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A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease.

Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohn's disease (CD) and ulcerative colitis (UC) following adalimumab, an anti-tumour necrosis factor (anti-TNF) treatment. We generated ~1 million single-cell transcriptomes, organised into 109 cell states, from 216 gut biopsies (41 subjects), revealing disease-specific differences. A systems biology-spatial analysis identified granuloma signatures in CD and interferon (IFN)-response signatures localising to T cell aggregates and epithelial damage in CD and UC. Pretreatment differences in epithelial and myeloid compartments were associated with remission outcomes in both diseases. Longitudinal comparisons demonstrated disease progression in nonremission: myeloid and T cell perturbations in CD and increased multi-cellular IFN signalling in UC. IFN signalling was also observed in rheumatoid arthritis (RA) synovium with a lymphoid pathotype. Our therapeutic atlas represents the largest cellular census of perturbation with the most common biologic treatment, anti-TNF, across multiple inflammatory diseases.

Sexual dimorphisms in fat distribution: investigating oestradiol’s depot-specific effects on preadipocyte and macrophage interactions

Fat distribution is a key regulator of cardiometabolic disease risk, with biological females typically favouring fat storage in the gluteofemoral region, while males tend to store fat around the abdomen. Accumulation of gluteofemoral adiposity, particularly through hyperplastic expansion, is metabolically favourable and is thought to be promoted by the sex hormone oestradiol in females. Alterations in oestradiol concentrations, such as those occurring at menopause or during oestradiol therapy, are associated with shifts in fat distribution and subsequent changes in cardiometabolic risk. However, the mechanisms underlying these oestradiol-induced changes remain poorly understood and are complicated by the controversial literature surrounding the effects of oestradiol on adipose tissue expansion. Given the documented role of oestradiol in modulating the inflammatory phenotypes of other cells within the adipose tissue stromovascular fraction (SVF), particularly macrophages, it is essential to investigate how oestradiol may influence signalling between adipocytes and macrophages to promote depot-specific changes in adipose expansion, favouring gluteofemoral adipose tissue growth and abdominal adipose tissue regression. This thesis aimed to first characterize the depot-specific SVF population landscape using single-cell RNA sequencing (scRNASeq) on paired abdominal and gluteal adipose tissue biopsies. It then assessed oestradiol signalling in abdominal and gluteal preadipocytes using in-vitro models, and established an in-vitro co-culture system between preadipocytes and macrophages. This system facilitated the identification of oestradiol-primed communication signals that may modulate depot-specific expansion through RNA sequencing approaches. The results reveal unique transcriptional landscapes of abdominal and gluteal adipose tissue SVF and demonstrate that preadipocyte responses to oestradiol are highly depot-specific. Additionally, this work identified a range of candidate signals exchanged between preadipocytes and macrophages that may contribute to oestradiol-primed, depots-specific adipose tissue expansion. Future research should aim to functionally test these signals using the in-vitro systems developed here.

Colonic goblet cell dysfunction and gastric intestinal metaplasia in patients with anterior gradient 2 defects and infantile Inflammatory bowel disease

Safe emergency general surgery-ASGBI statement.

Harnessing transcriptomic signals for amyotrophic lateral sclerosis to identify novel drugs and enhance risk prediction.

INTRODUCTION: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. This study integrates common genetic association results from the latest ALS genome-wide association study (GWAS) summary statistics with functional genomic annotations with the aim of providing mechanistic insights into ALS risk loci, inferring drug repurposing opportunities, and enhancing prediction of ALS risk and clinical characteristics. METHODS: Genes associated with ALS were identified using GWAS summary statistic methodology including SuSiE SNP-based fine-mapping, and transcriptome- and proteome-wide association study (TWAS/PWAS) analyses. Using several approaches, gene associations were integrated with the DrugTargetor drug-gene interaction database to identify drugs that could be repurposed for the treatment of ALS. Furthermore, ALS gene associations from TWAS were combined with observed blood expression in two external ALS case-control datasets to calculate polytranscriptomic scores and evaluate their utility for prediction of ALS risk and clinical characteristics, including site of onset, age at onset, and survival. RESULTS: SNP-based fine-mapping, TWAS and PWAS identified 118 genes associated with ALS, with TWAS and PWAS providing novel mechanistic insights. Drug repurposing analyses identified six drugs significantly enriched for interactions with ALS associated genes, though directionality could not be determined. Additionally, drug class enrichment analysis showed gene signatures linked to calcium channel blockers may reduce ALS risk, whereas antiepileptic drugs may increase ALS risk. Across the two observed expression target samples, ALS polytranscriptomic scores significantly predicted ALS risk (R 2 = 5.1 %; p-value = 3.2 × 10-27) and clinical characteristics. CONCLUSIONS: Functionally-informed analyses of ALS GWAS summary statistics identified novel mechanistic insights into ALS aetiology, highlighted several therapeutic research avenues, and enabled statistically significant prediction of ALS risk.

