Adoptive cellular therapy with T cells expressing the dendritic cell growth factor Flt3L drives epitope spreading and antitumor immunity.

Adoptive cell therapies using genetically engineered T cell receptor or chimeric antigen receptor T cells are emerging forms of immunotherapy that redirect T cells to specifically target cancer. However, tumor antigen heterogeneity remains a key challenge limiting their efficacy against solid cancers. Here, we engineered T cells to secrete the dendritic cell (DC) growth factor Fms-like tyrosine kinase 3 ligand (Flt3L). Flt3L-secreting T cells expanded intratumoral conventional type 1 DCs and substantially increased host DC and T cell activation when combined with immune agonists poly (I:C) and anti-4-1BB. Importantly, combination therapy led to enhanced inhibition of tumor growth and the induction of epitope spreading towards antigens beyond those recognized by adoptively transferred T cells in solid tumor models of T cell receptor and chimeric antigen receptor T cell therapy. Our data suggest that augmenting endogenous DCs is a promising strategy to overcome the clinical problem of antigen-negative tumor escape following adoptive cell therapy.

A central role for regulated protein stability in the control of TFE3 and MITF by nutrients.

The TFE3 and MITF master transcription factors maintain metabolic homeostasis by regulating lysosomal, melanocytic, and autophagy genes. Previous studies posited that their cytosolic retention by 14-3-3, mediated by the Rag GTPases-mTORC1, was key for suppressing transcriptional activity in the presence of nutrients. Here, we demonstrate using mammalian cells that regulated protein stability plays a fundamental role in their control. Amino acids promote the recruitment of TFE3 and MITF to the lysosomal surface via the Rag GTPases, activating an evolutionarily conserved phospho-degron and leading to ubiquitination by CUL1ß-TrCP and degradation. Elucidation of the minimal functional degron revealed a conserved alpha-helix required for interaction with RagA, illuminating the molecular basis for a severe neurodevelopmental syndrome caused by missense mutations in TFE3 within the RagA-TFE3 interface. Additionally, the phospho-degron is recurrently lost in TFE3 genomic translocations that cause kidney cancer. Therefore, two divergent pathologies converge on the loss of protein stability regulation by nutrients.

FOXO1 enhances CAR T cell stemness, metabolic fitness and efficacy.

Chimeric antigen receptor (CAR) T cell therapy has transformed the treatment of haematological malignancies such as acute lymphoblastic leukaemia, B cell lymphoma and multiple myeloma1-4, but the efficacy of CAR T cell therapy in solid tumours has been limited5. This is owing to a number of factors, including the immunosuppressive tumour microenvironment that gives rise to poorly persisting and metabolically dysfunctional T cells. Analysis of anti-CD19 CAR T cells used clinically has shown that positive treatment outcomes are associated with a more 'stem-like' phenotype and increased mitochondrial mass6-8. We therefore sought to identify transcription factors that could enhance CAR T cell fitness and efficacy against solid tumours. Here we show that overexpression of FOXO1 promotes a stem-like phenotype in CAR T cells derived from either healthy human donors or patients, which correlates with improved mitochondrial fitness, persistence and therapeutic efficacy in vivo. This work thus reveals an engineering approach to genetically enforce a favourable metabolic phenotype that has high translational potential to improve the efficacy of CAR T cells against solid tumours.

Protein degradation on the global scale.

Protein degradation occurs through proteasomal, endosomal, and lysosomal pathways. Technological advancements have allowed for the determination of protein copy numbers and turnover rates on a global scale, which has provided an overview of trends and rules governing protein degradation. Sharper chemical and gene-editing tools have enabled the specific perturbation of each degradation pathway, whose effects on protein dynamics can now be comprehensively analyzed. We review major studies and innovation in this field and discuss the interdependence between the major pathways of protein degradation.

Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer.

