Sequential requirements for distinct Polθ domains during theta-mediated end joining.

DNA polymerase θ (Polθ) plays a central role in a DNA double-strand break repair pathway termed theta-mediated end joining (TMEJ). TMEJ functions by pairing short-sequence "microhomologies" (MHs) in single-stranded DNA at each end of a break and subsequently initiating DNA synthesis. It is not known how the Polθ helicase domain (HD) and polymerase domain (PD) operate to bring together MHs and facilitate repair. To resolve these transient processes in real time, we utilized in vitro single-molecule FRET approaches and biochemical analyses. We find that the Polθ-HD mediates the initial capture of two ssDNA strands, bringing them in close proximity. The Polθ-PD binds and stabilizes pre-annealed MHs to form a synaptic complex (SC) and initiate repair synthesis. Individual synthesis reactions show that Polθ is inherently non-processive, accounting for complex mutational patterns during TMEJ. Binding of Polθ-PD to stem-loop-forming sequences can substantially limit synapsis, depending on the available dNTPs and sequence context.

Genome Protection by DNA Polymerase θ.

DNA polymerase θ (Pol θ) is a DNA repair enzyme widely conserved in animals and plants. Pol θ uses short DNA sequence homologies to initiate repair of double-strand breaks by theta-mediated end joining. The DNA polymerase domain of Pol θ is at the C terminus and is connected to an N-terminal DNA helicase-like domain by a central linker. Pol θ is crucial for maintenance of damaged genomes during development, protects DNA against extensive deletions, and limits loss of heterozygosity. The cost of using Pol θ for genome protection is that a few nucleotides are usually deleted or added at the repair site. Inactivation of Pol θ often enhances the sensitivity of cells to DNA strand-breaking chemicals and radiation. Since some homologous recombination-defective cancers depend on Pol θ for growth, inhibitors of Pol θ may be useful in treating such tumors.

Stepwise requirements for polymerases δ and θ in theta-mediated end joining.

Timely repair of chromosomal double-strand breaks is required for genome integrity and cellular viability. The polymerase theta-mediated end joining pathway has an important role in resolving these breaks and is essential in cancers defective in other DNA repair pathways, thus making it an emerging therapeutic target1. It requires annealing of 2-6 nucleotides of complementary sequence, microhomologies, that are adjacent to the broken ends, followed by initiation of end-bridging DNA synthesis by polymerase θ. However, the other pathway steps remain inadequately defined, and the enzymes required for them are unknown. Here we demonstrate requirements for exonucleolytic digestion of unpaired 3' tails before polymerase θ can initiate synthesis, then a switch to a more accurate, processive and strand-displacing polymerase to complete repair. We show the replicative polymerase, polymerase δ, is required for both steps; its 3' to 5' exonuclease activity for flap trimming, then its polymerase activity for extension and completion of repair. The enzymatic steps that are essential and specific to this pathway are mediated by two separate, sequential engagements of the two polymerases. The requisite coupling of these steps together is likely to be facilitated by physical association of the two polymerases. This pairing of polymerase δ with a polymerase capable of end-bridging synthesis, polymerase θ, may help to explain why the normally high-fidelity polymerase δ participates in genome destabilizing processes such as mitotic DNA synthesis2 and microhomology-mediated break-induced replication3.

Human DNA polymerase θ harbors DNA end-trimming activity critical for DNA repair.

Cancers with hereditary defects in homologous recombination rely on DNA polymerase θ (pol θ) for repair of DNA double-strand breaks. During end joining, pol θ aligns microhomology tracts internal to 5'-resected broken ends. An unidentified nuclease trims the 3' ends before synthesis can occur. Here we report that a nuclease activity, which differs from the proofreading activity often associated with DNA polymerases, is intrinsic to the polymerase domain of pol θ. Like the DNA synthesis activity, the nuclease activity requires conserved metal-binding residues, metal ions, and dNTPs and is inhibited by ddNTPs or chain-terminated DNA. Our data indicate that pol θ repurposes metal ions in the polymerase active site for endonucleolytic cleavage and that the polymerase-active and end-trimming conformations of the enzyme are distinct. We reveal a nimble strategy of substrate processing that allows pol θ to trim or extend DNA depending on the DNA repair context.

Dynamic stem-loop extension by Pol θ and templated insertion during DNA repair.

Theta-mediated end joining (TMEJ) is critical for survival of cancer cells when other DNA double-stranded break repair pathways are impaired. Human DNA polymerase theta (Pol θ) can extend ssDNA oligonucleotides, but little is known about preferred substrates and mechanism. We show that Pol θ can extend both ssDNA and RNA substrates by unimolecular stem-loop synthesis initiated by only two 3' terminal base pairs. Given sufficient time, Pol θ uses alternative pairing configurations that greatly expand the repertoire of sequence outcomes. Further primer-template adjustments yield low-fidelity outcomes when the nucleotide pool is imbalanced. Unimolecular stem-loop synthesis competes with bimolecular end joining, even when a longer terminal microhomology for end joining is available. Both reactions are partially suppressed by the ssDNA-binding protein replication protein A. Protein-primer grasp residues that are specific to Pol θ are needed for rapid stem-loop synthesis. The ability to perform stem-loop synthesis from a minimally paired primer is rare among human DNA polymerases, but we show that human DNA polymerases Pol η and Pol λ can catalyze related reactions. Using purified human Pol θ, we reconstituted in vitro TMEJ incorporating an insertion arising from a stem-loop extension. These activities may help explain TMEJ repair events that include inverted repeat sequences.

DNA polymerase zeta contributes to heterochromatin replication to prevent genome instability.

The DNA polymerase zeta (Polζ) plays a critical role in bypassing DNA damage. REV3L, the catalytic subunit of Polζ, is also essential in mouse embryonic development and cell proliferation for reasons that remain incompletely understood. In this study, we reveal that REV3L protein interacts with heterochromatin components including repressive histone marks and localizes in pericentromeric regions through direct interaction with HP1 dimer. We demonstrate that Polζ/REV3L ensures progression of replication forks through difficult-to-replicate pericentromeric heterochromatin, thereby preventing spontaneous chromosome break formation. We also find that Rev3l-deficient cells are compromised in the repair of heterochromatin-associated double-stranded breaks, eliciting deletions in late-replicating regions. Lack of REV3L leads to further consequences that may be ascribed to heterochromatin replication and repair-associated functions of Polζ, with a disruption of the temporal replication program at specific loci. This is correlated with changes in epigenetic landscape and transcriptional control of developmentally regulated genes. These results reveal a new function of Polζ in preventing chromosome instability during replication of heterochromatic regions.

Variability in Surveillance Strategies Following Resection of Sacrococcygeal Teratoma.

INTRODUCTION: Surveillance following sacrococcygeal teratoma (SCT) resection varies. The purpose of this study was to describe the clinical characteristics and outcomes of patients undergoing SCT resection and examine current institutional practices to detect recurrence. METHODS: A single-institution retrospective review of children who underwent resection of an SCT from January 1, 2010 to December 31, 2020 was performed. Data were summarized and surveillance strategies compared between histopathologic subtypes using nonparametric methods. RESULTS: Thirty six patients (75.0% female) underwent SCT removal at a median age of 8 d. Histopathology revealed 27 mature teratomas (75.0%), eight immature teratomas (22.2%), and one malignant germ cell tumor (2.8%). Median postoperative follow-up was 3.17 y (interquartile range [IQR]: 2.31-4.38 y). Patients had a median of 2.32 clinic visits per year (IQR: 2.00-2.70), alpha-fetoprotein levels were obtained at a median of 2.01 times per year (IQR: 0-1.66), and surveillance imaging was performed at a median of 2.31 times per year (IQR: 0-2.84). Patients with immature teratomas had alpha-fetoprotein laboratories obtained more frequently than patients with mature teratomas (3.10 times/year versus 0.93 times/year, P = 0.001). There was no significant difference in the number of imaging studies obtained between groups. Two patients (5.6%) developed recurrence, which were identified on magnetic resonance imaging at 191 and 104 d postresection, respectively. CONCLUSIONS: Postoperative surveillance practices varied widely. Recurrence was noted in a single malignant case in the first year following resection. Multi-institutional studies are needed to determine the optimal surveillance strategy to detect recurrence of SCT.

Significance of retrograde flow with antegrade continence enemas in children with fecal incontinence and constipation.

BACKGROUND: For children with constipation and fecal incontinence treated with antegrade continence enemas (ACE), a fluoroscopic study with contrast administered via appendicostomy/cecostomy can define the anatomy of the colon and simulate the flush to investigate associated symptoms or inadequate response. These studies can at times show retrograde flow into the small intestine. Our objective was to investigate the significance of this finding. METHODS: We reviewed studies at our institution with contrast administered via appendicostomy/cecostomy in children treated with ACE, identifying those demonstrating retrograde flow of contrast. We recorded demographics, medical history, interventions, and outcomes. RESULTS: We identified 162 studies (52% male, median age 10.7 years) with contrast via appendicostomy (76%) or cecostomy (24%). Diagnoses included anorectal malformation (38%), spinal cord anomaly (26%), functional constipation (24%), colonic dysmotility (18%), and Hirschsprung disease (12%). Fifty-nine (36%) studies showed retrograde flow: 28/59 children (48%) were not responding adequately and 21/59 (36%) had symptoms with ACE. Children with retrograde flow were more likely to have symptoms with ACE than those without (36% vs. 15%, p < 0.01). Fourteen children underwent interventions for this finding, including administering flushes more distally (4/8 responded), changing positioning of the child during flush administration, (1/2 responded), and slowing administration (1/1 responded). Retrograde flow was associated with younger age (p < 0.01), not sex or underlying diagnosis. CONCLUSION: Identifying retrograde flow during studies with contrast administered via appendicostomy/cecostomy can be useful for children with a poor response or symptoms associated with ACE, as adjustments to the mechanics of the flush can alleviate those symptoms. LEVEL OF EVIDENCE: Prognostic study, Level III.

Outcomes of children with constipation and autism spectrum disorder treated with antegrade continence enemas.

BACKGROUND: Treatment of functional constipation (FC) in children with autism spectrum disorder (ASD) is challenging due to sensory and behavioral issues. We aimed to understand whether antegrade continence enemas (ACEs) are successful in the treatment of FC in children with ASD. METHODS: A single-institution retrospective review was performed in children diagnosed with ASD and FC who underwent appendicostomy or cecostomy placement from 2007 to 2019. Descriptive statistics regarding soiling and complications were calculated. RESULTS: There were 33 patients included, with a median age of 9.7 years at the time of ACE initiation. The average intelligence quotient was 63.6 (SD = 18.0, n = 12), the average behavioral adaptive score was 59.9 (SD = 11.1, n = 13), and the average total Child Behavioral Checklist score was 72.5 (SD = 7.1, n = 10). Soiling rates were significantly lower following ACE initiation (42.3% vs. 14.8%, p = 0.04). Behavioral issues only prevented 1 patient (3.0%) from proper ACE use. Eleven patients (36.6%) were able to transition to laxatives. There were significant improvements in patient-reported outcomes measures and quality of life. CONCLUSION: Placement of an appendicostomy or cecostomy for management of FC in children with severe ASD was successful in treating constipation and improving quality of life.

Essential Roles for Polymerase θ-Mediated End Joining in the Repair of Chromosome Breaks.

