E2F1 proteolysis via SCF-cyclin F underlies synthetic lethality between cyclin F loss and Chk1 inhibition.

Cyclins are central engines of cell cycle progression in conjunction with cyclin-dependent kinases (CDKs). Among the different cyclins controlling cell cycle progression, cyclin F does not partner with a CDK, but instead forms via its F-box domain an SCF (Skp1-Cul1-F-box)-type E3 ubiquitin ligase module. Although various substrates of cyclin F have been identified, the vulnerabilities of cells lacking cyclin F are not known. Thus, we assessed viability of cells lacking cyclin F upon challenging them with more than 180 different kinase inhibitors. The screen revealed a striking synthetic lethality between Chk1 inhibition and cyclin F loss. Chk1 inhibition in cells lacking cyclin F leads to DNA replication catastrophe. Replication catastrophe depends on accumulation of the transcription factor E2F1 in cyclin F-depleted cells. We find that SCF-cyclin F controls E2F1 ubiquitylation and degradation during the G2/M phase of the cell cycle and upon challenging cells with Chk1 inhibitors. Thus, Cyclin F restricts E2F1 activity during the cell cycle and upon checkpoint inhibition to prevent DNA replication stress. Our findings pave the way for patient selection in the clinical use of checkpoint inhibitors.

A unified model for the G1/S cell cycle transition.

Efficient S phase entry is essential for development, tissue repair, and immune defences. However, hyperactive or expedited S phase entry causes replication stress, DNA damage and oncogenesis, highlighting the need for strict regulation. Recent paradigm shifts and conflicting reports demonstrate the requirement for a discussion of the G1/S transition literature. Here, we review the recent studies, and propose a unified model for the S phase entry decision. In this model, competition between mitogen and DNA damage signalling over the course of the mother cell cycle constitutes the predominant control mechanism for S phase entry of daughter cells. Mitogens and DNA damage have distinct sensing periods, giving rise to three Commitment Points for S phase entry (CP1-3). S phase entry is mitogen-independent in the daughter G1 phase, but remains sensitive to DNA damage, such as single strand breaks, the most frequently-occurring lesions that uniquely threaten DNA replication. To control CP1-3, dedicated hubs integrate the antagonistic mitogenic and DNA damage signals, regulating the stoichiometric cyclin: CDK inhibitor ratio for ultrasensitive control of CDK4/6 and CDK2. This unified model for the G1/S cell cycle transition combines the findings of decades of study, and provides an updated foundation for cell cycle research.

School closures during COVID-19: an overview of systematic reviews.

OBJECTIVES: To assess the benefits and drawbacks of school closures and in-school mitigations during the COVID-19 pandemic. DESIGN: Overview of systematic reviews (SRs). SEARCH METHODS: We searched six databases and additional resources on 29 July 2022: MEDLINE, Embase, Google Scholar, Cochrane Library, COVID-END inventory of evidence synthesis, and Epistemonikos. ELIGIBILITY CRITERIA: We selected SRs written in English that answered at least one of four specific questions concerning the efficacy and drawbacks of school closures. Their primary studies were conducted in primary and secondary schools, including pupils aged 5-18. Interventions included school closures or mitigations (such as mask usage) introduced in schools. DATA COLLECTION AND ANALYSIS: We used AMSTAR 2 to assess confidence in the included SRs, and GRADE was used to assess certainty of evidence. We performed a narrative synthesis of the results, prioritising higher-quality SRs, those which performed GRADE assessments and those with more unique primary studies. We also assessed the overlap between primary studies included in the SRs. MAIN OUTCOME MEASURES: Our framework for summarising outcome data was guided by the following questions: (1) What is the impact of school closures on COVID-19 transmission, morbidity or mortality in the community? (2) What is the impact of COVID-19 school closures on mental health (eg, anxiety), physical health (eg, obesity, domestic violence, sleep) and learning/achievement of primary and secondary pupils? (3) What is the impact of mitigations in schools on COVID-19 transmission, morbidity or mortality in the community? and (4) What is the impact of COVID-19 mitigations in schools on mental health, physical health and learning/achievement of primary and secondary pupils? RESULTS: We identified 578 reports, 26 of which were included. One SR was of high confidence, 0 moderate, 10 low and 15 critically low confidence. We identified 132 unique primary studies on the effects of school closures on transmission/morbidity/mortality, 123 on learning, 164 on mental health, 22 on physical health, 16 on sleep, 7 on domestic violence and 69 on effects of in-school mitigations on transmission/morbidity/mortality.Both school closures and in-school mitigations were associated with reduced COVID-19 transmission, morbidity and mortality in the community. School closures were also associated with reduced learning, increased anxiety and increased obesity in pupils. We found no SRs that assessed potential drawbacks of in-school mitigations on pupils. The certainty of evidence according to GRADE was mostly very low. CONCLUSIONS: School closures during COVID-19 had both positive and negative impacts. We found a large number of SRs and primary studies. However, confidence in the SRs was mostly low to very low, and the certainty of evidence was also mostly very low. We found no SRs assessing the potential drawbacks of in-school mitigations on children, which could be addressed moving forward. This overview provides evidence that could inform policy makers on school closures during future potential waves of COVID-19.

