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.

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.

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.

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.

Timing of minor and major amputation in patients with diabetes-related foot ulceration admitted to two public tertiary referral hospitals in Australia.

BACKGROUND: There is limited information regarding the number of patients with diabetes-related foot ulceration (DFU) who receive minor or major amputation, and how quickly these amputations occur. This study aimed to identify the incidence of index minor and major amputation among inpatients with DFU over 4 years, and where amputation occurred during the patient's index DFU-related admission, investigate prognostic factors. METHODS: The incidence of index minor and major amputation, and the admission sequence during which amputation occurred were identified from DFU-related admissions to two public hospitals during 2014-2018. Where minor or major amputation occurred during the patient's index DFU-related admission, prognostic factors were investigated using logistic regression. RESULTS: DFU-related hospital admissions were required by 564 patients. The incidence of minor amputation over 4 years was 34% (n = 193). The incidence of minor amputation during the patient's index DFU-related admission was 28% (n = 155), which was associated with requiring revascularisation (odds ratio [OR] 2.33, 95% CI 1.53-3.55, P < 0.001). The incidence of major amputation over 4 years was 8% (n = 45). The incidence of major amputation during the patient's index DFU-related admission was 6% (n = 31), which was associated with having more comorbidities (OR 1.58, 95% CI 1.10-2.26, P = 0.01) and receiving care for a mental health condition (OR 3.85, 95% CI 1.48-10.01, P = 0.006). CONCLUSION: Most amputations occurred during the patient's index DFU-related hospital admission. Major amputation during a patient's index admission was associated with more comorbidities and mental health conditions.

Frail patients having vascular surgery during the early COVID-19 pandemic experienced high rates of adverse perioperative events and amputation.

BACKGROUND: Frailty predicts adverse perioperative outcomes and increased mortality in patients having vascular surgery. Frailty assessment is a potential tool to inform resource allocation, and shared decision-making about vascular surgery in the resource constrained COVID-19 pandemic environment. This cohort study describes the prevalence of frailty in patients having vascular surgery and the association between frailty, mortality and perioperative outcomes. METHODS: The COVID-19 Vascular Service in Australia (COVER-AU) prospective cohort study evaluates 30-day and six-month outcomes for consecutive patients having vascular surgery in 11 Australian vascular units, March-July 2020. The primary outcome was mortality, with secondary outcomes procedure-related outcomes and hospital utilization. Frailty was assessed using the nine-point visual Clinical Frailty Score, scores of 5 or more considered frail. RESULTS: Of the 917 patients enrolled, 203 were frail (22.1%). The 30 day and 6 month mortality was 2.0% (n = 20) and 5.9% (n = 35) respectively with no significant difference between frail and non-frail patients (OR 1.68, 95%CI 0.79-3.54). However, frail patients stayed longer in hospital, had more perioperative complications, and were more likely to be readmitted or have a reoperation when compared to non-frail patients. At 6 months, frail patients had twice the odds of major amputation compared to non-frail patients, after adjustment (OR 2.01; 95% CI 1.17-3.78), driven by a high rate of amputation during the period of reduced surgical activity. CONCLUSION: Our findings highlight that older, frail patients, experience potentially preventable adverse outcomes and there is a need for targeted interventions to optimize care, especially in times of healthcare stress.

Coagulation factor V is a T-cell inhibitor expressed by leukocytes in COVID-19.

Clotting Factor V (FV) is primarily synthesized in the liver and when cleaved by thrombin forms pro-coagulant Factor Va (FVa). Using whole blood RNAseq and scRNAseq of peripheral blood mononuclear cells, we find that FV mRNA is expressed in leukocytes, and identify neutrophils, monocytes, and T regulatory cells as sources of increased FV in hospitalized patients with COVID-19. Proteomic analysis confirms increased FV in circulating neutrophils in severe COVID-19, and immunofluorescence microscopy identifies FV in lung-infiltrating leukocytes in COVID-19 lung disease. Increased leukocyte FV expression in severe disease correlates with T-cell lymphopenia. Both plasma-derived and a cleavage resistant recombinant FV, but not thrombin cleaved FVa, suppress T-cell proliferation in vitro. Anticoagulants that reduce FV conversion to FVa, including heparin, may have the unintended consequence of suppressing the adaptive immune system.