Fine needle aspiration of human lymph nodes reveals cell populations and soluble interactors pivotal to immunological priming.

Lymph node (LN) fine needle aspiration (LN FNA) represents a powerful technique for minimally invasive sampling of human LNs in vivo and has been used effectively to directly study aspects of the human germinal center response. However, systematic deep phenotyping of the cellular populations and cell-free proteins recovered by LN FNA has not been performed. Thus, we studied human cervical LN FNAs as a proof-of-concept and used single-cell RNA-sequencing and proteomic analysis to benchmark this compartment, define the purity of LN FNA material, and facilitate future studies in this immunologically pivotal environment. Our data provide evidence that LN FNAs contain bone-fide LN-resident innate immune populations, with minimal contamination of blood material. Examination of these populations reveals unique biology not predictable from equivalent blood-derived populations. LN FNA supernatants represent a specific source of lymph- and lymph node-derived proteins, and can, aided by transcriptomics, identify likely receptor-ligand interactions. This represents the first description of the types and abundance of immune cell populations and cell-free proteins that can be efficiently studied by LN FNA. These findings are of broad utility for understanding LN physiology in health and disease, including infectious or autoimmune perturbations, and in the case of cervical nodes, neuroscience.

Digital health interventions in primary care in low- and middle-income countries: a systematic scoping review protocol

Background The integration of digital health (eHealth) interventions into primary healthcare systems has gained recognition lately in Low-and Middle-Income Countries (LMICs) to enhance healthcare quality, accessibility, and efficiency. These interventions may offer effective strategies in mitigating the burden of chronic diseases by facilitating access to remote healthcare and optimising its processes. This scoping review aims to identify and assess eHealth interventions implemented in primary care settings in LMICs for further development and adaptation. Methods and analysis We will search two electronic databases, such as Scopus and Embase, to identify peer-reviewed studies reporting on eHealth interventions implemented in primary care settings within LMICs. This review will encompass evidence published in the English language without a time frame restriction. We will remove duplicates from the search, and two reviewers will independently assess all articles for eligibility by first screening the title and abstract, followed by a full-text review. Eligible articles will be extracted, and data will be charted according to types of intervention and settings using a standardised form. Ethics and dissemination There is no ethical review required for this scoping review. We plan to disseminate the findings by presentations at conferences and publishing in open-access journal.

Global estimates and determinants of antituberculosis drug pharmacokinetics in children and adolescents: a systematic review and individual patient data meta-analysis.

BACKGROUND: Suboptimal exposure to antituberculosis (anti-TB) drugs has been associated with unfavourable treatment outcomes. We aimed to investigate estimates and determinants of first-line anti-TB drug pharmacokinetics in children and adolescents at a global level. METHODS: We systematically searched MEDLINE, Embase and Web of Science (1990-2021) for pharmacokinetic studies of first-line anti-TB drugs in children and adolescents. Individual patient data were obtained from authors of eligible studies. Summary estimates of total/extrapolated area under the plasma concentration-time curve from 0 to 24 h post-dose (AUC0-24) and peak plasma concentration (C max) were assessed with random-effects models, normalised with current World Health Organization-recommended paediatric doses. Determinants of AUC0-24 and C max were assessed with linear mixed-effects models. RESULTS: Of 55 eligible studies, individual patient data were available for 39 (71%), including 1628 participants from 12 countries. Geometric means of steady-state AUC0-24 were summarised for isoniazid (18.7 (95% CI 15.5-22.6) h·mg·L-1), rifampicin (34.4 (95% CI 29.4-40.3) h·mg·L-1), pyrazinamide (375.0 (95% CI 339.9-413.7) h·mg·L-1) and ethambutol (8.0 (95% CI 6.4-10.0) h·mg·L-1). Our multivariate models indicated that younger age (especially <2 years) and HIV-positive status were associated with lower AUC0-24 for all first-line anti-TB drugs, while severe malnutrition was associated with lower AUC0-24 for isoniazid and pyrazinamide. N-acetyltransferase 2 rapid acetylators had lower isoniazid AUC0-24 and slow acetylators had higher isoniazid AUC0-24 than intermediate acetylators. Determinants of C max were generally similar to those for AUC0-24. CONCLUSIONS: This study provides the most comprehensive estimates of plasma exposures to first-line anti-TB drugs in children and adolescents. Key determinants of drug exposures were identified. These may be relevant for population-specific dose adjustment or individualised therapeutic drug monitoring.

Harnessing Transcriptomic Signals for Amyotrophic Lateral Sclerosis to Identify Novel Drugs and Enhance Risk Prediction.

INTRODUCTION: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. This study integrates the latest ALS genome-wide association study (GWAS) summary statistics with functional genomic annotations with the aim of providing mechanistic insights into ALS risk loci, inferring drug repurposing opportunities, and enhancing prediction of ALS risk and clinical characteristics. METHODS: Genes associated with ALS were identified using GWAS summary statistic methodology including SuSiE SNP-based fine-mapping, and transcriptome- and proteome-wide association study (TWAS/PWAS) analyses. Using several approaches, gene associations were integrated with the DrugTargetor drug-gene interaction database to identify drugs that could be repurposed for the treatment of ALS. Furthermore, ALS gene associations from TWAS were combined with observed blood expression in two external ALS case-control datasets to calculate polytranscriptomic scores and evaluate their utility for prediction of ALS risk and clinical characteristics, including site of onset, age at onset, and survival. RESULTS: SNP-based fine-mapping, TWAS and PWAS identified 117 genes associated with ALS, with TWAS and PWAS providing novel mechanistic insights. Drug repurposing analyses identified five drugs significantly enriched for interactions with ALS associated genes, with directional analyses highlighting α-glucosidase inhibitors may exacerbate ALS pathology. Additionally, drug class enrichment analysis showed calcium channel blockers may reduce ALS risk. Across the two observed expression target samples, ALS polytranscriptomic scores significantly predicted ALS risk (R2 = 4%; p-value = 2.1×10-21). CONCLUSIONS: Functionally-informed analyses of ALS GWAS summary statistics identified novel mechanistic insights into ALS aetiology, highlighted several therapeutic research avenues, and enabled statistically significant prediction of ALS risk.

Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

Alzheimer's disease (AD) is the most common form of dementia, and risk-influencing genetics implicates microglia and neuroimmunity in the pathogenesis of AD. Induced pluripotent stem cell (iPSC)-derived microglia (iPSC-microglia) are increasingly used as a model of AD, but the relevance of historical immune stimuli to model AD is unclear. We performed a detailed cross-comparison over time on the effects of combinatory stimulation of iPSC-microglia, and in particular their relevance to AD. We used single-cell RNA sequencing to measure the transcriptional response of iPSC-microglia after 24 h and 48 h of stimulation with prostaglandin E2 (PGE2) or lipopolysaccharide (LPS)+interferon gamma (IFN-γ), either alone or in combination with ATPγS. We observed a shared core transcriptional response of iPSC-microglia to ATPγS and to LPS+IFN-γ, suggestive of a convergent mechanism of action. Across all conditions, we observed a significant overlap, although directional inconsistency to genes that change their expression levels in human microglia from AD patients. Using a data-led approach, we identify a common axis of transcriptomic change across AD genetic mouse models of microglia and show that only LPS provokes a transcriptional response along this axis in mouse microglia and LPS+IFN-γ in human iPSC-microglia. This article has an associated First Person interview with the first author of the paper.

Gliotransmission of D-serine promotes thirst-directed behaviors in Drosophila.

Thirst emerges from a range of cellular changes that ultimately motivate an animal to consume water. Although thirst-responsive neuronal signals have been reported, the full complement of brain responses is unclear. Here, we identify molecular and cellular adaptations in the brain using single-cell sequencing of water-deprived Drosophila. Water deficiency primarily altered the glial transcriptome. Screening the regulated genes revealed astrocytic expression of the astray-encoded phosphoserine phosphatase to bi-directionally regulate water consumption. Astray synthesizes the gliotransmitter D-serine, and vesicular release from astrocytes is required for drinking. Moreover, dietary D-serine rescues aay-dependent drinking deficits while facilitating water consumption and expression of water-seeking memory. D-serine action requires binding to neuronal NMDA-type glutamate receptors. Fly astrocytes contribute processes to tripartite synapses, and the proportion of astrocytes that are themselves activated by glutamate increases with water deprivation. We propose that thirst elevates astrocytic D-serine release, which awakens quiescent glutamatergic circuits to enhance water procurement.

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly.

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

Integration of single-cell RNA-Seq and CyTOF data characterises heterogeneity of rare cell subpopulations

Background: The simultaneous measurement of cellular proteins and transcriptomes of single cell data has become an exciting new possibility with the advent of highly multiplexed multi-omics methodologies. However, mass cytometry (CyTOF) is a well-established, affordable technique for the analysis of proteomic data, which is well suited for the discovery and characterisation of very rare subpopulations of cells with a wealth of publicly available datasets. Methods: We present and evaluate the multimodal integration of single cell RNA-Seq and CyTOF datasets coming from both matched and unmatched samples, using two publicly available datasets. Results: We demonstrate that the integration of well annotated CyTOF data with single cell RNA sequencing can aid in the identification and annotation of cell populations with high accuracy. Furthermore, we show that the integration can provide imputed measurements of protein markers which are comparable to the current gold standard of antibody derived tags (ADT) from CITE-Seq for both matched and unmatched datasets. Using this methodology, we identify and transcriptionally characterise a rare subpopulation of CD11c positive B cells in high resolution using publicly available data and we unravel its heterogeneity in a single cell setting without the need to sort the cells in advance, in a manner which had not been previously possible. Conclusions: This approach provides the framework for using available proteomic and transcriptomic datasets in a unified and unbiased fashion to assist ongoing and future studies of cellular characterisation and biomarker identification.

The long-term sequelae of COVID-19: an international consensus on research priorities for patients with pre-existing and new-onset airways disease.

Persistent ill health after acute COVID-19-referred to as long COVID, the post-acute COVID-19 syndrome, or the post-COVID-19 condition-has emerged as a major concern. We undertook an international consensus exercise to identify research priorities with the aim of understanding the long-term effects of acute COVID-19, with a focus on people with pre-existing airways disease and the occurrence of new-onset airways disease and associated symptoms. 202 international experts were invited to submit a minimum of three research ideas. After a two-phase internal review process, a final list of 98 research topics was scored by 48 experts. Patients with pre-existing or post-COVID-19 airways disease contributed to the exercise by weighting selected criteria. The highest-ranked research idea focused on investigation of the relationship between prognostic scores at hospital admission and morbidity at 3 months and 12 months after hospital discharge in patients with and without pre-existing airways disease. High priority was also assigned to comparisons of the prevalence and severity of post-COVID-19 fatigue, sarcopenia, anxiety, depression, and risk of future cardiovascular complications in patients with and without pre-existing airways disease. Our approach has enabled development of a set of priorities that could inform future research studies and funding decisions. This prioritisation process could also be adapted to other, non-respiratory aspects of long COVID.

Phenotypic manifestation of α-synuclein strains derived from Parkinson's disease and multiple system atrophy in human dopaminergic neurons.

α-Synuclein is critical in the pathogenesis of Parkinson's disease and related disorders, yet it remains unclear how its aggregation causes degeneration of human dopaminergic neurons. In this study, we induced α-synuclein aggregation in human iPSC-derived dopaminergic neurons using fibrils generated de novo or amplified in the presence of brain homogenates from Parkinson's disease or multiple system atrophy. Increased α-synuclein monomer levels promote seeded aggregation in a dose and time-dependent manner, which is associated with a further increase in α-synuclein gene expression. Progressive neuronal death is observed with brain-amplified fibrils and reversed by reduction of intraneuronal α-synuclein abundance. We identified 56 proteins differentially interacting with aggregates triggered by brain-amplified fibrils, including evasion of Parkinson's disease-associated deglycase DJ-1. Knockout of DJ-1 in iPSC-derived dopaminergic neurons enhance fibril-induced aggregation and neuronal death. Taken together, our results show that the toxicity of α-synuclein strains depends on aggregate burden, which is determined by monomer levels and conformation which dictates differential interactomes. Our study demonstrates how Parkinson's disease-associated genes influence the phenotypic manifestation of strains in human neurons.

High-resolution transcriptional landscape of xeno-free human induced pluripotent stem cell-derived cerebellar organoids.

Current protocols for producing cerebellar neurons from human pluripotent stem cells (hPSCs) often rely on animal co-culture and mostly exist as monolayers, limiting their capability to recapitulate the complex processes in the developing cerebellum. Here, we employed a robust method, without the need for mouse co-culture to generate three-dimensional cerebellar organoids from hPSCs that display hallmarks of in vivo cerebellar development. Single-cell profiling followed by comparison to human and mouse cerebellar atlases revealed the presence and maturity of transcriptionally distinct populations encompassing major cerebellar cell types. Encapsulation with Matrigel aimed to provide more physiologically-relevant conditions through recapitulation of basement-membrane signalling, influenced both growth dynamics and cellular composition of the organoids, altering developmentally relevant gene expression programmes. We identified enrichment of cerebellar disease genes in distinct cell populations in the hPSC-derived cerebellar organoids. These findings ascertain xeno-free human cerebellar organoids as a unique model to gain insight into cerebellar development and its associated disorders.

Ductal variant prostate carcinoma is associated with a significantly shorter metastasis-free survival.

BACKGROUND: Ductal adenocarcinoma is an uncommon prostate cancer variant. Previous studies suggest that ductal variant histology may be associated with worse clinical outcomes, but these are difficult to interpret. To address this, we performed an international, multi-institutional study to describe the characteristics of ductal adenocarcinoma, particularly focussing on the effect of presence of ductal variant cancer on metastasis-free survival. METHODS: Patients with ductal variant histology from two institutional databases who underwent radical prostatectomies were identified and compared with an independent acinar adenocarcinoma cohort. After propensity score matching, the effect of the presence of ductal adenocarcinoma on time to biochemical recurrence, initiation of salvage therapy and the development of metastatic disease was determined. Deep whole-exome sequencing was performed for selected cases (n = 8). RESULTS: A total of 202 ductal adenocarcinoma and 2037 acinar adenocarcinoma cases were analysed. Survival analysis after matching demonstrated that patients with ductal variant histology had shorter salvage-free survival (8.1 versus 22.0 months, p = 0.03) and metastasis-free survival (6.7 versus 78.6 months, p 

Commissioning the H i Observing Mode of the Beam Former for the Cryogenically Cooled Focal L-band Array for the GBT (FLAG)

Abstract We present the results of commissioning observations for a new digital beam-forming back end for the Focal plane L-band Array for the Robert C. Byrd Green Bank Telescope (FLAG), a cryogenically cooled Phased Array Feed (PAF) with the lowest measured T sys/η of any PAF outfitted on a radio telescope to date. We describe the custom software used to apply beam-forming weights to the raw element covariances to create research-quality spectral-line images for the new fine-channel mode, study the stability of the beam weights over time, characterize FLAG’s sensitivity over a frequency range of 150 MHz, and compare the measured noise properties and observed distribution of neutral hydrogen emission from several extragalactic and Galactic sources with data obtained with the current single-pixel L-band receiver. These commissioning runs establish FLAG as the preeminent PAF receiver currently available for spectral-line observations on the world’s major radio telescopes.

Initial results from the ALFABURST survey

Here, we present initial results from the ALFABURST radio transient survey, which is currently running in a commensal mode with the ALFA receiver at the Arecibo telescope. We observed for a total of 1400 hours and have detected single pulses from known pulsars but did not detect any FRBs. The non-detection of FRBs is consistent with the current FRB sky rates.

Esophageal histoplasmosis in a renal allograft recipient.

Histoplasmosis is a progressive granulomatous disease caused by the intracellular dimorphic fungus Histoplasma capsulatum. We report a rare case of esophageal histoplasmosis in a renal allograft recipient. A 55-year-old male who received a live, unrelated renal allograft 20 years ago presented with complaints of recurrent fever for ten to 12 months, weight loss over six months, progressive dysphagia more for solids for five to six months and joint pain and swelling involving the bilateral metacarpo-phalangeal and proximal interphalangeal joints. Biopsy from the esophageal ulcers revealed dense inflammation infiltrated with lymphocytes and macrophages with clusters of strongly positive intracellular fungal spores with a clear area or "halo-like" zone suggestive of Histoplasma capsulatum invasion. The patient was treated with intravenous liposomal amphotericin B for ten days and later switched over to oral itraconazole. Repeated endoscopy revealed significant improvement of the lesions.