Vaccine-boosted CAR T crosstalk with host immunity to reject tumors with antigen heterogeneity.

Chimeric antigen receptor (CAR) T cell therapy effectively treats human cancer, but the loss of the antigen recognized by the CAR poses a major obstacle. We found that in vivo vaccine boosting of CAR T cells triggers the engagement of the endogenous immune system to circumvent antigen-negative tumor escape. Vaccine-boosted CAR T promoted dendritic cell (DC) recruitment to tumors, increased tumor antigen uptake by DCs, and elicited the priming of endogenous anti-tumor T cells. This process was accompanied by shifts in CAR T metabolism toward oxidative phosphorylation (OXPHOS) and was critically dependent on CAR-T-derived IFN-γ. Antigen spreading (AS) induced by vaccine-boosted CAR T enabled a proportion of complete responses even when the initial tumor was 50% CAR antigen negative, and heterogeneous tumor control was further enhanced by the genetic amplification of CAR T IFN-γ expression. Thus, CAR-T-cell-derived IFN-γ plays a critical role in promoting AS, and vaccine boosting provides a clinically translatable strategy to drive such responses against solid tumors.

Two subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans.

T cell memory relies on the generation of antigen-specific progenitors with stem-like properties. However, the identity of these progenitors has remained unclear, precluding a full understanding of the differentiation trajectories that underpin the heterogeneity of antigen-experienced T cells. We used a systematic approach guided by single-cell RNA-sequencing data to map the organizational structure of the human CD8+ memory T cell pool under physiological conditions. We identified two previously unrecognized subsets of clonally, epigenetically, functionally, phenotypically and transcriptionally distinct stem-like CD8+ memory T cells. Progenitors lacking the inhibitory receptors programmed death-1 (PD-1) and T cell immunoreceptor with Ig and ITIM domains (TIGIT) were committed to a functional lineage, whereas progenitors expressing PD-1 and TIGIT were committed to a dysfunctional, exhausted-like lineage. Collectively, these data reveal the existence of parallel differentiation programs in the human CD8+ memory T cell pool, with potentially broad implications for the development of immunotherapies and vaccines.

Tissue-specific abundance of interferon-gamma drives regulatory T cells to restrain DC1-mediated priming of cytotoxic T cells against lung cancer.

Local environmental factors influence CD8+ T cell priming in lymph nodes (LNs). Here, we sought to understand how factors unique to the tumor-draining mediastinal LN (mLN) impact CD8+ T cell responses toward lung cancer. Type 1 conventional dendritic cells (DC1s) showed a mLN-specific failure to induce robust cytotoxic T cells responses. Using regulatory T (Treg) cell depletion strategies, we found that Treg cells suppressed DC1s in a spatially coordinated manner within tissue-specific microniches within the mLN. Treg cell suppression required MHC II-dependent contact between DC1s and Treg cells. Elevated levels of IFN-γ drove differentiation Treg cells into Th1-like effector Treg cells in the mLN. In patients with cancer, Treg cell Th1 polarization, but not CD8+/Treg cell ratios, correlated with poor responses to checkpoint blockade immunotherapy. Thus, IFN-γ in the mLN skews Treg cells to be Th1-like effector Treg cells, driving their close interaction with DC1s and subsequent suppression of cytotoxic T cell responses.

TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures.

High-throughput 3' single-cell RNA-sequencing (scRNA-seq) allows cost-effective, detailed characterization of individual immune cells from tissues. Current techniques, however, are limited in their ability to elucidate essential immune cell features, including variable sequences of T cell antigen receptors (TCRs) that confer antigen specificity. Here, we present a strategy that enables simultaneous analysis of TCR sequences and corresponding full transcriptomes from 3'-barcoded scRNA-seq samples. This approach is compatible with common 3' scRNA-seq methods, and adaptable to processed samples post hoc. We applied the technique to identify transcriptional signatures associated with T cells sharing common TCRs from immunized mice and from patients with food allergy. We observed preferential phenotypes among subsets of expanded clonotypes, including type 2 helper CD4+ T cell (TH2) states associated with food allergy. These results demonstrate the utility of our method when studying diseases in which clonotype-driven responses are critical to understanding the underlying biology.

ATRX modulates the escape from a telomere crisis.

Telomerase activity is the principal telomere maintenance mechanism in human cancers, however 15% of cancers utilise a recombination-based mechanism referred to as alternative lengthening of telomeres (ALT) that leads to long and heterogenous telomere length distributions. Loss-of-function mutations in the Alpha Thalassemia/Mental Retardation Syndrome X-Linked (ATRX) gene are frequently found in ALT cancers. Here, we demonstrate that the loss of ATRX, coupled with telomere dysfunction during crisis, is sufficient to initiate activation of the ALT pathway and that it confers replicative immortality in human fibroblasts. Additionally, loss of ATRX combined with a telomere-driven crisis in HCT116 epithelial cancer cells led to the initiation of an ALT-like pathway. In these cells, a rapid and precise telomeric elongation and the induction of C-circles was observed; however, this process was transient and the telomeres ultimately continued to erode such that the cells either died or the escape from crisis was associated with telomerase activation. In both of these instances, telomere sequencing revealed that all alleles, irrespective of whether they were elongated, were enriched in variant repeat types, that appeared to be cell-line specific. Thus, our data show that the loss of ATRX combined with telomere dysfunction during crisis induces the ALT pathway in fibroblasts and enables a transient activation of ALT in epithelial cells.

Grazing herbivores reduce herbaceous biomass and fire activity across African savannas.

Fire and herbivory interact to alter ecosystems and carbon cycling. In savannas, herbivores can reduce fire activity by removing grass biomass, but the size of these effects and what regulates them remain uncertain. To examine grazing effects on fuels and fire regimes across African savannas, we combined data from herbivore exclosure experiments with remotely sensed data on fire activity and herbivore density. We show that, broadly across African savannas, grazing herbivores substantially reduce both herbaceous biomass and fire activity. The size of these effects was strongly associated with grazing herbivore densities, and surprisingly, was mostly consistent across different environments. A one-zebra increase in herbivore biomass density (~100 kg/km2 of metabolic biomass) resulted in a ~53 kg/ha reduction in standing herbaceous biomass and a ~0.43 percentage point reduction in burned area. Our results indicate that fire models can be improved by incorporating grazing effects on grass biomass.

Wild herbivores and cattle have differing effects on postfire herbaceous vegetation recovery in an African savanna.

Fire and herbivory have profound effects on vegetation in savanna ecosystems, but little is known about how different herbivore groups influence vegetation dynamics after fire. We assessed the separate and combined effects of herbivory by cattle and wild meso- and megaherbivores on postfire herbaceous vegetation cover, species richness, and species turnover in a savanna ecosystem in central Kenya. We measured these vegetation attributes for five sampling periods (from 2013 to 2017) in prescribed burns and unburned areas located within a series of replicated long-term herbivore exclosures that allow six different combinations of cattle and wild meso- and megaherbivores (elephants and giraffes). Vegetation cover (grasses, mainly) and species richness were initially reduced by burning but recovered by 15-27 months after fire, suggesting strong resilience to infrequent fire. However, the rates of recovery differed in plots accessible by different wild and domestic herbivore guilds. Wildlife (but not cattle) delayed postfire recovery of grasses, and the absence of wildlife (with or without cattle) delayed recovery of forbs. Herbivory by only cattle increased grass species richness in burned relative to unburned areas. Herbivory by cattle (with or without wildlife), however, reduced forb species richness in burned relative to unburned areas. Herbivory by wild ungulates (but not cattle) increased herbaceous species turnover in burned relative to unburned areas. Megaherbivores had negligible modifying effects on these results. This study demonstrates that savanna ecosystems are remarkably resilient to infrequent fires, but postfire grazing by cattle and wild mesoherbivores exerts different effects on recovery trajectories of herbaceous vegetation.

