The Role of Protein and Lipid Clustering in Lymphocyte Activation.

Lymphocytes must strike a delicate balance between activating in response to signals from potentially pathogenic organisms and avoiding activation from stimuli emanating from the body's own cells. For cells, such as T or B cells, maximizing the efficiency and fidelity, whilst minimizing the crosstalk, of complex signaling pathways is crucial. One way of achieving this control is by carefully orchestrating the spatiotemporal organization of signaling molecules, thereby regulating the rates of protein-protein interactions.

Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly.

Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography.

Structure and Inhibitor Binding Characterization of Oncogenic MLLT1 Mutants.

Dysfunction of YEATS-domain-containing MLLT1, an acetyl/acyl-lysine dependent epigenetic reader domain, has been implicated in the development of aggressive cancers. Mutations in the YEATS domain have been recently reported as a cause of MLLT1 aberrant reader function. However, the structural basis for the reported alterations in affinity for acetylated/acylated histone has remained elusive.

A deep survival interpretable radiomics model of hepatocellular carcinoma patients.

This work aims to identify a new radiomics signature using imaging phenotypes and clinical variables for risk prediction of overall survival (OS) in hepatocellular carcinoma (HCC) patients treated with stereotactic body radiation therapy (SBRT). 167 patients were retrospectively analyzed with repeated nested cross-validation to mitigate overfitting issues. 56 radiomic features were extracted from pre-treatment contrast-enhanced (CE) CT images.

Ablative radiotherapy for ultracentral lung cancers: Dosimetric, geometric, and volumetric predictors of outcomes and toxicity.

Background: Ultracentral lung cancers arise near the proximal bronchial tree (PBT), trachea, or esophagus, and have been associated with worse outcomes and increased toxicity after radiotherapy. We sought to associate dosimetric and anatomic factors with oncologic outcomes and toxicities.

Methods: One-hundred ten patients treated with ablative, curative-intent radiotherapy for ultracentral, node-negative, non-small cell lung cancer were included.

Asymmetric glycerophospholipids impart distinctive biophysical properties to lipid bilayers.

Phospholipids are a diverse group of biomolecules consisting of a hydrophilic headgroup and two hydrophobic acyl tails. The nature of the head and length and saturation of the acyl tails are important for defining the biophysical properties of lipid bilayers. It has recently been shown that the membranes of certain yeast species contain high levels of unusual asymmetric phospholipids consisting of one long and one medium-chain acyl moiety, a configuration not common in mammalian cells or other well-studied model yeast species.

Functional neurological disorders: effective teaching for health professionals.

Objectives: To provide an outline for the delivery of an educational course or lecture about functional neurological disorders (FND) that is directed towards health professionals with varying clinical knowledge and to highlight the educational efficacy that can be derived from a well-designed educational platform.

Method: Through multidisciplinary collaboration, a course designed to develop the skills for diagnosis and management of FND was created. Elements essential to the delivery of education are: (A) knowledge creation; (B) facilitating multidisciplinary cross-pollination; (C) listening to patients' experiences; (D) communication skills practice; (E) case studies; (F) discipline specific mentoring; (G) establishing and addressing participant learning goals and (H) developing collegial and referral networks.

Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM).

Motivation: Many recent advancements in single-molecule localization microscopy exploit the stochastic photoswitching of fluorophores to reveal complex cellular structures beyond the classical diffraction limit. However, this same stochasticity makes counting the number of molecules to high precision extremely challenging, preventing key insight into the cellular structures and processes under observation.

Results: Modelling the photoswitching behaviour of a fluorophore as an unobserved continuous time Markov process transitioning between a single fluorescent and multiple dark states, and fully mitigating for missed blinks and false positives, we present a method for computing the exact probability distribution for the number of observed localizations from a single photoswitching fluorophore.

Computational fluid dynamics of the right atrium: Assessment of modelling criteria for the evaluation of dialysis catheters.

Central venous catheters are widely used in haemodialysis therapy, having to respect design requirements for appropriate performance. These are placed within the right atrium (RA); however, there is no prior computational study assessing different catheter designs while mimicking their native environment. Here, a computational fluid dynamics model of the RA, based on realistic geometry and transient physiological boundary conditions, was developed and validated.

Checkpoint inhibitor immunotherapy toxicity and overall survival among older adults with advanced cancer.