The NUCKS1-SKP2-p21/p27 axis controls S phase entry.

Efficient entry into S phase of the cell cycle is necessary for embryonic development and tissue homoeostasis. However, unscheduled S phase entry triggers DNA damage and promotes oncogenesis, underlining the requirement for strict control. Here, we identify the NUCKS1-SKP2-p21/p27 axis as a checkpoint pathway for the G1/S transition. In response to mitogenic stimulation, NUCKS1, a transcription factor, is recruited to chromatin to activate expression of SKP2, the F-box component of the SCFSKP2 ubiquitin ligase, leading to degradation of p21 and p27 and promoting progression into S phase. In contrast, DNA damage induces p53-dependent transcriptional repression of NUCKS1, leading to SKP2 downregulation, p21/p27 upregulation, and cell cycle arrest. We propose that the NUCKS1-SKP2-p21/p27 axis integrates mitogenic and DNA damage signalling to control S phase entry. The Cancer Genome Atlas (TCGA) data reveal that this mechanism is hijacked in many cancers, potentially allowing cancer cells to sustain uncontrolled proliferation.

Enhancing Traceability in Clinical Research Data through a Metadata Framework.

BACKGROUND: The clinical research data lifecycle, from data collection to analysis results, functions in silos that restrict traceability. Traceability is a requirement for regulated clinical research studies and an important attribute of nonregulated studies. Current clinical research software tools provide limited metadata traceability capabilities and are unable to query variables across all phases of the data lifecycle. OBJECTIVES: To develop a metadata traceability framework that can help query and visualize traceability metadata, identify traceability gaps, and validate metadata traceability to improve data lineage and reproducibility within clinical research studies. METHODS: This research follows the design science research paradigm where the objective is to create and evaluate an information technology (IT) artifact that explicitly addresses an organizational problem or opportunity. The implementation and evaluation of the IT artifact demonstrate the feasibility of both the design process and the final designed product. RESULTS: We present Trace-XML, a metadata traceability framework that extends standard clinical research metadata models and adapts graph traversal algorithms to provide clinical research study traceability queries, validation, and visualization. Trace-XML was evaluated using analytical and qualitative methods. The analytical methods show that Trace-XML accurately and completely assesses metadata traceability within a clinical research study. A qualitative study used thematic analysis of interview data to show that Trace-XML adds utility to a researcher's ability to evaluate metadata traceability within a study. CONCLUSION: Trace-XML benefits include features that (1) identify traceability gaps in clinical study metadata, (2) validate metadata traceability within a clinical study, and (3) query and visualize traceability metadata. The key themes that emerged from the qualitative evaluation affirm that Trace-XML adds utility to the task of creating and assessing end-to-end clinical research study traceability.

TEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts.