Therapies that boost the anti-tumor responses of cytotoxic T lymphocytes (CTLs) have shown promise; however, clinical responses to the immunotherapeutic agents currently available vary considerably, and the molecular basis of this is unclear. We performed transcriptomic profiling of tumor-infiltrating CTLs from treatment-naive patients with lung cancer to define the molecular features associated with the robustness of anti-tumor immune responses. We observed considerable heterogeneity in the expression of molecules associated with activation of the T cell antigen receptor (TCR) and of immunological-checkpoint molecules such as 4-1BB, PD-1 and TIM-3. Tumors with a high density of CTLs showed enrichment for transcripts linked to tissue-resident memory cells (TRM cells), such as CD103, and CTLs from CD103hi tumors displayed features of enhanced cytotoxicity. A greater density of TRM cells in tumors was predictive of a better survival outcome in lung cancer, and this effect was independent of that conferred by CTL density. Here we define the 'molecular fingerprint' of tumor-infiltrating CTLs and identify potentially new targets for immunotherapy.

ERα-associated translocations underlie oncogene amplifications in breast cancer.

Focal copy-number amplification is an oncogenic event. Although recent studies have revealed the complex structure1-3 and the evolutionary trajectories4 of oncogene amplicons, their origin remains poorly understood. Here we show that focal amplifications in breast cancer frequently derive from a mechanism-which we term translocation-bridge amplification-involving inter-chromosomal translocations that lead to dicentric chromosome bridge formation and breakage. In 780 breast cancer genomes, we observe that focal amplifications are frequently connected to each other by inter-chromosomal translocations at their boundaries. Subsequent analysis indicates the following model: the oncogene neighbourhood is translocated in G1 creating a dicentric chromosome, the dicentric chromosome is replicated, and as dicentric sister chromosomes segregate during mitosis, a chromosome bridge is formed and then broken, with fragments often being circularized in extrachromosomal DNAs. This model explains the amplifications of key oncogenes, including ERBB2 and CCND1. Recurrent amplification boundaries and rearrangement hotspots correlate with oestrogen receptor binding in breast cancer cells. Experimentally, oestrogen treatment induces DNA double-strand breaks in the oestrogen receptor target regions that are repaired by translocations, suggesting a role of oestrogen in generating the initial translocations. A pan-cancer analysis reveals tissue-specific biases in mechanisms initiating focal amplifications, with the breakage-fusion-bridge cycle prevalent in some and the translocation-bridge amplification in others, probably owing to the different timing of DNA break repair. Our results identify a common mode of oncogene amplification and propose oestrogen as its mechanistic origin in breast cancer.

Integrated loss- and gain-of-function screens define a core network governing human embryonic stem cell behavior.

Understanding the genetic control of human embryonic stem cell function is foundational for developmental biology and regenerative medicine. Here we describe an integrated genome-scale loss- and gain-of-function screening approach to identify genetic networks governing embryonic stem cell proliferation and differentiation into the three germ layers. We identified a deep link between pluripotency maintenance and survival by showing that genetic alterations that cause pluripotency dissolution simultaneously increase apoptosis resistance. We discovered that the chromatin-modifying complex SAGA and in particular its subunit TADA2B are central regulators of pluripotency, survival, growth, and lineage specification. Joint analysis of all screens revealed that genetic alterations that broadly inhibit differentiation across multiple germ layers drive proliferation and survival under pluripotency-maintaining conditions and coincide with known cancer drivers. Our results show the power of integrated multilayer genetic screening for the robust mapping of complex genetic networks.

Microtubule association of TRIM3 revealed by differential extraction proteomics.

The microtubule network is formed from polymerised tubulin subunits and associating proteins, which govern microtubule dynamics and a diverse array of functions. To identify novel microtubule-binding proteins, we have developed an unbiased biochemical assay, which relies on the selective extraction of cytosolic proteins from U2OS cells, while leaving behind the microtubule network. Candidate proteins are linked to microtubules by their sensitivities to the depolymerising drug nocodazole or the microtubule-stabilising drug taxol, which is quantitated by mass spectrometry. Our approach is benchmarked by co-segregation of tubulin and previously established microtubule-binding proteins. We then identify several novel candidate microtubule-binding proteins, from which we have selected the ubiquitin E3 ligase tripartite motif-containing protein 3 (TRIM3) for further characterisation. We map TRIM3 microtubule binding to its C-terminal NHL-repeat region. We show that TRIM3 is required for the accumulation of acetylated tubulin, following treatment with taxol. Furthermore, loss of TRIM3 partially recapitulates the reduction in nocodazole-resistant microtubules characteristic of α-tubulin acetyltransferase 1 (ATAT1) depletion. These results can be explained by a decrease in ATAT1 following depletion of TRIM3 that is independent of transcription.