Objectives: Despite growing evidence that checkpoint inhibitor immunotherapy (IO) toxicity is associated with improved treatment response, the relationship between immune-related adverse events (irAEs) and overall survival (OS) among older adults [age ≥ 70 years (y)] remains unknown. The study goal was to determine differences in OS based on age and ≥ grade 3 (G3) irAEs.

Materials And Methods: This was a retrospective cohort study of 673 patients with advanced cancer.

Comparative assessment of manual chart review and ICD claims data in evaluating immunotherapy-related adverse events.

Background: The aim of this retrospective study was to demonstrate that irAEs, specifically gastrointestinal and pulmonary, examined through International Classification of Disease (ICD) data leads to underrepresentation of true irAEs and overrepresentation of false irAEs, thereby concluding that ICD claims data are a poor approach to electronic health record (EHR) data mining for irAEs in immunotherapy clinical research.

Methods: This retrospective analysis was conducted in 1,063 cancer patients who received ICIs between 2011 and 2017. We identified irAEs by manual review of medical records to determine the incidence of each of our endpoints, namely colitis, hepatitis, pneumonitis, other irAE, or no irAE.

Mapping lung ventilation through stress maps derived from biomechanical models of the lung.

Purpose: Most existing computed tomography (CT)-ventilation imaging techniques are based on deformable image registration (DIR) of different respiratory phases of a four-dimensonal CT (4DCT) scan of the lung, followed by the quantification of local breathing-induced changes in Hounsfield Units (HU) or volume. To date, only moderate correlations have been reported between these CT-ventilation metrics and standard ventilation imaging modalities for adaptive lung radiation therapy. This study evaluates the use of stress maps derived from biomechanical model-based DIR as an alternative CT-ventilation metric.

The structure and function of protein kinase C-related kinases (PRKs).

The protein kinase C-related kinase (PRK) family of serine/threonine kinases, PRK1, PRK2 and PRK3, are effectors for the Rho family small G proteins. An array of studies have linked these kinases to multiple signalling pathways and physiological roles, but while PRK1 is relatively well-characterized, the entire PRK family remains understudied. Here, we provide a holistic overview of the structure and function of PRKs and describe the molecular events that govern activation and autoregulation of catalytic activity, including phosphorylation, protein interactions and lipid binding.

Radiation Therapy for Small-Cell Lung Cancer: ASCO Guideline Endorsement of an ASTRO Guideline.

Purpose: The American Society for Radiation Oncology (ASTRO) produced an evidence-based guideline on radiation therapy (RT) for small-cell lung cancer (SCLC). Because of the relevance of this topic to ASCO membership, ASCO reviewed the guideline, applying a set of procedures and policies used to critically examine guidelines developed by other organizations.

Methods: The ASTRO guideline on RT for SCLC was reviewed for developmental rigor by methodologists.

Design and optimisation of dendrimer-conjugated Bcl-2/x inhibitor, AZD0466, with improved therapeutic index for cancer therapy.

Dual Bcl-2/Bcl-x inhibitors are expected to deliver therapeutic benefit in many haematological and solid malignancies, however, their use is limited by tolerability issues. AZD4320, a potent dual Bcl-2/Bcl-x inhibitor, has shown good efficacy however had dose limiting cardiovascular toxicity in preclinical species, coupled with challenging physicochemical properties, which prevented its clinical development. Here, we describe the design and development of AZD0466, a drug-dendrimer conjugate, where AZD4320 is chemically conjugated to a PEGylated poly-lysine dendrimer.

Elements of a counter-exhibition: Excavating and countering a Canadian history and legacy of eugenics.

Into the Light, a recently mounted collectively curated museum exhibition, exposed and countered histories and legacies of 20th-century "race betterment" pedagogies taught in Ontario's postsecondary institutions that targeted some groups of people, including Anishinaabe, Black, and other racialized populations, and disabled and poor people, with dehumanizing ideas and practices. This article advances understandings of the transformative potential of centralizing marginalized stories in accessible and creative ways to disrupt, counter, and draw critical attention to the brutal impacts of oppressive knowledge. The "counter-exhibition" prioritized stories of groups unevenly targeted by such oppression to contest and defy singular narratives circulating in institutional knowledge systems of what it means to be human.