Stereocontrolled synthesis of the aconitine D ring from D-glucose.

The synthesis of a fully oxygenated aconitine D ring precursor from (D)-(+)-glucose is described. The route features a highly diastereoselective alkynyl Grignard ketone addition and a base-mediated enelactone to 1,3-diketone rearrangement.

Dysgu: efficient structural variant calling using short or long reads.

Structural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer. Long-read sequencing technologies have led to improvements in the characterization of structural variants (SVs), although paired-end sequencing offers better scalability. Here, we present dysgu, which calls SVs or indels using paired-end or long reads. Dysgu detects signals from alignment gaps, discordant and supplementary mappings, and generates consensus contigs, before classifying events using machine learning. Additional SVs are identified by remapping of anomalous sequences. Dysgu outperforms existing state-of-the-art tools using paired-end or long-reads, offering high sensitivity and precision whilst being among the fastest tools to run. We find that combining low coverage paired-end and long-reads is competitive in terms of performance with long-reads at higher coverage values.

Help-seeking intentions of UK construction workers: a cross-sectional study.

BACKGROUND: In response to the high rates of poor mental health in the construction industry, numerous workplace interventions have been designed to address the known and suspected risk factors to employee mental health and well-being. A key challenge of these strategies is low engagement in support services. AIMS: The goals of this research were to investigate the help-seeking intentions of employees in the construction industry, explore levels of mental well-being in this population and provide insight into employee engagement with mental health support strategies. METHODS: Employees from two UK construction companies completed an online cross-sectional questionnaire (n = 119), designed to measure help-seeking intentions, levels of mental well-being and worker attitudes towards workplace mental health support strategies. RESULTS: One-third of the sample reported experiencing an episode of mental health difficulties in the past 6 months. Employees reported a greater preference for seeking support from informal versus formal help sources. Participants were most likely to seek help from a partner and least likely to seek help from a Mental Health First Aider/ Champion. The study also showed some association between help-seeking intention and age of employees. CONCLUSIONS: Given the poor levels of mental well-being in this population, it is essential that adequate workplace support is provided. Whilst formal help sources are important for this population, our study highlights the potential benefits of informal help sources to support employees. Future interventions may therefore wish to consider developing tailored, informal workplace support networks and programmes.

Associations between levels of physical literacy and adherence to the 24-h movement guidelines among university students: A cross-sectional study.

Objectives: Emerging evidence indicates that the composition of movement behaviours within a 24-h period is associated with multiple health benefits across the lifespan. A concept that emphasises an individual's active lifestyle is physical literacy (PL), yet empirical research exploring the potential associations between PL and 24-h movement guidelines remains scarce. This study aimed to evaluate the associations between levels of PL and adherence to the guidelines among Chinese university students. Study design: A cross-sectional study. Methods: Seven hundred and ninety-eight university students (390 male, 19.2 ± 1.2 years) completed all the measurements. Levels of PL and participants' adherence to guidelines including physical activity, sedentary behaviour and sleep were self-reported through Perceived Physical Literacy Instrument, International Physical Activity Questionnaire and Pittsburgh Sleep Quality Index, respectively. Two-way ANOVA was conducted to determine the associations between the number of guidelines met (0, 1, 2, or 3) and levels of PL. Results: The results demonstrate that 36.5% (n = 291) of the participants met all the three guidelines, while 4.1% (n = 33) met none. Further analysis indicated that meeting physical activity or sedentary behaviour guidelines was associated with significantly higher total PL scores, and scores in the sub-domains of Confidence and Physical Competence and Motivation. Conclusions: The findings provide evidence that young adults who obtained higher PL scores may meet more guidelines during a 24-h period. Future studies should incorporate accelerometer-based physical activity measurements and investigate the causal relationship between PL and adherence to the movement guidelines.

Catastrophic Endgames: Emerging Mechanisms of Telomere-Driven Genomic Instability.

When cells progress to malignancy, they must overcome a final telomere-mediated proliferative lifespan barrier called replicative crisis. Crisis is characterized by extensive telomere fusion that drives widespread genomic instability, mitotic arrest, hyperactivation of autophagy, and cell death. Recently, it has become apparent that that the resolution of dicentric chromosomes, which arise from telomere fusions during crisis, can initiate a sequence of events that leads to chromothripsis, a form of extreme genomic catastrophe. Chromothripsis is characterized by localized genomic regions containing tens to thousands of rearrangements and it is becoming increasingly apparent that chromothripsis occurs widely across tumor types and has a clinical impact. Here we discuss how telomere dysfunction can initiate genomic complexity and the emerging mechanisms of chromothripsis.

WAT3R: recovery of T-cell receptor variable regions from 3' single-cell RNA-sequencing.

SUMMARY: Diversity of the T-cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of α and ß chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3'-based single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3' scRNA-seq is not available. Here, we present an analysis pipeline to process TCR variable regions enriched from 3' scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T-cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells from a healthy donor and detect TCR sequences in a high proportion of single T cells. Detection of TCR sequences is low in non-T-cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T cells than in other T-cell types, indicating an association between T-cell clonotypes and differentiation states. AVAILABILITY AND IMPLEMENTATION: The Workflow for Association of T-cell receptors from 3' single-cell RNA-seq (WAT3R), including test data, is available on GitHub (https://github.com/mainciburu/WAT3R), Docker Hub (https://hub.docker.com/r/mainciburu/wat3r) and a workflow on the Terra platform (https://app.terra.bio). The test dataset is available on GEO (accession number GSE195956). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cognitive mechanisms and resilience in UK-based general practitioners: cross-sectional findings.

BACKGROUND: Being a general practitioner (GP) is a stressful occupation, and the strain GPs are under can have negative effects on their psychological well-being, as well as on the patients' experience of healthcare. Resilience can help buffer against this and is a dynamic process by which one can cope with adversity and stress. AIMS: This study aimed to identify modifiable cognitive mechanisms related to resilience in GPs, specifically interpretation bias and cognitive reappraisal. METHODS: One hundred and fourteen GPs completed an online cross-sectional correlational study. This comprised questionnaires assessing resilience, emotional distress, work environment and cognitive mechanisms (emotion regulation), as well as a task assessing interpretation bias. RESULTS: Resilience of GPs was negatively correlated with measures of emotional distress. Furthermore, resilience was positively correlated with positive interpretation bias (r = 0.60, ρ = 0.60, P < 0.01) and cognitive reappraisal (r = 0.39, ρ = 0.40, P < 0.01). In a hierarchical regression, positive interpretation bias (B = 0.25, SE B = 0.06, ß = 0.39, P < 0.01) was a significant independent predictor of resilience when controlling for depression, anxiety and stress. CONCLUSIONS: This is the first study to establish an association between resilience and positive interpretation bias and cognitive reappraisal in GPs. Future research should use longitudinal designs to determine if they have a causal role in promoting resilience, and importantly whether interventions focusing on these processes may foster resilience in less resilient GPs.

Revealing the heterogeneity of CD4+ T cells through single-cell transcriptomics.

Single-cell RNA sequencing (scRNA-seq) offers the ability to resolve whole transcriptomes of single cells with substantial throughput, and it has revolutionized studies of gene expression. The transcriptional resolution available can uncover fine structures of biologic heterogeneity that are manifest among cell populations. Here, we review the applications of scRNA-seq to profile the phenotypes and clonotypes of CD4+ T cells. First, we describe challenges inherent to scRNA-seq that are important for analysis of CD4+ T cells, as well as the technical solutions that are emerging to address these challenges. We then consider major themes of the application of scRNA-seq to CD4+ T cells, including investigation of CD4+ T-cell heterogeneity in model systems, analysis of populations from the peripheral blood, and the profiling of tissue-resident populations. We place emphasis on capabilities unique to scRNA-seq, such as the ability to obtain paired T-cell receptor and transcriptome information from single T cells and the potential to elucidate interactions between CD4+ T cells and other cells in their environment. Finally, we conclude by considering future areas of technologic advancement and innovation through which scRNA-seq may further shape our understanding of the roles of CD4+ T cells in health and disease.

E-cigarette vapor exposure in utero causes long-term pulmonary effects in offspring.

The in utero environment is sensitive to toxicant exposure, altering the health and growth of the fetus, and thus sensitive to contaminant exposure. Though recent clinical data suggest that e-cigarette use does no further harm to birth outcomes than a nicotine patch, this does not account for the effects of vaping during pregnancy on the long-term health of offspring. Pregnant mice were exposed to: 1) e-cigarette vapor with nicotine (PV + Nic; 2% Nic in 50:50 propylene glycol: vegetable glycerin), 2) e-cigarette vapor without nicotine [PV; (50:50 propylene glycol:vegetable glycerin)], or 3) HEPA filtered air (FA). Dams were removed from exposure upon giving birth. At 5 mo of age, pulmonary function tests on the offspring revealed female and male mice from the PV group had greater lung stiffness (Ers) and alveolar stiffness (H) compared with the FA group. Furthermore, baseline compliance (Crs) was reduced in female mice from the PV group and in male mice from the PV and PV + Nic groups. Lastly, female mice had decreased forced expiratory volume (FEV0.1) in the PV group, but not in the male groups, compared with the FA group. Lung histology revealed increased collagen deposition around the vessels/airways and in alveolar tissue in PV and PV + Nic groups. Furthermore, goblet hyperplasia was observed in PV male and PV/PV + Nic female mice. Our work shows that in utero exposure to e-cigarette vapor, regardless of nicotine presence, causes lung dysfunction and structural impairments that persist in the offspring to adulthood.

Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin.

Telomere erosion, dysfunction, and fusion can lead to a state of cellular crisis characterized by large-scale genome instability. We investigated the impact of a telomere-driven crisis on the structural integrity of the genome by undertaking whole-genome sequence analyses of clonal populations of cells that had escaped crisis. Quantification of large-scale structural variants revealed patterns of rearrangement consistent with chromothripsis but formed in the absence of functional nonhomologous end-joining pathways. Rearrangements frequently consisted of short fragments with complex mutational patterns, with a repair topology that deviated from randomness showing preferential repair to local regions or exchange between specific loci. We find evidence of telomere involvement with an enrichment of fold-back inversions demarcating clusters of rearrangements. Our data suggest that chromothriptic rearrangements caused by a telomere crisis arise via a replicative repair process involving template switching.

Integrative analysis of spontaneous CLL regression highlights genetic and microenvironmental interdependency in CLL.

Spontaneous regression is a recognized phenomenon in chronic lymphocytic leukemia (CLL) but its biological basis remains unknown. We undertook a detailed investigation of the biological and clinical features of 20 spontaneous CLL regression cases incorporating phenotypic, functional, transcriptomic, and genomic studies at sequential time points. All spontaneously regressed tumors were IGHV-mutated with no restricted IGHV usage or B-cell receptor (BCR) stereotypy. They exhibited shortened telomeres similar to nonregressing CLL, indicating prior proliferation. They also displayed low Ki-67, CD49d, cell-surface immunoglobulin M (IgM) expression and IgM-signaling response but high CXCR4 expression, indicating low proliferative activity associated with poor migration to proliferation centers, with these features becoming increasingly marked during regression. Spontaneously regressed CLL displayed a transcriptome profile characterized by downregulation of metabolic processes as well as MYC and its downstream targets compared with nonregressing CLL. Moreover, spontaneous regression was associated with reversal of T-cell exhaustion features including reduced programmed cell death 1 expression and increased T-cell proliferation. Interestingly, archetypal CLL genomic aberrations including HIST1H1B and TP53 mutations and del(13q14) were found in some spontaneously regressing tumors, but genetic composition remained stable during regression. Conversely, a single case of CLL relapse following spontaneous regression was associated with increased BCR signaling, CLL proliferation, and clonal evolution. These observations indicate that spontaneously regressing CLL appear to undergo a period of proliferation before entering a more quiescent state, and that a complex interaction between genomic alterations and the microenvironment determines disease course. Together, the findings provide novel insight into the biological processes underpinning spontaneous CLL regression, with implications for CLL treatment.

BMI is dead; long live waist-circumference indices: But which index should we choose to predict cardio-metabolic risk?

BACKGROUND AND AIMS: There is growing evidence that Body Mass Index (BMI) is unfit for purpose. Waist circumference (WC) indices appear to be the preferred alternative, although it is not clear which WC index is optimal at predicting cardio-metabolic risk (CMR) and associated health outcomes. METHODS AND RESULTS: We obtained a stratified random probability sample of 53,390 participants from the Health Survey for England (HSE), 2008-2018. The four available CMR factors were; high-density lipoproteins (HDL) cholesterol, glycated haemoglobin (HbA1c), systolic (SBP) and diastolic blood pressure (DBP). Strength of association between the four cardio-metabolic risk factors and competing anthropometric indicators of weight status [BMI, Waist-to-height ratio (WHTR), unadjusted WC, and a new WC index independent of height, WHT·5R = WC/height0.5] was assessed separately, using simple correlations and ANCOVAs, and together (combined) using MANCOVA, controlling for age, sex and ethnicity. Centile curves for the new index WHT·5R = WC/height0.5were also provided. CONCLUSIONS: Waist-circumference indices were superior to BMI when explaining/predicting our CMR factors, before and after controlling for age, sex and ethnicity. No single WC index was consistently superior. Results suggest that WHTR is the strongest predictor of HbA1c, confirming that shorter individuals are at great risk of diabetes. The most appropriate WC index associated with blood pressure was WHT·5R for DBP, or unadjusted WC for SBP. Given HDL cholesterol is independent of height, the best predictor of HDL was WHT.5R. Clearly, "no one size fits all!". MANCOVA identified WHT·5R to be the best single WC index associated with a composite of all four CMR factors.

High-throughput STELA provides a rapid test for the diagnosis of telomere biology disorders.

Telomere biology disorders are complex clinical conditions that arise due to mutations in genes required for telomere maintenance. Telomere length has been utilised as part of the diagnostic work-up of patients with these diseases; here, we have tested the utility of high-throughput STELA (HT-STELA) for this purpose. HT-STELA was applied to a cohort of unaffected individuals (n = 171) and a retrospective cohort of mutation carriers (n = 172). HT-STELA displayed a low measurement error with inter- and intra-assay coefficient of variance of 2.3% and 1.8%, respectively. Whilst telomere length in unaffected individuals declined as a function of age, telomere length in mutation carriers appeared to increase due to a preponderance of shorter telomeres detected in younger individuals (< 20 years of age). These individuals were more severely affected, and age-adjusted telomere length differentials could be used to stratify the cohort for overall survival (Hazard Ratio = 5.6 (1.5-20.5); p < 0.0001). Telomere lengths of asymptomatic mutation carriers were shorter than controls (p < 0.0001), but longer than symptomatic mutation carriers (p < 0.0001) and telomere length heterogeneity was dependent on the diagnosis and mutational status. Our data show that the ability of HT-STELA to detect short telomere lengths, that are not readily detected with other methods, means it can provide powerful diagnostic discrimination and prognostic information. The rapid format, with a low measurement error, demonstrates that HT-STELA is a new high-quality laboratory test for the clinical diagnosis of an underlying telomeropathy.