The dependence of CD4 T cell development and activation on the kinetics of the TCR:pMHC interaction

The T cell is a critical player in the adaptive immune response. T cells function by stimulating antibody production by B cells, secreting cytokines to attract other immune cells, regulating the response of other T cells, and directly killing infected or damaged targets. The role of the adaptive immune response depends on the specific recognition of foreign antigenic epitopes by the T cell. A T cell\u27s specificity for antigen is conferred by the T cell receptor: TCR). The TCR is designed to bind a peptide antigen presented on an MHC molecule by an antigen presenting cell: APC). The strength of this interaction is determined by the ratio of the rate of dissociation: koff) and the rate of association: kon) between the TCR and the pMHC. The overall affinity of the complex must be sufficient for productive transmission of signals through the TCR to activate a T cell. However, the precise regulation of this event is not fully understood. Structural changes are thought to occur once the TCR encounters pMHC. Because of the energetics involved, kinetic and thermodynamic parameters have been correlated with the pattern and strength of T cell activation but these relationships do not explain all TCR:pMHC. The contact duration or dwell time of the TCR with pMHC takes into account the potential for rebinding events, which can enhance the signal strength and are related to the kon and koff of the complex. A faster kon can balance out a fast koff to have sufficient interaction between the TCR and pMHC for complete T cell activation. The kon also controls the number of rebinding events that can occur. Even so, the role of kon in T cell biology has not been explored independently of changes in koff. Presented in this thesis is a system using two TCRs with specificity for the same antigen to compare how changes in kon alter T cell development and function. The n3.L2 and a mutant version, M2, recognize the Hbd(64-76) antigen presented on the I-Ek MHC class II molecule. M2 had a 3.7 fold stronger affinity for Hb(64-76)/I-Ek due solely to a faster kon. As a consequence, the M2 TCR responded more strongly to a broader range of altered Hb peptide ligands: APLs). While this presumably was due to an overall increased association with the MHC molecule, which could result from increased kon, the M2 TCR still retained antigen specificity and did not respond strongly to all Hb APLs. N3.L2 hybridomas and double positive thymocytes responded more strongly to two APLs of the P2 TCR contact residue. Therefore the changes between the n3.L2 and M2 TCR structures only allow certain residues to productively bind. By measuring the kinetics of n3.L2 and M2 in association with APL/I-Ek, the maximal IL-2 response is accurately predicted by the koff. No kinetic parameter correlated with the amount of APL needed to stimulate IL-2 production, suggesting other factors may be involved. Since the response to APLs can mimic the ability of a TCR to recognize selecting self-peptides in the thymus, peripheral T cell responsiveness may be developmentally controlled. TCR transgenic mice were generated expressing either the n3.L2 or M2 TCR. M2 thymocytes had stronger recognition of endogenous peptides and were deleted through negative selection when exposed to Hb(64-76) as a self peptide. N3.L2 thymocytes underwent full development and were not completely deleted by Hb(64-76). Interestingly, this difference in T cell selection led to functional consequences in peripheral T cells. Ca2+, an early activation signal, was more sustained in n3.L2 CD4 T cells and more oscillatory in M2 CD4 T cells. Interestingly, M2 CD4 T cells failed to proliferate in response to antigen. Therefore, the TCR sensitivity set during T cell selection leads to qualitatively different signaling cascades in the periphery and can generate an anergic population with increased kon for pMHC recognition

Using video consultation technology between care homes and health and social care professionals: a scoping review and interview study during COVID-19 pandemic

© 2022 The Author(s). Published by Oxford University Press on behalf of the British Geriatrics Society. This is the accepted manuscript version of an article which has been published in final form athttps://doi.org/10.1093/ageing/afab279Background the COVID-19 pandemic disproportionately affected care home residents’ and staffs’ access to health care and advice. Health and social care professionals adapted rapidly to using video consultation (videoconferencing) technology without guidance. We sought to identify enablers and barriers to their use in supporting care home residents and staff. Methods a scoping review of the evidence on remote consultations between healthcare services and care homes. Interviews with English health and social care professionals about their experiences during the pandemic. Findings were synthesised using the non-adoption, abandonment, scale-up, spread, sustainability framework. Results 18 papers were included in the review. Twelve interviews were completed. Documented enablers and barriers affecting the uptake and use of technology (e.g. reliable internet; reduced travelling) resonated with participants. Interviews demonstrated rapid, widespread technology adoption overcame barriers anticipated from the literature, often strengthening working relationships with care homes. Novel implementation issues included using multiple platforms and how resident data were managed. Healthcare professionals had access to more bespoke digital platforms than their social care counterparts. Participants alternated between platforms depending on individual context or what their organisation supported. All participants supported ongoing use of technologies to supplement in-person consultations. Conclusions the evidence on what needs to be in place for video consultations to work with care homes was partly confirmed. The pandemic context demolished many documented barriers to engagement and provided reassurance that residents’ assessments were possible. It exposed the need to study further differing resident requirements and investment in digital infrastructure for adequate information management between organisations.Peer reviewe

Renin-angiotensin system blockers and susceptibility to COVID-19:an international, open science, cohort analysis