Geriatric Comanagement of Older Vascular Surgery Inpatients Reduces Hospital-Acquired Geriatric Syndromes.

OBJECTIVE: This study evaluates the impact of a novel model of care called Geriatric Comanagement of Older Vascular surgery inpatients on clinical outcomes. DESIGN, SETTING, AND PARTICIPANTS: A pre-post study of geriatric comanagement, comparing prospectively recruited preintervention (February-October 2019) and prospectively recruited postintervention (January-December 2020) cohorts. Consecutively admitted vascular surgery patients age ≥65 years at a tertiary academic hospital in Concord and with an expected length of stay (LOS) greater than 2 days were recruited. INTERVENTION: A comanagement model where a geriatrician was embedded within the vascular surgery team and delivered proactive comprehensive geriatric assessment based interventions. METHODS: Primary outcomes of incidence of hospital-acquired geriatric syndromes, delirium, and LOS were compared between groups using univariable and multivariable logistic regression analyses. Prespecified subgroup analysis was performed by frailty status. RESULTS: There were 150 patients in the preintervention group and 152 patients in the postintervention group. The postintervention group were more frail [66 (43.4%) vs 45 (30.0%)], urgently admitted [72 (47.4%) vs 56 (37.3%)], and nonoperatively managed [52 (34.2%) vs 33 (22.0%)]. These differences were attributed to the coronavirus disease 2019 pandemic during the postintervention phase. The postintervention group had fewer hospital-acquired geriatric syndromes [74 (48.7%) vs 97 (64.7%); P = .005] and reduced incident delirium [5 (3.3%) vs 15 (10.0%); P = .02], in unadjusted and adjusted analyses. Cardiac [8 (5.3%) vs 30 (20.0%); P < .001] and infective complications [4 (2.6%) vs 12 (8.0%); P = .04] were also fewer. LOS was unchanged. Frail patients in the postintervention group experienced significantly fewer geriatric syndromes including delirium. CONCLUSIONS AND IMPLICATIONS: This is the first prospective study of inpatient geriatric comanagement for older vascular surgery patients. Reductions in hospital-acquired geriatric syndromes including delirium, and cardiac and infective complications were observed after implementing geriatric comanagement. These benefits were also demonstrated in the frail subgroup.

Convergent somatic mutations in metabolism genes in chronic liver disease.

The progression of chronic liver disease to hepatocellular carcinoma is caused by the acquisition of somatic mutations that affect 20-30 cancer genes1-8. Burdens of somatic mutations are higher and clonal expansions larger in chronic liver disease9-13 than in normal liver13-16, which enables positive selection to shape the genomic landscape9-13. Here we analysed somatic mutations from 1,590 genomes across 34 liver samples, including healthy controls, alcohol-related liver disease and non-alcoholic fatty liver disease. Seven of the 29 patients with liver disease had mutations in FOXO1, the major transcription factor in insulin signalling. These mutations affected a single hotspot within the gene, impairing the insulin-mediated nuclear export of FOXO1. Notably, six of the seven patients with FOXO1S22W hotspot mutations showed convergent evolution, with variants acquired independently by up to nine distinct hepatocyte clones per patient. CIDEB, which regulates lipid droplet metabolism in hepatocytes17-19, and GPAM, which produces storage triacylglycerol from free fatty acids20,21, also had a significant excess of mutations. We again observed frequent convergent evolution: up to fourteen independent clones per patient with CIDEB mutations and up to seven clones per patient with GPAM mutations. Mutations in metabolism genes were distributed across multiple anatomical segments of the liver, increased clone size and were seen in both alcohol-related liver disease and non-alcoholic fatty liver disease, but rarely in hepatocellular carcinoma. Master regulators of metabolic pathways are a frequent target of convergent somatic mutation in alcohol-related and non-alcoholic fatty liver disease.

