Strand-resolved mutagenicity of DNA damage and repair.

DNA base damage is a major source of oncogenic mutations1. Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation2. Here we exploited these properties to reveal how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair. Despite distinct mechanisms of leading and lagging strand replication3,4, we observe identical fidelity and damage tolerance for both strands. For small alkylation adducts of DNA, our results support a model in which the same translesion polymerase is recruited on-the-fly to both replication strands, starkly contrasting the strand asymmetric tolerance of bulky UV-induced adducts5. The accumulation of multiple distinct mutations at the site of persistent lesions provides the means to quantify the relative efficiency of repair processes genome wide and at single-base resolution. At multiple scales, we show DNA damage-induced mutations are largely shaped by the influence of DNA accessibility on repair efficiency, rather than gradients of DNA damage. Finally, we reveal specific genomic conditions that can actively drive oncogenic mutagenesis by corrupting the fidelity of nucleotide excision repair. These results provide insight into how strand-asymmetric mechanisms underlie the formation, tolerance and repair of DNA damage, thereby shaping cancer genome evolution.

DNA lesion bypass and the stochastic dynamics of transcription-coupled repair.

DNA base damage is a major source of oncogenic mutations and disruption to gene expression. The stalling of RNA polymerase II (RNAP) at sites of DNA damage and the subsequent triggering of repair processes have major roles in shaping the genome-wide distribution of mutations, clearing barriers to transcription, and minimizing the production of miscoded gene products. Despite its importance for genetic integrity, key mechanistic features of this transcription-coupled repair (TCR) process are controversial or unknown. Here, we exploited a well-powered in vivo mammalian model system to explore the mechanistic properties and parameters of TCR for alkylation damage at fine spatial resolution and with discrimination of the damaged DNA strand. For rigorous interpretation, a generalizable mathematical model of DNA damage and TCR was developed. Fitting experimental data to the model and simulation revealed that RNA polymerases frequently bypass lesions without triggering repair, indicating that small alkylation adducts are unlikely to be an efficient barrier to gene expression. Following a burst of damage, the efficiency of transcription-coupled repair gradually decays through gene bodies with implications for the occurrence and accurate inference of driver mutations in cancer. The reinitation of transcription from the repair site is not a general feature of transcription-coupled repair, and the observed data is consistent with reinitiation never taking place. Collectively, these results reveal how the directional but stochastic activity of TCR shapes the distribution of mutations following DNA damage.

Patient Factors Influencing Prescription of Antithrombotic Medication After Lower Limb Endovascular Intervention.

OBJECTIVE: There is significant practice variation in the use of antithrombotic therapy after endovascular intervention for lower limb peripheral arterial disease, with differences in medication choice and duration. Prescriber decision making is complex, and patient factors have been shown to substantially contribute to prescribing variation. To determine the influence of patient factors on antithrombotic prescribing, a discrete choice experiment was distributed to vascular surgeons and trainees across Australia and Aotearoa New Zealand. METHODS: After pilot testing, the discrete choice experiment questionnaire was distributed to 300 vascular surgeons and trainee members of the Australian and New Zealand Society for Vascular Surgery. Multinomial logistic regression models were used to analyse patient factors that had the most influence on decisions to prescribe a second antithrombotic agent, and the preferred choice of antithrombotic (clopidogrel 75 mg daily or rivaroxaban 2.5 mg twice daily) in addition to aspirin 100 mg daily. The odds ratio (OR) with 95% confidence interval (CI) reported preference strength. RESULTS: A total of 44 questionnaires were completed between September and October 2023, reaching the 15% targeted response rate. Prescribing a second antithrombotic was more likely after femoropopliteal stenting compared with angioplasty (OR 1.89, 95% CI 1.20 - 2.13), and in chronic limb threatening ischaemia compared with intermittent claudication (OR 1.58, 95% CI 1.20 - 2.13). Most respondents preferred clopidogrel over rivaroxaban (62%), with over a third of respondents exclusively prescribing clopidogrel. Patients with stents (OR 1.77, 95% CI 1.32 - 2.37) or moderate bleeding risk (OR 1.38, 95% CI 0.97 - 1.84) were more likely to receive clopidogrel than rivaroxaban. CONCLUSION: This study demonstrates that vascular surgeons primarily prioritise antithrombotic prescribing decisions by procedure type. Clopidogrel is more likely to be prescribed than rivaroxaban as a second agent in combination with aspirin, especially after stenting. Knowing these clinician preferences can target implementation strategies towards supporting decision making in subgroups of patients according to individual risk profiles.

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair.

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, during single mitoses and at single-strand resolution. To distinguish between chronic (reactive oxygen species (ROS)) and acute (ultraviolet light (UV)) mutagenesis, we microfluidically separate pairs of sister cells from the first mitosis following burst UV damage. Strikingly, UV mutations manifest as sister-specific events, revealing mirror-image mutation phasing genome-wide. In contrast, ROS mutagenesis in transcribed regions is reduced strand agnostically. Successive rounds of genome replication over persisting UV damage drives multiallelic variation at CC dinucleotides. Finally, we show that mutation phasing can be resolved to single strands across the entire genome of liver tumors from F1 mice. This strategy can be broadly used to distinguish the contributions of overlapping cancer relevant mutational processes.

Codesign of health technology interventions to support best-practice perioperative care and surgical waitlist management.

OBJECTIVES: This project aimed to determine where health technology can support best-practice perioperative care for patients waiting for surgery. METHODS: An exploratory codesign process used personas and journey mapping in three interprofessional workshops to identify key challenges in perioperative care across four health districts in Sydney, Australia. Through participatory methodology, the research inquiry directly involved perioperative clinicians. In three facilitated workshops, clinician and patient participants codesigned potential digital interventions to support perioperative pathways. Workshop output was coded and thematically analysed, using design principles. RESULTS: Codesign workshops, involving 51 participants, were conducted October to November 2022. Participants designed seven patient personas, with consumer representatives confirming acceptability and diversity. Interprofessional team members and consumers mapped key clinical moments, feelings and barriers for each persona during a hypothetical perioperative journey. Six key themes were identified: 'preventative care', 'personalised care', 'integrated communication', 'shared decision-making', 'care transitions' and 'partnership'. Twenty potential solutions were proposed, with top priorities a digital dashboard and virtual care coordination. DISCUSSION: Our findings emphasise the importance of interprofessional collaboration, patient and family engagement and supporting health technology infrastructure. Through user-based codesign, participants identified potential opportunities where health technology could improve system efficiencies and enhance care quality for patients waiting for surgical procedures. The codesign approach embedded users in the development of locally-driven, contextually oriented policies to address current perioperative service challenges, such as prolonged waiting times and care fragmentation. CONCLUSION: Health technology innovation provides opportunities to improve perioperative care and integrate clinical information. Future research will prototype priority solutions for further implementation and evaluation.

Prescriber decision-making on antithrombotic therapy after endovascular intervention for peripheral artery disease: a protocol for a discrete choice experiment.

INTRODUCTION: Peripheral artery disease (PAD) is a major risk factor for cardiovascular morbidity and mortality, despite surgical and endovascular treatments. Emerging evidence supports the use of immediate antithrombotic medications after endovascular intervention for PAD, however, there is a lack of consensus regarding choice and duration of antithrombotic therapy. Prescriber decision-making is a complex process, with prior studies demonstrating patient factors can influence variability in antithrombotic therapy for PAD. However, it remains unclear the relative contribution of these factors. This paper describes a planned study that aims to (1) determine the influence of patient factors on clinician preference for antithrombotic therapy following endovascular intervention and (2) compare differences in prescribing preferences between consultant vascular surgeons and trainees. METHODS AND ANALYSIS: This cross-sectional survey will evaluate antithrombotic prescribing choices using a discrete choice experiment (DCE) that has been developed and piloted for this study. A list of attributes and levels was generated using a mixed-methods approach. This included an extensive literature review and semistructured interviews with prescribing clinicians. Following final selection of included attributes, specialised software was used to construct a D-efficient design for the DCE questionnaire. The electronic questionnaire will be administered to vascular trainees and consultant surgeons across Australia. These data will be analysed using multinomial logistic regression, treating the decision to prescribe antithrombotic therapy as a function of both the attributes of the two alternatives, as well as characteristics of the respondent. Latent class analysis will be used to explore heterogeneity of responses. ETHICS AND DISSEMINATION: Ethics approval was obtained from the University of Sydney Human Ethics committee (2023/474). The results of this study will be published in peer-reviewed journals and presented at national vascular surgical conferences. These results will be used to improve understanding how clinicians make prescribing decisions and to inform future strategy to enhance guideline-directed prescribing.