Small Differences and Big Changes: The Many Variables of MicroRNA Expression and Function in the Brain.

MicroRNAs are emerging as crucial regulators within the complex, dynamic environment of the synapse, and they offer a promising new avenue for the treatment of neurological disease. These small noncoding RNAs modify gene expression in several ways, including posttranscriptional modulation via binding to complementary and semicomplementary sites on target mRNAs. This rapid, finely tuned regulation of gene expression is essential to meet the dynamic demands of the synapse. Here, we provide a detailed review of the multifaceted world of synaptic microRNA regulation. We discuss the many mechanisms by which microRNAs regulate gene expression at the synapse, particularly in the context of neuronal plasticity. We also describe the various factors, such as age, sex, and neurological disease, that can influence microRNA expression and activity in neurons. In summary, microRNAs play a crucial role in the intricate and quickly changing functional requirements of the synapse, and context is essential in the study of microRNAs and their potential therapeutic applications.

Membrane compartmentalisation of the ubiquitin system.

We now have a comprehensive inventory of ubiquitin system components. Understanding of any system also needs an appreciation of how components are organised together. Quantitative proteomics has provided us with a census of their relative populations in several model cell types. Here, by examining large scale unbiased data sets, we seek to identify and map those components, which principally reside on the major organelles of the endomembrane system. We present the consensus distribution of > 50 ubiquitin modifying enzymes, E2s, E3s and DUBs, that possess transmembrane domains. This analysis reveals that the ER and endosomal compartments have a diverse cast of resident E3s, whilst the Golgi and mitochondria operate with a more restricted palette. We describe key functions of ubiquitylation that are specific to each compartment and relate this to their signature complement of ubiquitin modifying components.

Comparison of dopamine release and uptake parameters across sex, species and striatal subregions.

For over four decades, fast-scan cyclic voltammetry (FSCV) has been used to selectively measure neurotransmitters such as dopamine (DA) with high spatial and temporal resolution, providing detailed information about the regulation of DA in the extracellular space. FSCV is an optimal method for determining concentrations of stimulus-evoked DA in brain tissue. When modelling diseases involving disturbances in DA transmission, preclinical rodent models are especially useful because of the availability of specialized tools and techniques that serve as a foundation for translational research. There is known heterogeneity in DA dynamics between and within DA-innervated brain structures and between males and females. However, systematic evaluations of sex- and species-differences across multiple areas are lacking. Therefore, using FSCV, we captured a broad range of DA dynamics across five sub-regions of the dorsal and ventral striatum of males and females of both rats and mice that reflect the functional heterogeneity of DA kinetics and dynamics within these structures. While numerous differences were found, in particular, we documented a strong, consistent pattern of increased DA transporter activity in females in all of the regions surveyed. The data herein are intended to be used as a resource for further investigation of DA terminal function.

OFFSPRING: A SPRING Follow-Up Study Assessing the Efficacy of Maternal Probiotics and Allergic Disease in the Child.

INTRODUCTION: There are a variety of factors that contribute to the development of allergic diseases in children, including environmental exposures during the maternal prenatal period. It has been proposed that probiotic supplementation during pregnancy could be used as a possible preventative measure to target childhood allergic disease. METHODS: Participants from a previously conducted prospective double-blind randomised control trial of probiotics versus placebo study (Study of PRrobiotics IN Gestation) were sent electronic questionnaires to complete about their child, who are now between 3 and 7 years of age. Demographic data and rates of allergic diseases were compared between the two groups. RESULTS: One hundred and seven women responded to the questionnaires. Between the two groups, there was no difference in the frequency of allergic diseases, with similar rates of eczema, asthma, and hospital presentations seen. CONCLUSION: In this follow-up study, infants of mothers who were exposed to probiotics during their pregnancy do not appear to have any paediatric health advantages in terms of allergic diseases.

Estimating the effect of latent time-varying count exposures using multiple lists.

A major challenge in longitudinal built-environment health studies is the accuracy of commercial business databases that are used to characterize dynamic food environments. Different databases often provide conflicting exposure measures on the same subject due to different source credibilities. As on-site verification is not feasible for historical data, we suggest combining multiple databases to correct the bias in health effect estimates due to measurement error in any 1 datasource. We propose a joint model for the time-varying health outcomes, observed count exposures, and latent true count exposures. Our model estimates the time-specific quality of sources and incorporates time dependence of true count exposure by Poisson integer-valued first-order autoregressive process. We take a Bayesian nonparametric approach to flexibly account for location-specific exposures. By resolving the discordance between different databases, our method reduces the bias in the longitudinal health effect of the true exposures. Our method is demonstrated with childhood obesity data in California public schools with respect to convenience store exposures in school neighborhoods from 2001 to 2008.

Age differences in priming as a function of processing at encoding.

It is unclear whether implicit memory (priming) is affected by aging. Some studies have reported no difference between young and older adults, while others have uncovered reliable reductions. An important factor that may explain these discrepancies is the manner of encoding. Processing requirements (perceptual/conceptual) have varied considerably between studies, yet processing abilities are not equally affected by aging. This study examined whether processing during encoding moderates age effects on priming. Young and older participants studied object-word pairs and made natural/manufactured (conceptual) and left/right rotation (perceptual) judgements in relation to the word or object. Objects served as targets on a subsequent continuous identification with recognition task to assess priming and recognition. Priming and recognition were greater in young than older adults for attended items, with a larger effect size in the conceptual than the perceptual condition. Findings suggest that age differences in priming may be a function of processing at encoding.

ISGylation-independent protection of cell growth by USP18 following interferon stimulation.

Type 1 interferon stimulation highly up-regulates all elements of a ubiquitin-like conjugation system that leads to ISGylation of target proteins. An ISG15-specific member of the deubiquitylase family, USP18, is up-regulated in a co-ordinated manner. USP18 can also provide a negative feedback by inhibiting JAK-STAT signalling through protein interactions independently of DUB activity. Here, we provide an acute example of this phenomenon, whereby the early expression of USP18, post-interferon treatment of HCT116 colon cancer cells is sufficient to fully suppress the expression of the ISG15 E1 enzyme, UBA7. Stimulation of lung adenocarcinoma A549 cells with interferon reduces their growth rate but they remain viable. In contrast, A549 USP18 knock-out cells show similar growth characteristics under basal conditions, but upon interferon stimulation, a profound inhibition of cell growth is observed. We show that this contingency on USP18 is independent of ISGylation, suggesting non-catalytic functions are required for viability. We also demonstrate that global deISGylation kinetics are very slow compared with deubiquitylation. This is not influenced by USP18 expression, suggesting that enhanced ISGylation in USP18 KO cells reflects increased conjugating activity.

Temporal Patterns in Fruit and Vegetable Intake Among Racially and Ethnically Diverse Children and Adolescents in California.

Introduction: Childhood dietary behaviors, including fruit and vegetable intake, are associated with adult health. Most children do not meet daily recommended servings of fruits and vegetables. Less is known about temporal patterns in fruit and vegetable consumption or if they vary by race and ethnicity. We investigated temporal patterns in fruit and vegetable intake among California school-age children and adolescents overall and by race and ethnicity. Methods: We used 2-year cross-sectional datasets from the child and adolescent samples in the California Health Interview Surveys from 2011-2012 through 2019-2020 and modified Poisson regression models to estimate the likelihood of consuming 5 or more servings of fruits and vegetables in 2013-2016 and 2017-2020 compared with 2011-2012. Models controlled for age, race and ethnicity, gender, citizenship status, family income, and adult education and tested for differences by race and ethnicity. The samples included 16,125 children aged 5 to 11 years and 9,672 adolescents aged 12 to 17 years. Results: Overall, 29.3% of children and 25.9% of adolescents reported intake of 5 or more fruits and vegetables per day. Among children, adjusted prevalence ratios (PR) of fruit and vegetable intake were higher in 2013-2016 (PR,1.25; 95% CI, 1.11-1.42) and 2017-2020 (PR,1.13; 95% CI, 0.99-1.30) compared with 2011-2012. Among adolescents, the adjusted prevalence did not differ significantly over time. We found no evidence of differential associations by race and ethnicity for children and adolescents. Conclusion: We found favorable temporal changes in fruit and vegetable consumption among children, but not among adolescents. Monitoring temporal patterns in fruit and vegetable intake remains critical for planning population-level interventions to increase consumption.