DNA polymerase theta (Pol θ)-mediated end joining (TMEJ) has been implicated in the repair of chromosome breaks, but its cellular mechanism and role relative to canonical repair pathways are poorly understood. We show that it accounts for most repairs associated with microhomologies and is made efficient by coupling a microhomology search to removal of non-homologous tails and microhomology-primed synthesis across broken ends. In contrast to non-homologous end joining (NHEJ), TMEJ efficiently repairs end structures expected after aborted homology-directed repair (5' to 3' resected ends) or replication fork collapse. It typically does not compete with canonical repair pathways but, in NHEJ-deficient cells, is engaged more frequently and protects against translocation. Cell viability is also severely impaired upon combined deficiency in Pol θ and a factor that antagonizes end resection (Ku or 53BP1). TMEJ thus helps to sustain cell viability and genome stability by rescuing chromosome break repair when resection is misregulated or NHEJ is compromised.

The cost of keeping patients waiting: retrospective treatment-control study of additional healthcare utilisation for UK patients awaiting elective treatment.

OBJECTIVE: Long waiting times for elective hospital treatments are common in many countries. This study seeks to address a deficit in the literature concerning the effect of long waits on the wider consumption of healthcare resources. METHODS: We carried out a retrospective treatment-control study in a healthcare system in South West England from 15 June 2021 to 15 December 2021. We compared weekly contacts with health services of patients waiting over 18 weeks for treatment ('Treatments') and people not on a waiting list ('Controls'). Controls were matched to Treatments based on age, sex, deprivation and multimorbidity. Treatments were stratified by the clinical specialty of the awaited hospital treatment, with healthcare usage assessed over various healthcare settings. Wilcoxon signed-rank tests assessed whether there was an increase in healthcare utilisation and bootstrap resampling was used to estimate the magnitude of any differences. RESULTS: A total of 44,616 patients were waiting over 18 weeks (the constitutional target in England) for treatment during the study period. There was an increase (p < 0.0004) in healthcare utilisation for all specialties. Patients in the Cardiothoracic Surgery specialty had the largest increase, with 17.9 [interquartile-range: 4.3, 33.8] additional contacts with secondary care and 17.3 [-1.1, 34.1] additional prescriptions per year. CONCLUSION: People waiting for treatment consume higher levels of healthcare than comparable individuals not on a waiting list. These findings are relevant for clinicians and managers in better understanding patient need and reducing harm. Results also highlight the possible 'false economy' in failing to promptly resolve long elective waits.

Histone H3K4 methylation regulates deactivation of the spindle assembly checkpoint through direct binding of Mad2.

Histone H3 methylation on Lys4 (H3K4me) is associated with active gene transcription in all eukaryotes. In Saccharomyces cerevisiae, Set1 is the sole lysine methyltransferase required for mono-, di-, and trimethylation of this site. Although H3K4me3 is linked to gene expression, whether H3K4 methylation regulates other cellular processes, such as mitosis, is less clear. Here we show that both Set1 and H3K4 mutants display a benomyl resistance phenotype that requires components of the spindle assembly checkpoint (SAC), including Bub3 and Mad2. These proteins inhibit Cdc20, an activator of the anaphase-promoting complex/cyclosome (APC/C). Mutations in Cdc20 that block Mad2 interactions suppress the benomyl resistance of both set1 and H3K4 mutant cells. Furthermore, the HORMA domain in Mad2 directly binds H3, identifying a new histone H3 "reader" motif. Mad2 undergoes a conformational change important for execution of the SAC. We found that the closed (active) conformation of both yeast and human Mad2 is capable of binding methylated H3K4, but, in contrast, the open (inactive) Mad2 conformation limits interaction with methylated H3. Collectively, our data indicate that interactions between Mad2 and H3K4 regulate resolution of the SAC by limiting closed Mad2 availability for Cdc20 inhibition.

Utilization Trends and Volume-outcomes Relationship of Endoscopic Resection for Early Stage Esophageal Cancer.

OBJECTIVES: We describe utilization trends and center volume-outcomes relationship of ER of early stage esophageal cancer using a large hospitalbased registry. SUMMARY OF BACKGROUND DATA: ER is increasingly accepted as the preferred treatment for early stage esophageal cancer, however its utilization and the center volume-outcomes relationship in the United States is unknown. METHODS: The National Cancer Database was used to identify patients with cT1N0M0 esophageal cancer treated with ER or esophagectomy between 2004 and 2015. Relative frequencies were plotted over time. Restricted cubic splines and maximally selected rank statistics were used to identify an inflection point of center volume and survival. RESULTS: A total of 1136 patients underwent ER and 2829 patients underwent esophagectomy during the study period. Overall utilization of ER, and relative use compared to esophagectomy, increased throughout the study period. Median annualized center ER volume was 1.9 cases per year (interquartile range 0.5-5.8). Multivariable Cox regression showed increasing annualized center volume by 1 case per year was associated with improved survival. Postoperative 30- or 90-day mortality, 30-day readmission, and pathologic T upstaging rates were similar irrespective of center volume. CONCLUSIONS: Utilization of ER compared to esophagectomy for stage I esophageal cancer has increased over the past decade, though many individual centers perform fewer than 1 case annually. increasing annualized center volume by one procedure per year was associated with improved survival. increased volume beyond this was not associated with survival benefit. Referral to higher volume centers for treatment of superficial esophageal cancer should be considered.

Effects of Circularity Interventions in the European Plastic Packaging Sector.

Low levels of plastics circularity today reflect major challenges for the sector to reduce environmental impacts and a need for wider systemic change. In this work, we investigated the potential for climate and socioeconomic benefits of circular economy (CE) interventions in the plastic packaging system. By means of a mixed-unit input-output (IO) model, we performed a comparative scenario analysis for the development of demand and waste management up to 2030 within the EU-28 (EU27 + United Kingdom). We modeled the development of material flows and assessed the effects of both demand-side and end-of-life interventions. Different levels of ambition toward 2030 based on EU circular economy strategies were tested. Results showed that on reaching high levels of circularity, between 14 and 22 Mt CO2-eq/year could be reduced by 2030 (20-30% of the total sector impact in 2018) compared to business-as-usual. Demand change (e.g., by decreasing product packaging intensities) showed similar emission-saving potential as achieving the current recycling target of 55%, which emphasizes the role of demand-side actions. Most scenarios displayed moderate employment gains and potential economic losses, pertaining to both direct and indirect activity shifts in the economy. While considering model limitations, the approach is useful in indicating potential first-order effects of system changes.

Material and Carbon Footprints of Machinery Capital.

Machinery and equipment, integral as technology-specific capital goods, play a dual role in climate change: it acts as both a mitigator and an exacerbator due to its carbon-intensive life cycle. Despite their importance, current climate mitigation analyses often overlook these items, leaving a gap in comprehensive analyses of their material stock and environmental impacts. To address this, our research integrates input-output analysis (IOA) with dynamic material flow analysis (d-MFA) to assess the carbon and material footprints of machinery. It finds that in 2019, machinery production required 30% of global metal production and 8% of global carbon emissions. Between 2000 and 2019, the metal footprint of the stock of machinery grew twice as fast as the economy. To illustrate the global implications and scale, we spotlight key countries. China's rise in machinery material stock is noteworthy, surpassing the United States in 2008 in total amount and achieving half of the US per capita level by 2019. Our study also contrasts economic depreciation─a value-centric metric─with the tangible lifespan of machinery, revealing how much the physical size of the capital stock exceeds its book values. As physical machinery stocks saturate, new machinery can increasingly be built from metals recycled from retired machinery.

Long-Term Outcomes of Antegrade Continence Enemas to Treat Constipation and Fecal Incontinence in Children.

OBJECTIVES: The objective of this study is to investigate long-term outcomes of antegrade continence enema (ACE) treatment in children with constipation or fecal incontinence. METHODS: Prospective cohort study including pediatric patients with organic or functional defecation disorders who started ACE treatment. Data were collected at baseline and at follow-up (FU) from 6 weeks until 60 months. We assessed parent and patient-reported gastrointestinal health-related quality of life (HRQoL) using the Pediatric Quality of Life Inventory Gastrointestinal Symptoms Module (PedsQL-GI), gastrointestinal symptoms, adverse events, and patient satisfaction. RESULTS: Thirty-eight children were included (61% male, median age 7.7 years, interquartile range 5.5-12.2). Twenty-two children (58%) were diagnosed with functional constipation (FC), 10 (26%) with an anorectal malformation, and 6 (16%) with Hirschsprung disease. FU questionnaires were completed by 22 children (58%) at 6 months, 16 children (42%) at 12 months, 20 children (53%) at 24 months, and 10 children (26%) at 36 months. PedsQL-GI scores improved overall with a significant increase at 12- and 24-month FU for children with FC and a significant increase in parent reported PedsQL-GI score at 36-month FU for children with organic causes. Minor adverse events, such as granulation tissue, were reported in one-third of children, and 10% of children needed a surgical revision of their ACE. The majority of all parents and children reported that they would "probably" or "definitely" choose ACE again. CONCLUSION: ACE treatment is perceived positively by patients and parents and can lead to long-term improvement in gastrointestinal HRQoL in children with organic or functional defecation disorders.

Acid exposure time is sensitive for detecting gastroesophageal reflux disease and is associated with long-term survival after lung transplant.

Gastroesophageal reflux disease (GERD) is common in patients who have undergone lung transplantation and is associated with poorer outcomes, but guidelines are lacking to direct management strategies in this population. We assessed the diagnostic yield of impedance metrics compared to pH-metry alone for detecting GERD among lung transplant recipients and evaluated their association with clinical outcomes. We performed a retrospective cohort study of consecutive patients who underwent lung transplantation. Demographic data, acid exposure time (AET), number of reflux episodes, mean nocturnal baseline impedance (MNBI), post-reflux swallowing-induced peristaltic wave index (PSPWI), and clinical outcomes including mortality were collected. The relationship between GERD metrics and clinical outcomes was assessed using Wilcoxon signed-rank test and Fisher's exact test as appropriate. Of the 76 patients studied, 29 (38%) had GERD based on abnormal AET after lung transplantation. One (1.3%) patient had GERD based on elevated number of reflux episodes and abnormal distal MNBI detected GERD in 19 (26%) patients, resulting in 62% sensitivity and 94% specificity. Two (2.6%) patients had normal PSPWI. Patients with low distal MNBI had significantly decreased forced expiratory volume in 1 second (FEV1) at 3-year posttransplant compared to those without low distal MNBI (P = 0.03). Three-year survival was significantly worse among patients with elevated AET (66.7% vs. 89.1%, P = 0.03) but not with low distal MNBI (68.4% vs. 84.3%, P = 0.18). Abnormal AET is more sensitive for detecting GERD than other reflux metrics studied and is associated with survival, suggesting pH-metry alone may be sufficient to guide GERD management after lung transplant.

DNA polymerase ι compensates for Fanconi anemia pathway deficiency by countering DNA replication stress.

Fanconi anemia (FA) is caused by defects in cellular responses to DNA crosslinking damage and replication stress. Given the constant occurrence of endogenous DNA damage and replication fork stress, it is unclear why complete deletion of FA genes does not have a major impact on cell proliferation and germ-line FA patients are able to progress through development well into their adulthood. To identify potential cellular mechanisms that compensate for the FA deficiency, we performed dropout screens in FA mutant cells with a whole genome guide RNA library. This uncovered a comprehensive genome-wide profile of FA pathway synthetic lethality, including POLI and CDK4 As little is known of the cellular function of DNA polymerase iota (Pol ι), we focused on its role in the loss-of-function FA knockout mutants. Loss of both FA pathway function and Pol ι leads to synthetic defects in cell proliferation and cell survival, and an increase in DNA damage accumulation. Furthermore, FA-deficient cells depend on the function of Pol ι to resume replication upon replication fork stalling. Our results reveal a critical role for Pol ι in DNA repair and replication fork restart and suggest Pol ι as a target for therapeutic intervention in malignancies carrying an FA gene mutation.