Eukaryotic topoisomerase 1 (TOP1) regulates DNA topology to ensure efficient DNA replication and transcription. TOP1 is also a major driver of endogenous genome instability, particularly when its catalytic intermediate-a covalent TOP1-DNA adduct known as a TOP1 cleavage complex (TOP1cc)-is stabilised. TOP1ccs are highly cytotoxic and a failure to resolve them underlies the pathology of neurological disorders but is also exploited in cancer therapy where TOP1ccs are the target of widely used frontline anti-cancer drugs. A critical enzyme for TOP1cc resolution is the tyrosyl-DNA phosphodiesterase (TDP1), which hydrolyses the bond that links a tyrosine in the active site of TOP1 to a 3' phosphate group on a single-stranded (ss)DNA break. However, TDP1 can only process small peptide fragments from ssDNA ends, raising the question of how the ~90 kDa TOP1 protein is processed upstream of TDP1. Here we find that TEX264 fulfils this role by forming a complex with the p97 ATPase and the SPRTN metalloprotease. We show that TEX264 recognises both unmodified and SUMO1-modifed TOP1 and initiates TOP1cc repair by recruiting p97 and SPRTN. TEX264 localises to the nuclear periphery, associates with DNA replication forks, and counteracts TOP1ccs during DNA replication. Altogether, our study elucidates the existence of a specialised repair complex required for upstream proteolysis of TOP1ccs and their subsequent resolution.

CDISC SHARE, a Global, Cloud-based Resource of Machine-Readable CDISC Standards for Clinical and Translational Research.

The Clinical Data Interchange Standards Consortium (CDISC) is a global non-profit standards development organization that creates consensus-based standards for clinical and translational research. Several of these standards are now required by regulators for electronic submissions of regulated clinical trials' data and by government funding agencies. These standards are free and open, available for download on the CDISC Website as PDFs. While these documents are human readable, they are not amenable to ready use by electronic systems. CDISC launched the CDISC Shared Health And Research Electronic library (SHARE) to provide the standards metadata in machine-readable formats to facilitate the automated management and implementation of the standards. This paper describes how CDISC SHARE'S standards can facilitate collecting, aggregating and analyzing standardized data from early design to end analysis; and its role as a central resource providing information systems with metadata that drives process automation including study setup and data pipelining.

Interplay between base excision repair protein XRCC1 and ALDH2 predicts overall survival in lung and liver cancer patients.

BACKGROUND: To deliver efficacious personalised cancer treatment, it is essential to characterise the cellular metabolism as well as the genetic stability of individual tumours. In this study, we describe a new axis between DNA repair and detoxification of aldehyde derivatives with important implications for patient prognosis and treatment. METHODS: Western blot and qPCR analyses were performed in relevant non-transformed and cancer cell lines from lung and liver tissue origin in combination with bioinformatics data mining of The Cancer Genome Atlas database from lung and hepatocellular cancer patients. RESULTS: Using both biochemical and bioinformatics approaches, we revealed an association between the levels of expression of the aldehyde detoxifying enzyme aldehyde dehydrogenase 2 (ALDH2) and the key DNA base excision repair protein XRCC1. Across cancer types, we found that if one of the corresponding genes exhibits a low expression level, the level of the other gene is increased. Surprisingly, we found that low ALDH2 expression levels associated with high XRCC1 expression levels are indicative for a poor overall survival, particularly in lung and liver cancer patients. In addition, we found that Mithramycin A, a XRCC1 expression inhibitor, efficiently kills cancer cells expressing low levels of ALDH2. CONCLUSIONS: Our data suggest that lung and liver cancers require efficient single-strand break repair for their growth in order to benefit from a low aldehyde detoxification metabolism. We also propose that the ratio of XRCC1 and ALDH2 levels may serve as a useful prognostic tool in these cancer types.

Visceral leishmaniasis due to Leishmania donovani in a patient with advanced HIV infection.

An Eritrean-born man observed over an extended period had upper gastrointestinal symptoms, fever, hepatosplenomegaly and pancytopenia in the setting of advanced HIV infection and poor adherence to antiretroviral therapy. Despite thorough investigation, it was not until a repeat gastroscopic examination and gastric biopsy were performed 18 months after initial presentation that Leishmania infection was diagnosed. The species was identified by polymerase chain reaction assay as L. donovani. Physicians managing HIV-infected patients from regions where Leishmania is endemic should consider visceral leishmaniasis, even in patients who have not lived in a Leishmania-endemic region for many years.