The prevalent causes of death in patients with peripheral artery disease undergoing revascularisation or amputation.

OBJECTIVE: Preventing untimely death in patients with peripheral artery disease (PAD) requires a detailed understanding of the predominant causes of death (COD). This literature review aims to describe how short- and long-term COD are reported in patients who had surgery for PAD. METHODS: A literature review was conducted according to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines for articles reporting specific causes of mortality in patients who had surgery for all stages of PAD. Articles were included if they reported COD after open surgical or endovascular revascularisation, or major or minor amputation for PAD. Critical appraisals were conducted according to included study types, using the Joanna Briggs Institute tools. RESULTS: Cause of death was reported in 21 publications. Twenty were observational and one was a randomised control trial. Study size ranged from 25 to 10,505 patients. Cardiovascular disease was the most prevalent COD in perioperative periods (42.5% from 13 studies). Long-term follow-up ranged from 1 month and 7 years with 15 studies reporting cardiac related mortality as the most frequent cause of death. However, mortality from neoplasia, respiratory disease (including pneumonia and pulmonary emboli), stroke and sepsis were prevalent. Many studies were low-average quality, with few population-based observational studies. CONCLUSION: Whilst cardiovascular COD are the most prevalent reasons for mortality in patients with PAD, the proportion of patients dying from neoplasia and respiratory disease is high. Improved reporting standards for COD in studies examining PAD are needed.

The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma.

The introduction of the International Association for the Study of Lung Cancer grading system has furthered interest in histopathological grading for risk stratification in lung adenocarcinoma. Complex morphology and high intratumoral heterogeneity present challenges to pathologists, prompting the development of artificial intelligence (AI) methods. Here we developed ANORAK (pyrAmid pooliNg crOss stReam Attention networK), encoding multiresolution inputs with an attention mechanism, to delineate growth patterns from hematoxylin and eosin-stained slides. In 1,372 lung adenocarcinomas across four independent cohorts, AI-based grading was prognostic of disease-free survival, and further assisted pathologists by consistently improving prognostication in stage I tumors. Tumors with discrepant patterns between AI and pathologists had notably higher intratumoral heterogeneity. Furthermore, ANORAK facilitates the morphological and spatial assessment of the acinar pattern, capturing acinus variations with pattern transition. Collectively, our AI method enabled the precision quantification and morphology investigation of growth patterns, reflecting intratumoral histological transitions in lung adenocarcinoma.

Cancer Evolution: A Multifaceted Affair.

Cancer cells adapt and survive through the acquisition and selection of molecular modifications. This process defines cancer evolution. Building on a theoretical framework based on heritable genetic changes has provided insights into the mechanisms supporting cancer evolution. However, cancer hallmarks also emerge via heritable nongenetic mechanisms, including epigenetic and chromatin topological changes, and interactions between tumor cells and the tumor microenvironment. Recent findings on tumor evolutionary mechanisms draw a multifaceted picture where heterogeneous forces interact and influence each other while shaping tumor progression. A comprehensive characterization of the cancer evolutionary toolkit is required to improve personalized medicine and biomarker discovery. SIGNIFICANCE: Tumor evolution is fueled by multiple enabling mechanisms. Importantly, genetic instability, epigenetic reprogramming, and interactions with the tumor microenvironment are neither alternative nor independent evolutionary mechanisms. As demonstrated by findings highlighted in this perspective, experimental and theoretical approaches must account for multiple evolutionary mechanisms and their interactions to ultimately understand, predict, and steer tumor evolution.

Sex, Endothelial Cell Functions, and Peripheral Artery Disease.

Peripheral artery disease (PAD) is caused by blocked arteries due to atherosclerosis and/or thrombosis which reduce blood flow to the lower limbs. It results in major morbidity, including ischemic limb, claudication, and amputation, with patients also suffering a heightened risk of heart attack, stroke, and death. Recent studies suggest women have a higher prevalence of PAD than men, and with worse outcomes after intervention. In addition to a potential unconscious bias faced by women with PAD in the health system, with underdiagnosis, and lower rates of guideline-based therapy, fundamental biological differences between men and women may be important. In this review, we highlight sexual dimorphisms in endothelial cell functions and how they may impact PAD pathophysiology in women. Understanding sex-specific mechanisms in PAD is essential for the development of new therapies and personalized care for patients with PAD.

Infigratinib, a selective FGFR1-3 tyrosine kinase inhibitor, alters dentoalveolar development at high doses.

BACKGROUND: Fibroblast growth factor receptor-3 (FGFR3) gain-of-function mutations are linked to achondroplasia. Infigratinib, a FGFR1-3 tyrosine kinase inhibitor, improves skeletal growth in an achondroplasia mouse model. FGFs and their receptors have critical roles in developing teeth, yet effects of infigratinib on tooth development have not been assessed. Dentoalveolar and craniofacial phenotype of Wistar rats dosed with low (0.1 mg/kg) and high (1.0 mg/kg) dose infigratinib were evaluated using micro-computed tomography, histology, and immunohistochemistry. RESULTS: Mandibular third molars were reduced in size and exhibited aberrant crown and root morphology in 100% of female rats and 80% of male rats at high doses. FGFR3 and FGF18 immunolocalization and extracellular matrix protein expression were unaffected, but cathepsin K (CTSK) was altered by infigratinib. Cranial vault bones exhibited alterations in dimension, volume, and density that were more pronounced in females. In both sexes, interfrontal sutures were significantly more patent with high dose vs vehicle. CONCLUSIONS: High dose infigratinib administered to rats during early stages affects dental and craniofacial development. Changes in CTSK from infigratinib in female rats suggest FGFR roles in bone homeostasis. While dental and craniofacial disruptions are not expected at therapeutic doses, our findings confirm the importance of dental monitoring in clinical studies.

A hidden problem: peripheral artery disease in women.

Peripheral artery disease (PAD) has a huge social and economic burden and is an important contributor to the global health burden. Sex differences in PAD are apparent, with recent data suggesting equal if not greater prevalence in women, and women having worse clinical outcomes. Why this occurs is not clear. To identify underlying reasons for gender inequalities in PAD, we executed a deeper exploration through a social constructive perspective. A scoping review was conducted using the World Health Organization model for analysis of gender-related needs in healthcare. Complex interacting factors, including biological, clinical, and societal variables, were reviewed to highlight gender-related inequities in the diagnosis, treatment, and management of PAD. Current gaps in knowledge were identified and insights into future directions aimed at improving these inequalities were discussed. Our findings highlight the multi-level complexities that need to be considered for strategies to improve gender-related needs in PAD healthcare.

Optimising Medications in Older Vascular Surgery Patients Through Geriatric Co-management.

BACKGROUND: Prescribing of potentially inappropriate medications and under-prescribing of guideline-recommended medications for cardiovascular risk modification have both been associated with negative outcomes in older adults. Hospitalisation represents an important opportunity to optimise medication use and may be achieved through geriatrician-led interventions. OBJECTIVE: We aimed to evaluate whether implementation of a novel model of care called Geriatric Comanagement of older Vascular (GeriCO-V) surgery patients is associated with improvements in medication prescribing. METHODS: We used a prospective pre-post study design. The intervention was a geriatric co-management model, where a geriatrician delivered comprehensive geriatric assessment-based interventions including a routine medication review. We included consecutively admitted patients to the vascular surgery unit at a tertiary academic centre aged ≥ 65 years with an expected length of stay of ≥ 2 days and who were discharged from hospital. Outcomes of interest were the prevalence of at least one potentially inappropriate medication as defined by the Beers Criteria at admission and discharge, and rates of cessation of at least one potentially inappropriate medication present on admission. In the subgroup of patients with peripheral arterial disease, the prevalence of guideline-recommended medications on discharge was determined. RESULTS: There were 137 patients in the pre-intervention group (median [interquartile range] age: 80.0 [74.0-85.0] years, 83 [60.6%] with peripheral arterial disease) and 132 patients in the post-intervention group (median [interquartile range] age: 79.0 (73.0-84.0) years, 75 [56.8%] with peripheral arterial disease). There was no change in the prevalence of potentially inappropriate medication use from admission to discharge in either group (pre-intervention: 74.5% on admission vs 75.2% on discharge; post-intervention: 72.0% vs 72.7%, p = 0.65). Forty-five percent of pre-intervention group patients had at least one potentially inappropriate medication present on admission ceased, compared with 36% of post-intervention group patients (p = 0.11). A higher number of patients with peripheral arterial disease in the post-intervention group were discharged on antiplatelet agent therapy (63 [84.0%] vs 53 [63.9%], p = 0.004) and lipid-lowering therapy (58 [77.3%] vs 55 [66.3%], p = 0.12). CONCLUSIONS: Geriatric co-management was associated with an improvement in guideline-recommended antiplatelet agent prescribing aimed at cardiovascular risk modification for older vascular surgery patients. The prevalence of potentially inappropriate medications was high in this population, and was not reduced with geriatric co-management.