Background: Angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) have been postulated to affect susceptibility to COVID-19. Observational studies so far have lacked rigorous ascertainment adjustment and international generalisability. We aimed to determine whether use of ACEIs or ARBs is associated with an increased susceptibility to COVID-19 in patients with hypertension.Methods: In this international, open science, cohort analysis, we used electronic health records from Spain (Information Systems for Research in Primary Care [SIDIAP]) and the USA (Columbia University Irving Medical Center data warehouse [CUIMC] and Department of Veterans Affairs Observational Medical Outcomes Partnership [VA-OMOP]) to identify patients aged 18 years or older with at least one prescription for ACEIs and ARBs (target cohort) or calcium channel blockers (CCBs) and thiazide or thiazide-like diuretics (THZs; comparator cohort) between Nov 1, 2019, and Jan 31, 2020. Users were defined separately as receiving either monotherapy with these four drug classes, or monotherapy or combination therapy (combination use) with other antihypertensive medications. We assessed four outcomes: COVID-19 diagnosis; hospital admission with COVID-19; hospital admission with pneumonia; and hospital admission with pneumonia, acute respiratory distress syndrome, acute kidney injury, or sepsis. We built large-scale propensity score methods derived through a data-driven approach and negative control experiments across ten pairwise comparisons, with results meta-analysed to generate 1280 study effects. For each study effect, we did negative control outcome experiments using a possible 123 controls identified through a data-rich algorithm. This process used a set of predefined baseline patient characteristics to provide the most accurate prediction of treatment and balance among patient cohorts across characteristics. The study is registered with the EU Post-Authorisation Studies register, EUPAS35296.Findings: Among 1 355 349 antihypertensive users (363 785 ACEI or ARB monotherapy users, 248 915 CCB or THZ monotherapy users, 711 799 ACEI or ARB combination users, and 473 076 CCB or THZ combination users) included in analyses, no association was observed between COVID-19 diagnosis and exposure to ACEI or ARB monotherapy versus CCB or THZ monotherapy (calibrated hazard ratio [HR] 0·98, 95% CI 0·84-1·14) or combination use exposure (1·01, 0·90-1·15). ACEIs alone similarly showed no relative risk difference when compared with CCB or THZ monotherapy (HR 0·91, 95% CI 0·68-1·21; with heterogeneity of &gt;40%) or combination use (0·95, 0·83-1·07). Directly comparing ACEIs with ARBs demonstrated a moderately lower risk with ACEIs, which was significant with combination use (HR 0·88, 95% CI 0·79-0·99) and non-significant for monotherapy (0·85, 0·69-1·05). We observed no significant difference between drug classes for risk of hospital admission with COVID-19, hospital admission with pneumonia, or hospital admission with pneumonia, acute respiratory distress syndrome, acute kidney injury, or sepsis across all comparisons.Interpretation: No clinically significant increased risk of COVID-19 diagnosis or hospital admission-related outcomes associated with ACEI or ARB use was observed, suggesting users should not discontinue or change their treatment to decrease their risk of COVID-19.</p

Fc-Optimized Anti-CD25 Depletes Tumor-Infiltrating Regulatory T Cells and Synergizes with PD-1 Blockade to Eradicate Established Tumors

CD25 is expressed at high levels on regulatory T (Treg) cells and was initially proposed as a target for cancer immunotherapy. However, anti-CD25 antibodies have displayed limited activity against established tumors. We demonstrated that CD25 expression is largely restricted to tumor-infiltrating Treg cells in mice and humans. While existing anti-CD25 antibodies were observed to deplete Treg cells in the periphery, upregulation of the inhibitory Fc gamma receptor (FcγR) IIb at the tumor site prevented intra-tumoral Treg cell depletion, which may underlie the lack of anti-tumor activity previously observed in pre-clinical models. Use of an anti-CD25 antibody with enhanced binding to activating FcγRs led to effective depletion of tumor-infiltrating Treg cells, increased effector to Treg cell ratios, and improved control of established tumors. Combination with anti-programmed cell death protein-1 antibodies promoted complete tumor rejection, demonstrating the relevance of CD25 as a therapeutic target and promising substrate for future combination approaches in immune-oncology

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.

The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies

Fc Effector Function Contributes to the Activity of Human Anti-CTLA-4 Antibodies.

With the use of a mouse model expressing human Fc-gamma receptors (FcγRs), we demonstrated that antibodies with isotypes equivalent to ipilimumab and tremelimumab mediate intra-tumoral regulatory T (Treg) cell depletion in vivo, increasing the CD8+ to Treg cell ratio and promoting tumor rejection. Antibodies with improved FcγR binding profiles drove superior anti-tumor responses and survival. In patients with advanced melanoma, response to ipilimumab was associated with the CD16a-V158F high affinity polymorphism. Such activity only appeared relevant in the context of inflamed tumors, explaining the modest response rates observed in the clinical setting. Our data suggest that the activity of anti-CTLA-4 in inflamed tumors may be improved through enhancement of FcγR binding, whereas poorly infiltrated tumors will likely require combination approaches

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure