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Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches.
No full textHighly multiplexed imaging assays allow simultaneous quantification of multiple protein and phosphorylation markers, providing a static snapshots of cell types and states. Pseudo-time techniques can transform these static snapshots of unsynchronized cells into dynamic trajectories, enabling the study of dynamic processes such as development trajectories and the cell cycle. Such ordering also enables training of mathematical models on these data, but technical challenges have hitherto made it difficult to integrate multiple experimental conditions, limiting the predictive power and insights these models can generate. In this work, we propose data processing and model training approaches for integrating multiplexed, multi-condition immunofluorescence data with mathematical modelling. We devise training strategies for mathematical models that are applicable to datasets where cells exhibit oscillatory as well as arrested dynamics and use them to train a cell cycle model on a dataset of MCF-10A mammary epithelial exposed to cell-cycle arresting small molecules. We validate the model by investigating predicted growth factor sensitivities and responses to inhibitors of cells at different initial conditions. We anticipate that our framework will generalise to other highly multiplexed measurement techniques such as mass-cytometry, rendering larger bodies of data accessible to dynamic modelling and paving the way to deeper biological insights
A putative hepatitis B virus sequence motif associated with hepatocellular carcinoma in South African adults.
No full textINTRODUCTION AND OBJECTIVES: Chronic hepatitis B virus (HBV) infection is a major risk factor for hepatocellular carcinoma (HCC). In African populations, HCC frequently presents at an advanced stage with poor outcomes. We applied whole genome sequencing (WGS) to compare HBV genomes in individuals with and without HCC. MATERIALS AND METHODS: We identified adults with HBV infection, with and without complicating HCC, in Cape Town, South Africa. We generated HBV WGS using pan-genotypic probe-based enrichment followed by Illumina sequencing. RESULTS: Compared to the non-HCC group, HCC patients were more likely to be male (p<0.0001), older (p=0.01), HIV-negative (p=0.006), and have higher HBV viral loads (p<0.0001). Among 19 HCC and 12 non-HCC patients for whom WGS was obtained, genotype A dominated (74%), of which 96% were subgenotype A1. PreS2 deletions (Δ38-55) were enriched in HBV sequences from HCC patients (n=7). The sequence motif most strongly associated with HCC comprised either a deletion or polymorphism at site T53 in PreS2 - collectively coined 'non-T53' - together with a basal core promoter (BCP) mutation G1764A (AUROC = 0.79). CONCLUSIONS: In this setting, HBV sequence polymorphisms and deletions are associated with HCC, and 'non-T53+G1764A' represents a putative signature motif for HCC. Additional investigations are needed to disaggregate the impact of other demographic, clinical, and environmental influences, to ascertain the extent to which viral polymorphisms contribute to oncogenesis, and to determine whether HBV sequence is a useful biomarker for HCC risk stratification
Imperfect wound healing sets the stage for chronic diseases.
No full textAlthough the age of the genome gave us much insight about how our organs fail with disease, it also suggested that diseases do not arise from mutations alone; rather, they develop as we age. In this Review, we examine how wound healing might act to ignite disease. Wound healing works well when we are younger, repairing damage from accidents, environmental assaults, and battles with pathogens. Yet, with age and accumulation of mutations and tissue damage, the repair process can devolve, leading to inflammation, fibrosis, and neoplastic signaling. We discuss healthy wound responses and how our bodies might misappropriate these pathways in disease. Although we focus predominantly on epithelial-based (lung and skin) diseases, similar pathways might operate in cardiac, muscle, and neuronal diseases
Data associated with "Functional specialisation of multisensory temporal integration in the mouse superior colliculus"
