Enhancing transcription-replication conflict targets ecDNA-positive cancers.

Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. ecDNA renders tumours treatment resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival. At present, there are no ecDNA-specific treatments.

Coordinated inheritance of extrachromosomal DNAs in cancer cells.

The chromosomal theory of inheritance dictates that genes on the same chromosome segregate together while genes on different chromosomes assort independently. Extrachromosomal DNAs (ecDNAs) are common in cancer and drive oncogene amplification, dysregulated gene expression and intratumoural heterogeneity through random segregation during cell division. Distinct ecDNA sequences, termed ecDNA species, can co-exist to facilitate intermolecular cooperation in cancer cells.

Disparate Pathways for Extrachromosomal DNA Biogenesis and Genomic DNA Repair.

Our study harnesses a CRISPR-based method to examine ecDNA biogenesis, uncovering efficient circularization between double-strand breaks. ecDNAs and their corresponding chromosomal scars can form via nonhomologous end joining or microhomology-mediated end joining, but the ecDNA and scar formation processes are distinct. Based on our findings, we establish a mechanistic model of excisional ecDNA formation.

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in ∼15% of early-stage cancers and ∼30% of late-stage cancers. ecDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies.

Exceeding the limit for microscopic image translation with a deep learning-based unified framework.

Deep learning algorithms have been widely used in microscopic image translation. The corresponding data-driven models can be trained by supervised or unsupervised learning depending on the availability of paired data. However, general cases are where the data are only roughly paired such that supervised learning could be invalid due to data unalignment, and unsupervised learning would be less ideal as the roughly paired information is not utilized.

Lung Cancer Diagnosis on Virtual Histologically Stained Tissue Using Weakly Supervised Learning.

Lung adenocarcinoma (LUAD) is the most common primary lung cancer and accounts for 40% of all lung cancer cases. The current gold standard for lung cancer analysis is based on the pathologists' interpretation of hematoxylin and eosin (H&E)-stained tissue slices viewed under a brightfield microscope or a digital slide scanner. Computational pathology using deep learning has been proposed to detect lung cancer on histology images.

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.

Extrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in approximately 15% of early stage cancers and 30% of late-stage cancers. EcDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating oncogene copy-number and rewiring gene-regulatory networks. Elucidating the genomic architecture of ecDNA amplifications is critical for understanding tumor pathology and developing more effective therapies.

Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair.

Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for induction of ecDNA with extensive characterization of newly formed ecDNA to examine ecDNA biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of a 1 Mb and 1.

Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.

Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis.

Coordinated inheritance of extrachromosomal DNA species in human cancer cells.

The chromosomal theory of inheritance has dominated human genetics, including cancer genetics. Genes on the same chromosome segregate together while genes on different chromosomes assort independently, providing a fundamental tenet of Mendelian inheritance. Extrachromosomal DNA (ecDNA) is a frequent event in cancer that drives oncogene amplification, dysregulated gene expression and intratumoral heterogeneity, including through random segregation during cell division.

KIBRA repairs synaptic plasticity and promotes resilience to tauopathy-related memory loss.

Synaptic plasticity is obstructed by pathogenic tau in the brain, representing a key mechanism that underlies memory loss in Alzheimer's disease (AD) and related tauopathies. Here, we define a mechanism for plasticity repair in vulnerable neurons using the C-terminus of the KIdney/BRAin (KIBRA) protein (CT-KIBRA). We show that CT-KIBRA restores plasticity and memory in transgenic mice expressing pathogenic human tau; however, CT-KIBRA did not alter tau levels or prevent tau-induced synapse loss.

Redesigning primary care: Provider perspectives on the clinical utility of virtual visits.

Objective: To explore primary care physician (PCP) perspectives on the clinical utility of virtual visits.

Design: Qualitative design involving semistructured interviews.

Setting: Primary care practices within 5 regions in southern Ontario.

Impact of virtual visits on primary care physician work flows.

Objective: To understand the impact of virtual visits on primary care physician (PCP) work flows.

Design: Qualitative semistructured interviews.

Setting: Primary care practices within 5 regions in southern Ontario.

Mailed Letter Versus Phone Call to Increase Diabetic-Related Retinopathy Screening Engagement by Patients in a Team-Based Primary Care Practice: Prospective, Single-Masked, Randomized Trial.

Background: Vision loss from diabetic-related retinopathy (DR) is preventable through regular screening.

Objective: The purpose of this study was to test different patient engagement approaches to expand a teleophthalmology program at a primary care clinic in the city of Toronto, Canada.

Methods: A teleophthalmology program was set up in a large, urban, academic, team-based primary care practice.

Translational rapid ultraviolet-excited sectioning tomography for whole-organ multicolor imaging with real-time molecular staining.

Rapid multicolor three-dimensional (3D) imaging for centimeter-scale specimens with subcellular resolution remains a challenging but captivating scientific pursuit. Here, we present a fast, cost-effective, and robust multicolor whole-organ 3D imaging method assisted with ultraviolet (UV) surface excitation and vibratomy-assisted sectioning, termed translational rapid ultraviolet-excited sectioning tomography (TRUST). With an inexpensive UV light-emitting diode (UV-LED) and a color camera, TRUST achieves widefield exogenous molecular-specific fluorescence and endogenous content-rich autofluorescence imaging simultaneously while preserving low system complexity and system cost.

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH.

Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment and pulsed field gel electrophoresis of agarose-entrapped genomic DNA, previously developed for bacterial chromosome segments, to isolate megabase-sized human ecDNAs. We demonstrate strong enrichment of ecDNA molecules containing EGFR, FGFR2 and MYC from human cancer cells and NRAS ecDNA from human metastatic melanoma with acquired therapeutic resistance.

Predictive Values of Nocturia and Its Voiding Frequency on the Aging Males' Symptoms.

Background: The link between nocturia and aging male symptoms (AMS) has not been scientifically established. This study aimed to measure the degree of severity of AMS that impacts health-related quality of life (HRQoL) in adult males living with nocturia and to determine the predictive values of nocturnal factors on AMS.

Methods: This is an extended analysis of new data collected by using the Hong Kong Traditional AMS (HK-AMS) scale and the Cantonese version of the Pittsburgh Sleep Quality Index (PSQI) in a recently published cross-sectional population-based survey.

Perceptions of a Teleophthalmology Screening Program for Diabetic Retinopathy in Adults With Type 1 and Type 2 Diabetes in Urban Primary Care Settings.

Objectives: Teleophthalmology has improved diabetic retinopathy screening, and should be expanded in urban areas, where most unscreened individuals reside. In this study, we explored facilitators of and barriers to teleophthalmology in primary care settings in Toronto, Canada.

Methods: Semistructured interviews were conducted with 7 health-care providers and 7 individuals with diabetes to explore their perspectives of teleophthalmology in urban primary care settings.

ecDNA hubs drive cooperative intermolecular oncogene expression.

Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression.

Ultraviolet photoacoustic microscopy with tissue clearing for high-contrast histological imaging.

Ultraviolet photoacoustic microscopy (UV-PAM) has been investigated to provide label-free and registration-free volumetric histological images for whole organs, offering new insights into complex biological organs. However, because of the high UV absorption of lipids and pigments in tissue, UV-PAM suffers from low image contrast and shallow image depth, hindering its capability for revealing various microstructures in organs. To improve the UV-PAM imaging contrast and imaging depth, here we propose to implement a state-of-the-art optical clearing technique, CUBIC (clear, unobstructed brain/body imaging cocktails and computational analysis), to wash out the lipids and pigments from tissues.