The experience of hospital care for older surgical patients and their carers: A mixed-methods study.

OBJECTIVE: A growing proportion of older adults are undergoing surgery, but there is a paucity of patient and carer experience research in this group. This study investigated the experience of hospital care in an older vascular surgery population for patients and their carers. METHODS: This was a mixed-methods convergent design, including simultaneous collection of quantitative and qualitative research strands by combining open-ended questions with rating scales in a questionnaire. Recently hospitalised vascular surgery patients aged ≥65 years at a major teaching hospital were recruited. Carers were also approached to participate. RESULTS: Forty-seven patients (mean age 77 years, 77% male, 20% with a Clinical Frailty Scale score >4) and nine carers participated. The majority of patients reported that their views were listened to (n = 42, 89%), they were kept informed (n = 39, 83%), and were asked about their pain (n = 37, 79%). Among carers, seven reported their views were listened to and that they were kept informed. Thematic analysis of patients' and carers' responses to open-ended questions about their experience of hospital care revealed four themes in terms of what mattered to them: fundamental care including hygiene and nutrition, comfort of the hospital environment such as sleep and meals, being informed and involved in health-care decision-making, and treating pain and deconditioning to help recovery. CONCLUSIONS: Older adults admitted to hospital for vascular surgery and their carers, valued highly the care that met both their fundamental needs and facilitated shared decisions for care and recovery. These priorities can be addressed through Age-Friendly Health System initiatives.

Postoperative complications and hospital costs following open radical cystectomy: A retrospective study.

OBJECTIVES: To evaluate primarily the relationship between postoperative complications and hospital costs, and secondarily the relationship between postoperative complications and mortality, following radical cystectomy. METHODS: Postoperative complications were retrospectively examined for 147 patients undergoing radical cystectomy at a university hospital between January 2012 and July 2021. Complications were defined and graded using the Clavien-Dindo classification system. In-hospital cost was calculated using an activity-based costing methodology. Regression modelling was used to investigate the relationships among a priori selected perioperative variables, complications, and costs. The effect of complications on postoperative mortality was ascertained using time-dependent coefficients in a Cox proportional hazards regression model. RESULTS: 135 (92%) patients experienced one or more postoperative complications. The medians of hospital cost for patients who experienced no complications and those who experienced complications were $42,796.3 (29,222.9-53,532.5) and $81,050.1 (49,614.8-122,533.6) respectively, p < 0.001. Hospital costs were strongly associated with complication severity: Clavien-Dindo grade II complications increased costs by 45.2% (p < 0.001, 95% CI 19.1%-76.6%), and Clavien-Dindo grade III to V complications increased costs by 107.5% (p < 0.001, 95% CI 52.4%-181.8%). Each additional count of complication and increase in Clavien-Dindo complication grade increased the risk of mortality 1.28-fold (RR = 1.28, p = 0.006, 95% CI 1.08-1.53) and 2.50-fold (RR = 2.50, p = 0.012 95% CI 1.23-5.07) respectively. CONCLUSIONS: These findings demonstrate a high prevalence of complications following cystectomy and significant associated increases in hospital costs and mortality. Postoperative complications are a key target for cost-containment strategies. TRIAL REGISTRATION: Trial Registration: Australian New Zealand Clinical Trials Registry (ACTRN:12622000057785.