Three-dimensional total-internal reflection fluorescence nanoscopy with nanometric axial resolution by photometric localization of single molecules.

Single-molecule localization microscopy enables far-field imaging with lateral resolution in the range of 10 to 20 nanometres, exploiting the fact that the centre position of a single-molecule's image can be determined with much higher accuracy than the size of that image itself. However, attaining the same level of resolution in the axial (third) dimension remains challenging. Here, we present Supercritical Illumination Microscopy Photometric z-Localization with Enhanced Resolution (SIMPLER), a photometric method to decode the axial position of single molecules in a total internal reflection fluorescence microscope.

Medical management of children with type 1 diabetes on low-carbohydrate or ketogenic diets.

Objectives: Low-carbohydrate and ketogenic diets are becoming increasingly popular choices for people with type 1 diabetes (T1D) aiming to achieve optimal glycemic control. A carbohydrate-restricted diet in children has been associated with negative health effects including poor linear growth and inadequate bone mineralization. Guidelines for monitoring children and adolescents choosing to follow a carbohydrate-restricted diet do not exist.

Cellular sources of TSPO expression in healthy and diseased brain.

The 18 kDa translocator protein (TSPO) is a highly conserved protein located in the outer mitochondrial membrane. TSPO binding, as measured with positron emission tomography (PET), is considered an in vivo marker of neuroinflammation. Indeed, TSPO expression is altered in neurodegenerative, neuroinflammatory, and neuropsychiatric diseases.

The Kinase Chemogenomic Set (KCGS): An Open Science Resource for Kinase Vulnerability Identification.

We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases.

Treatment of Non-Small-Cell Lung Cancer Based on Circulating Cell-Free DNA and Impact of Variation Allele Frequency.

Background: Next-generation sequencing of circulating cell-free DNA (cfDNA) can identify sensitizing and resistance mutations in non-small-cell lung cancer (NSCLC). cfDNA is helpful when tissue is insufficient for genomic testing or repeat biopsy is not feasible or poses unacceptable risk. Here we report the experience of cfDNA testing at the time of diagnosis and how this intervention can help avoid further invasive interventions, how it can be used to determine initiation of therapy, and how variation allele frequency of the somatic alteration affects response to subsequent treatment.

Linton Mark Traub (1962-2020).

Meir Aridor and David Owen discuss the life and achievements of Linton Traub, who passed away on October 19, 2020.

TNFR1 and the TNFα axis as a targetable mediator of liver injury from stereotactic body radiation therapy.

Introduction: Radiation therapy for the management of intrahepatic malignancies can adversely affect liver function. Liver damage has been associated with increased levels of inflammatory cytokines, including tumor necrosis factor alpha (TNFα). We hypothesized that an inflammatory state, characterized by increased soluble TNFα receptor (sTNFR1), mediates sensitivity of the liver to radiation.

Multi-color Molecular Visualization of Signaling Proteins Reveals How C-Terminal Src Kinase Nanoclusters Regulate T Cell Receptor Activation.

Elucidating the mechanisms that controlled T cell activation requires visualization of the spatial organization of multiple proteins on the submicron scale. Here, we use stoichiometrically accurate, multiplexed, single-molecule super-resolution microscopy (DNA-PAINT) to image the nanoscale spatial architecture of the primary inhibitor of the T cell signaling pathway, Csk, and two binding partners implicated in its membrane association, PAG and TRAF3. Combined with a newly developed co-clustering analysis framework, we find that Csk forms nanoscale clusters proximal to the plasma membrane that are lost post-stimulation and are re-recruited at later time points.

Combination of a Big Data Analytics Resource System With an Artificial Intelligence Algorithm to Identify Clinically Actionable Radiation Dose Thresholds for Dysphagia in Head and Neck Patients.

Purpose: We combined clinical practice changes, standardizations, and technology to automate aggregation, integration, and harmonization of comprehensive patient data from the multiple source systems used in clinical practice into a big data analytics resource system (BDARS). We then developed novel artificial intelligence algorithms, coupled with the BDARS, to identify structure dose volume histograms (DVH) metrics associated with dysphagia.

Methods And Materials: From the BDARS harmonized data of ≥22,000 patients, we identified 132 patients recently treated for head and neck cancer who also demonstrated dysphagia scores that worsened from base line to a maximum grade ≥2.