No full textDataset from Bianchini et al., "Functional specialisation of multisensory temporal integration in the mouse superior colliculus" available at https://www.biorxiv.org/content/10.1101/2025.02.11.637674v3.Companion code at https://github.com/gaiabianchini/Bianchini2025_SC/tree/main.The data is organised into four subfolders:neurons_datasetsdecoder_datasetsconnectivity_datasetsmovement_control_datasetsEach folder contains the main datasets along with intermediate datasets obtained at different stages of pre-processing. Each dataset is clearly referenced in the corresponding analysis step.Below is a short description of the datasets contained in each folder.1.neurons_datasetsContains three datasets:retinotopy_dataset:Data from 979 neurons across 11 sessions in 9 mice, using high-resolution receptive field mapping across 35 locations (5 elevations × 7 azimuths), with 25 repetitions per auditory, visual, and multisensory condition.Used in: Figure 1E–L; Figure 3C–D; Supplementary Figure 2A.delay_tuning_dataset:Data from 5,360 neurons across 92 sessions in 24 mice, during presentation of audiovisual stimuli with multiple visual-leading temporal delays at a single spatial location.Used in: Figure 1C–D; Figure 2 (all panels); Supplementary Figure 2B–D, 3 (all panels), Supplementary Figure 5 (all panels).delayBA_tuning_dataset:Data from 1,104 neurons across 22 sessions in 6 mice, during presentation of audiovisual stimuli including both auditory-leading and visual-leading conditions.Used in: Supplementary Figure 4 (all panels).2.decoder_datasetsContains outputs of classification algorithms trained on the delay_tuning_dataset.Used in: Figure 4 (all panels); Figure 5 (all panels); Figure 6 (all panels); Supplementary Figures 8–10 (all panels).3.connectivivty_datasetsContains cross-correlation analyses:CCG_dataset_baeline_RF_mapping: based on retinotopy_datasetCCG_dataset_baseline: based on delay_tuning_datasetUsed in: Figure 3 (all panels); Supplementary Figure 6 (all panels).4.movement_control_datasetsContains data from 9 sessions in 7 animals, used for analysis of sound-induced behavioural responses.Used in: Supplementary Figures 1 and 7 (all panels).</p
Sequential transcriptional programs underpin activation of hippocampal stem cells.
No full textAdult neural stem cells exist on a continuum from deep to shallow quiescence that changes in response to injury or aging; however, the transcription factors controlling these stepwise transitions have not been identified. Single-cell transcriptomic analyses of mice with loss of function or increased levels of the essential activation factor Ascl1 reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression in this state. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow quiescent states toward a proliferating state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation and establish a combinatorial code for classifying these cells into deep and shallow quiescence
A stromal inflammasome Ras safeguard against Myc-driven lymphomagenesis.
No full textThe inflammasome plays multifaceted roles in cancer, but less is known about its function during premalignancy upon initial cell transformation. We report a homeostatic function of the inflammasome in suppressing malignant transformation through Ras inhibition. We identified increased hematopoietic stem cell (HSC) proliferation within the bone marrow of inflammasome-deficient mice. HSCs within an inflammasome-deficient stroma expressed a Ras signature associated with increased Ras pathway- and cancer-related transcripts and heightened levels of cytokine, chemokine and growth factor receptors. Stromal inflammasome deficiency established a poised Ras-dependent mitogenic state within HSCs, which fueled progeny B cell lymphomagenesis upon Myc deregulation in a spontaneous model of B cell lymphoma, and shortened its premalignant stage leading to faster onset of malignancy. Thus, the stromal inflammasome preserves tissue balance by restraining Ras to disrupt the most common oncogenic Myc-Ras cooperation and establish a natural defense against transition to malignancy. These findings should inform preventative therapies against hematological malignancies.</p
A CRISPR view on genetic screens in Toxoplasma gondii.
No full textGenome editing technologies, such as CRISPR-Cas9, have revolutionised the study of genes in a variety of organisms, including unicellular parasites. Today, the CRISPR-Cas9 technology is vastly applied in high-throughput screens to investigate interactions between the Apicomplexan parasite Toxoplasma gondii and its hosts. In vitro and in vivo T. gondii screens performed in naive and restrictive conditions have led to the discovery of essential and fitness-conferring T. gondii genes, as well as factors important for virulence and dissemination. Recent studies have adapted the CRISPR-Cas9 screening technology to study T. gondii genes based on phenotypes unrelated to parasite survival. These advances were achieved by using conditional systems coupled with imaging, as well as single-cell RNA sequencing and phenotypic selection. Here, we review the state-of-the-art of CRISPR-Cas9 screening technologies with a focus on T. gondii, highlighting strengths, current limitations and future avenues for its development, including its application to other Apicomplexan species
Using laboratory test results for surveillance during a new outbreak of acute hepatitis in 3-week- to 5-year-old children in the United Kingdom, the Netherlands, Ireland, and Curaçao: Observational cohort study.
