitor cells and increased the number of regenerative crypt colonies thereby mitigating IR-induced gastrointestinal syndrome. Moreover, RS1 pretreatment could increase the survival and regeneration of irradiated intestinal organoid in vitro, which can be rescued by RAD51 inhibitor. However, pretreatment with RS-1 in vivo did not elevate nucleated cell count or HSPCs in bone marrow after 6Gy irradiation. Additionally, there was no impact on mouse survival due to drug treatment observed. Thus, our data suggest that targeting HR as a strategy to prevent tissue damage from acute irradiation exposure may depend on cell cycling rates and intrinsic DNA repair mechanisms.

Longitudinal analysis of genetic and epigenetic changes in human pluripotent stem cells in the landscape of culture-induced abnormality.

Human embryonic stem cells (hESCs) are naturally equipped to maintain genome integrity to minimize genetic mutations during early embryo development. However, genetic aberration risks and subsequent cellular changes in hESCs during in vitro culture pose a significant threat to stem cell therapy. While a few studies have reported specific somatic mutations and copy number variations (CNVs), the molecular mechanisms underlying the acquisition of 'culture-adapted phenotypes' by hESCs are largely unknown. Therefore, we conducted comprehensive genomic, single-cell transcriptomic, and single-cell ATAC-seq analyses of an isogenic hESC model displaying definitive 'culture-adapted phenotypes'. We found that hESCs lacking TP53, in which loss-of-function mutations were identified in human pluripotent stem cells (hPSCs), presented a surge in somatic mutations. Notably, hPSCs with a copy number gain of 20q11.21 during early passage did not present 'culture-adapted phenotypes' or BCL2L1 induction. Single-cell RNA-seq and ATAC-seq analyses revealed active transcriptional regulation at the 20q11.21 locus. Furthermore, the induction of BCL2L1 and TPX2 to trigger 'culture-adapted phenotypes' was associated with epigenetic changes facilitating TEA domain (TEAD) binding. These results suggest that 20q11.21 copy number gain and additional epigenetic changes are necessary for expressing 'culture-adapted phenotypes' by activating gene transcription at this specific locus.

A p38 MAPK-ROS axis fuels proliferation stress and DNA damage during CRISPR-Cas9 gene editing in hematopoietic stem and progenitor cells.

Exvivo activation is a prerequisite to reaching adequate levels of gene editing by homology-directed repair (HDR) for hematopoietic stem and progenitor cell (HSPC)-based clinical applications. Here, we show that shortening culture time mitigates the p53-mediated DNA damage response to CRISPR-Cas9-induced DNA double-strand breaks, enhancing the reconstitution capacity of edited HSPCs. However, this results in lower HDR efficiency, rendering exvivo culture necessary yet detrimental. Mechanistically, exvivo activation triggers a multi-step process initiated by p38 mitogen-activated protein kinase (MAPK) phosphorylation, which generates mitogenic reactive oxygen species (ROS), promoting fast cell-cycle progression and subsequent proliferation-induced DNA damage. Thus, p38 inhibition before gene editing delays G1/S transition and expands transcriptionally defined HSCs, ultimately endowing edited cells with superior multi-lineage differentiation, persistence throughout serial transplantation, enhanced polyclonal repertoire, and better-preserved genome integrity. Our data identify proliferative stress as a driver of HSPC dysfunction with fundamental implications for designing more effective and safer gene correction strategies for clinical applications.

Optimizing the New Model of Nurse Practitioner Regulation in Canada to Support the Integration of Genomics

Optimizing the New Model of Nurse Practitioner Regulation in Canada to Support the Integration of Genomics

Cohesin complex oligomerization maintains end-tethering at DNA double-strand breaks.

DNA double-strand breaks (DSBs) must be repaired to ensure genome stability. Crucially, DSB-ends must be kept together for timely repair. In Saccharomyces cerevisiae, two pathways mediate DSB end-tethering. One employs the Mre11-Rad50-Xrs2 (MRX) complex to physically bridge DSB-ends. Another requires the conversion of DSB-ends into single-strand DNA (ssDNA) by Exo1, but the bridging proteins are unknown. We uncover that cohesin, its loader and Smc5/6 act with Exo1 to tether DSB-ends. Remarkably, cohesin specifically impaired in oligomerization fails to tether DSB-ends, revealing a function for cohesin oligomerization. In addition to the known importance of sister chromatid cohesion, microscopy-based microfluidic experiments unveil a role for cohesin in repair by ensuring DSB end-tethering. Altogether, our findings demonstrate that oligomerization of cohesin prevents DSB end-separation and promotes DSB repair, revealing a previously undescribed mode of action and role for cohesin in safeguarding genome integrity.

Senataxin Attenuates DNA Damage Response Activation and Suppresses Senescence

Oxidative stress, driven by reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), induces DNA double-strand breaks (DSBs) that compromise genomic integrity. The DNA Damage Response (DDR), primarily mediated by ATM and ATR kinases, is crucial for recognizing and repairing DSBs. Senataxin (SETX), a DNA/RNA helicase, is critical in resolving R-loops, with mutations in SETX associated with neurodegenerative diseases. This study uncovers a novel function of senataxin in modulating DDR and its impact on cellular senescence. Senataxin is shown to be crucial not only for DSB repair but also for determining cell fate under oxidative stress. SETX knockout cells show impaired DSB repair and prolonged ATM/ATR signaling detected by Western blotting, leading to increased senescence, as indicated by elevated β-galactosidase activity following H2O2 exposure and I-PpoI-induced DSBs. Wild-type cells exhibit higher apoptosis levels compared to SETX knockout cells under H2O2 treatment, suggesting that senataxin promotes apoptosis over senescence in oxidative stress. This indicates that senataxin plays a protective role against the accumulation of senescent cells, potentially mitigating age-related cellular decline and neurodegenerative disease progression. These findings highlight senataxin as a critical mediator in DDR pathways and a potential therapeutic target for conditions where cellular senescence contributes to disease pathology.