2020 Asian Pacific Society of Cardiology Consensus Recommendations on Antithrombotic Management for High-risk Chronic Coronary Syndrome.

The unique characteristics of patients with chronic coronary syndrome (CCS) in the Asia-Pacific region, heterogeneous approaches because of differences in accesses and resources and low number of patients from the Asia-Pacific region in pivotal studies, mean that international guidelines cannot be routinely applied to these populations. The Asian Pacific Society of Cardiology developed these consensus recommendations to summarise current evidence on the management of CCS and provide recommendations to assist clinicians treat patients from the region. The consensus recommendations were developed by an expert consensus panel who reviewed and appraised the available literature, with focus on data from patients in Asia-Pacific. Consensus statements were developed then put to an online vote. The resulting recommendations provide guidance on the assessment and management of bleeding and ischaemic risks in Asian CCS patients. Furthermore, the selection of long-term antithrombotic therapy is discussed, including the role of single antiplatelet therapy, dual antiplatelet therapy and dual pathway inhibition therapy.

Understanding the Role and Value of Process Quality Indicators in Older Vascular Surgery Inpatients.

BACKGROUND: Despite the development of geriatrics surgery process quality indicators (QIs), few studies have reported on these QIs in routine surgical practice. Even less is known about the links between these QIs and clinical outcomes, and patient characteristics. We aimed to measure geriatrics surgery process QIs, and investigate the association between process QIs and outcomes, and QIs and patient characteristics, in hospitalized older vascular surgery patients. METHODS: This was a prospective cohort study of 150 consecutive patients aged ≥ 65 years admitted to a tertiary vascular surgery unit. Occurrence of geriatrics surgery process QIs as part of routine vascular surgery care was measured. Associations between QIs and high-risk patient characteristics, and QIs and clinical outcomes were assessed using clustered heatmaps. RESULTS: QI occurrence rate varied substantially from 2% to 93%. Some QIs, such as cognition and delirium screening, documented treatment preferences, and geriatrician consultation were infrequent and clustered with high-risk patient characteristcs. There were two major process-outcome clusters: (a) multidisciplinary consultations, communication and screening-based process QIs with multiple adverse outcomes, and (b) documentation and prescribing-related QIs with fewer adverse outcomes. CONCLUSIONS: Clustering patterns of process QIs with clinical outcomes are complex, and there is a differential occurrence of QIs by patient characteristics. Prospective intervention studies that report on implemented QIs, outcomes and patient characteristics are needed to better understand the causal pathways between process QIs and outcomes, and to help prioritize targets for quality improvement in the care of older surgical patients.

Variation in treatment and outcomes for patients with chronic limb-threatening ischaemia in New South Wales, Australia.

BACKGROUND: Chronic limb-threatening ischaemia (CLTI) carries significant amputation and mortality risks. Australian population-based outcomes for CLTI are inadequately known. This study aimed to distinguish factors associated with outcomes in the first 2 years after CLTI surgery. METHODS: By linking routinely collected health administrative and mortality data from New South Wales, this population-based cohort study identified patients with ischaemic rest pain, gangrene or ulceration undergoing vascular surgery in public hospitals between 2010 and 2012. The primary outcome was 2-year amputation-free survival (AFS), and secondary outcomes included readmission and reoperation rates. Multivariable regression analysis identified prognostic factors adjusted for patient, hospital and geographic factors. RESULTS: Primary CLTI surgery was performed on 4898 patients. Almost half the cohort had minor amputations without concurrent revascularization (2398, 49%), and the remaining patients had open (652, 13%) or endovascular (1848, 38%) surgery. At 2-years, the AFS rate was 72%. Significant disparity was seen between age groups, with the 2-year AFS 71% in patients aged 75 years or older, compared to 95% in patients aged less than 75 years (P < 0.001). Place of residence or hospital training status did not significantly influence AFS or readmission, but non-training hospitals had higher rates of reoperation. CONCLUSION: This population-based cohort study demonstrated variable outcomes for patients with CLTI, particularly with respect to older age, admission acuity and comorbidity. Results may guide service improvements however further research is needed into how population-wide health initiatives can address age-related disparities in CLTI.