No full textBACKGROUND: In March 2022, a concerning rise in cases of unexplained pediatric hepatitis was reported in multiple countries. Cases were defined as acute hepatitis with serum transaminases >500 U/L (aspartate transaminase [AST] or alanine transaminase [ALT]) in children aged 16 years or younger. We explored a simple federated data analytics method to search for evidence of unreported cases using routinely held data. We conducted a pragmatic survey to analyze changes in the proportion of hospitalized children with elevated AST or ALT over time. In addition, we studied the feasibility of using routinely collected clinical laboratory results to detect or follow-up the outbreak of an infectious disease. OBJECTIVE: We explored a simple federated data analytics method to search for evidence of unreported cases using routinely held data. METHODS: We provided hospitals with a simple computational tool to enable laboratories to share nondisclosive summary-level data. Summary statistics for AST and ALT measurements were collected from the last 10 years across all age groups. Measurements were considered elevated if ALT or AST was >200 U/L. The rate of elevated AST or ALT test for 3-week- to 5-year-olds was compared between a period of interest in which cases of hepatitis were reported (December 1, 2021, to August 31, 2022) and a prepandemic baseline period (January 1, 2012, to December 31, 2019). We calculated a z score, which measures the extent to which the rate for elevated ALT or AST was higher or lower in the period of interest compared to a baseline period, for the 3-week- to 5-year-olds. RESULTS: Our approach of sharing a simple software tool for local use enabled rapid, federated data analysis. A total of 34 hospitals in the United Kingdom, the Netherlands, Ireland, and Curaçao were asked to contribute summary data, and 30 (88%) submitted their data. For all locations combined, the rate of elevated AST or ALT measurements in the period of interest was not elevated (z score=-0.46; P=.64). Results from individual regions were discordant, with a higher rate of elevated AST or ALT values in the Netherlands (z score=4.48; P<.001), driven by results from a single center in Utrecht. We did not observe any clear indication of changes in primary care activity or test results in the same period. CONCLUSIONS: Hospital laboratories collect large amounts of data on a daily basis that can potentially be of use for disease surveillance, but these are currently not optimally used. Federated analytics using nondisclosive, summary-level laboratory data sharing was successful, safe, and efficient. The approach holds potential as a tool for pandemic surveillance in future outbreaks. Our findings do not indicate the presence of a broader outbreak of mild hepatitis cases among young children, although there was an increase in elevated AST or ALT values locally in the Netherlands
Cancer gene identification from RNA variant allelic frequencies using RVdriver.
No full textExisting approaches to identifying cancer genes rely overwhelmingly on DNA sequencing data. Here, we introduce RVdriver, a computational tool that leverages paired bulk genomic and transcriptomic data to classify RNA variant allele frequencies (VAFs) of non-synonymous mutations relative to a synonymous mutation background. We analyze 7882 paired exomes and transcriptomes from 31 cancer types and identify novel, as well as known, cancer genes, complementing other DNA-based approaches. Furthermore, RNA VAFs of individual mutations are able to distinguish "driver" from "passenger" mutations within established cancer genes. This approach highlights the value of multi-omic approaches for cancer gene discovery
DNA damage and replication stress checkpoints.
No full textDNA damage checkpoints are key regulatory signaling cascades that arrest cell cycle progression upon DNA damage or upon DNA replication stalling and allow time for repair or correction. Failure to elicit these checkpoints can lead to genomic instability that can result in cell death or mutations, ultimately leading to diseases such as cancer. Components of the DNA damage checkpoint are attractive targets for precision medicine to treat cancers. Over the last several years, cutting-edge structural techniques have provided molecular insights into the highly coordinated checkpoint signaling that occurs in response to DNA damage or other obstacles to replication progression. This review summarizes our current mechanistic understanding of the DNA damage checkpoint in eukaryotes, with an emphasis on the sensor kinases ATM (Tel1) and ATR (Mec1), highlighting structure-function and cellular studies