'Communication is difficult': Speech, language and communication needs of people with young onset or rarer forms of non-language led dementia.

BACKGROUND: People with behavioural variant frontotemporal dementia, Lewy body dementia, posterior cortical atrophy and young onset Alzheimer's disease may experience language and communication difficulties. However, the role of speech and language interventions for people with these non-language led dementias has received little attention. AIMS: This study aimed to explore the experiences and perspectives of people living with these conditions, and their families, regarding their language and communication difficulties and how speech and language therapy could address these needs. METHODS: This study employed a qualitative design to explore the experiences of people living with or caring for somebody with behavioural variant frontotemporal dementia, Lewy body dementia, posterior cortical atrophy or young onset Alzheimer's disease, and to understand their opinions about speech and language therapy. Participants were recruited from a support service connected to a dementia clinic to attend one of five focus group meetings. Videorecorded focus groups and interviews were transcribed, and reflexive thematic analysis was used to analyse data from people affected by each type of dementia. RESULTS: A total of 25 participants were recruited to the study, with representation across the different forms of non-language led dementias. The four main themes identified were: (1) communication difficulties as a key difficulty, (2) loss and loneliness, (3) speech and language therapy, and (4) the role of the caregiver. Sixteen subthemes were also identified which highlighted individual issues across disease types. DISCUSSION: Although all the forms of dementia studied here are not considered to be language-led, people with these conditions and/or their care partners identified speech, language and communication as common challenges. These communication difficulties were reported to have a negative impact on their social participation and mental health and participants felt speech and language interventions could help. There is a need for research exploring speech and language interventions developed for and with people with non-language led dementias and their care partners, to ensure they meet the needs of the people they are designed for. WHAT THIS PAPER ADDS: What is already known on the subject People with primary progressive aphasia present with speech, language and communication difficulties, and several speech and language interventions have been developed to meet the needs of this population. However, people with non-language led dementias may also experience speech, language and communication difficulties, and little is known about interventions that may address these difficulties. What this paper adds to existing knowledge People living with or caring for somebody with behavioural variant frontotemporal dementia, Lewy body dementia, posterior cortical atrophy and young onset Alzheimer's disease report experiencing speech, language and communication difficulties that impact on the person with dementia's social participation and mood. Participants in this study also shared their opinions about how speech and language interventions could help, from the earliest stages of the disease. What are the potential or actual clinical implications of this work? Speech and language therapists need to address the individual speech, language and communication needs of people with dementias, even those that are not thought to be language-led. Current speech and language therapy service provision does not meet the needs of people with non-language led dementias and further research is required to develop interventions and services to meet these needs.

An overview of outputs of Aboriginal- and Torres Strait Islander-related publications from University Departments of Rural Health in Australia; 2010-2021.

INTRODUCTION: Disparities in the health of Indigenous people and in the health of rural populations are well described. University Departments of Rural Health (UDRHs) in Australia are federally funded under a program to address ongoing challenges with health workforce distribution for rural and remote areas. They have a significant role in research in regional, rural and remote areas, including research related to Indigenous health. However, a comprehensive analysis of their contributions to original Indigenous health related to Indigenous health is lacking. OBJECTIVE: This study examines the contributions of UDRHs to Indigenous issues through analysis of publications of UDRHs focused on Indigenous health during the period 2010-2021. DESIGN: This paper examines a database of UDRH Indigenous-related publications from 2010 to 2021. FINDINGS: A total of 493 publications to which UDRHs contributed were analysed, including 354 original research articles. Health services research was the most common category, followed by epidemiology and papers exploring Indigenous culture and health. While health services research substantially increased over the period, the numbers of original research papers specifically focused on Indigenous workforce issues, whether related to Indigenous people, students or existing workforce was relatively small. DISCUSSION: This broad overview shows the nature and trends in Indigenous health research by UDRHs and makes evident a substantial contribution to Indigenous health research, reflecting their commitment to improving the health and well-being of Indigenous communities. CONCLUSIONS: The analysis can help direct future efforts, and future analyses should delve deeper into the impact of this research and further engage Indigenous researchers.