The Prognostic Performance of Frailty for Delirium and Functional Decline in Vascular Surgery Patients.

BACKGROUND: Frailty in older vascular surgery patients is associated with increased mortality, hospital stay, and morbidity. The association of frailty with hospital-acquired geriatric syndromes such as delirium and functional decline has not been well studied. OBJECTIVES: To investigate the association between frailty and hospital-acquired geriatric syndromes in older hospitalized vascular surgery patients, and to evaluate the prognostic performance of the frailty index (FI) and the Clinical Frailty Scale (CFS) for delirium and functional decline. DESIGN: Prospective cohort study. SETTING: Acute care academic hospital. PARTICIPANTS: Patients aged 65 years or more admitted to a tertiary vascular surgery unit (N=150). MEASUREMENTS: Frailty was assessed using the FI and CFS. The adjusted association of frailty status with delirium and functional decline was assessed using logistic regression analysis. The prognostic performance of FI and CFS was determined by assessing C-statistic and positive and negative predictive values (PPV and NPV). RESULTS: Of 150 participants, FI identified 34 (23%) and CFS identified 45 (30%) as frail. Frailty was an independent predictor of delirium (FI adjusted odds ratio, odds ratio (OR) = 5.66, 95% confidence interval (CI) = 1.53-21.03; CFS adjusted OR = 4.07, 95% CI = 1.14-14.50), but not functional decline. FI and CFS showed acceptable prognostic performance for delirium (C-statistic 0.74), but not functional decline (C-statistic 0.63-0.64). For both outcomes, the FI and CFS had high NPV (86-96%), and low PPV (22-29%). CONCLUSION: Frail older vascular surgery patients are more likely to develop hospital-acquired geriatric syndromes. The FI and CFS have acceptable prognostic performance for predicting delirium but not all individuals who are identified as frail develop delirium. Ongoing research is needed to identify interventions that improve outcomes in patients who screen positive for frailty.

IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis.

The cytokine interleukin-6 (IL6) and its downstream effector STAT3 constitute a key oncogenic pathway, which has been thought to be functionally connected to estrogen receptor α (ER) in breast cancer. We demonstrate that IL6/STAT3 signaling drives metastasis in ER+ breast cancer independent of ER. STAT3 hijacks a subset of ER enhancers to drive a distinct transcriptional program. Although these enhancers are shared by both STAT3 and ER, IL6/STAT3 activity is refractory to standard ER-targeted therapies. Instead, inhibition of STAT3 activity using the JAK inhibitor ruxolitinib decreases breast cancer invasion in vivo. Therefore, IL6/STAT3 and ER oncogenic pathways are functionally decoupled, highlighting the potential of IL6/STAT3-targeted therapies in ER+ breast cancer.

Pervasive lesion segregation shapes cancer genome evolution.

Cancers arise through the acquisition of oncogenic mutations and grow by clonal expansion1,2. Here we reveal that most mutagenic DNA lesions are not resolved into a mutated DNA base pair within a single cell cycle. Instead, DNA lesions segregate, unrepaired, into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations. We characterize this process in mutagen-induced mouse liver tumours and show that DNA replication across persisting lesions can produce multiple alternative alleles in successive cell divisions, thereby generating both multiallelic and combinatorial genetic diversity. The phasing of lesions enables accurate measurement of strand-biased repair processes, quantification of oncogenic selection and fine mapping of sister-chromatid-exchange events. Finally, we demonstrate that lesion segregation is a unifying property of exogenous mutagens, including UV light and chemotherapy agents in human cells and tumours, which has profound implications for the evolution and adaptation of cancer genomes.