Heroin- and Fentanyl-Induced Respiratory Depression in a Rat Plethysmography Model: Potency, Tolerance, and Sex Differences.

The opioid overdose death toll in the United States is an ongoing public health crisis. We characterized the magnitude and duration of respiratory depression, the leading cause of death in opioid overdose cases, induced by heroin or fentanyl and the development of tolerance in male and female rats. We used whole-body plethysmography to first establish dose-response curves by recording breathing for 60 minutes post-intravenous opioid injection. We then tested the development of respiratory tolerance to acute heroin or fentanyl over several weeks and to chronic fentanyl with acute fentanyl or heroin challenge. Heroin and fentanyl each provoked dose-dependent respiratory depression. Heroin caused prolonged (45-60 minute) respiratory depression in female and male rats, characterized by decreased frequency, tidal volume, and minute ventilation and increased inspiratory time and apneic pause. Fentanyl produced similar changes with a shorter duration (10-15 minutes). High-dose heroin or fentanyl produced robust respiratory depression that was slightly more severe in females and, when given intermittently (acute doses 2 to 3 weeks apart), did not lead to tolerance. In contrast, chronic fentanyl delivered with an osmotic minipump resulted in tolerance to acute fentanyl and heroin, characterized by a shorter duration of respiratory depression. This effect persisted during withdrawal in males only. Our model and experimental design will allow for investigation of the neurobiology of opioid-induced respiratory depression and for testing potential therapeutics to reverse respiratory depression or stimulate breathing. SIGNIFICANCE STATEMENT: Fentanyl was more potent and had shorter duration in producing respiratory depression than heroin in both sexes, whereas female rats were more sensitive than males to heroin-induced respiratory depression. Tolerance/cross-tolerance develops in chronic fentanyl administration but is minimized with long interadministration intervals.

Uropathogenic Escherichia coli population structure and antimicrobial susceptibility in Norfolk, UK.

BACKGROUND: Urinary tract infections (UTIs) are a frequent cause for visits to primary care providers. In alignment globally, uropathogenic Escherichia coli (UPEC) are the main aetiological agent for UTIs in Norfolk and are increasingly difficult to treat due to multi-drug resistance. OBJECTIVES: We set out to identify which clonal groups and resistance genes are disseminating in the community and hospitals in Norfolk, the first study of its kind for UPEC in this region. METHODS: We collected 199 clinical E. coli isolates causing UTIs in the community and hospital from the Clinical Microbiology laboratory at Norfolk and Norwich University Hospital between August 2021 and January 2022. These were whole-genome sequenced using the Illumina and MinION platforms for in silico MLST and antibiotic resistance determinant detection. RESULTS: The isolates were composed of 70 STs; 8 lineages represented 56.7% of this population: ST73, ST12, ST69, ST131, ST404, ST95, ST127 and ST1193. Importantly, primary UTI screening deemed 6.5% of isolates to be multidrug resistant (MDR), with high rates of resistance to ampicillin (52.1%) and trimethoprim (36.2%) in hospitals. Of concern is the probable clonal expansion of MDR groups ST131 and ST1193 in hospitals and community settings with chromosomally encoded blaCTX-M-15, blaOXA-1 and aac(6')-Ib-cr5. CONCLUSIONS: The burden of reported UTIs in Norfolk is largely caused by non-MDR isolates and mirrors similar UPEC studies nationally and internationally. Continually monitoring samples with consideration of sources will help reduce burden of disease.