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A computational pipeline for spatial mechano-transcriptomics.
Advances in spatial profiling technologies are providing insights into how molecular programs are influenced by local signaling and environmental cues. However, cell fate specification and tissue patterning involve the interplay of biochemical and mechanical feedback. Here we develop a computational framework that enables the joint statistical analysis of transcriptional and mechanical signals in the context of spatial transcriptomics. To illustrate the application and utility of the approach, we use spatial transcriptomics data from the developing mouse embryo to infer the forces acting on individual cells, and use these results to identify mechanical, morphometric and gene expression signatures that are predictive of tissue compartment boundaries. In addition, we use geoadditive structural equation modeling to identify gene modules that predict the mechanical behavior of cells in an unbiased manner. This computational framework is easily generalized to other spatial profiling contexts, providing a generic scheme for exploring the interplay of biomolecular and mechanical cues in tissues.
Clinical predictors of flare and drug-free remission in rheumatoid arthritis: preliminary results from the prospective BIO-FLARE experimental medicine study.
OBJECTIVES: Huge advances in rheumatoid arthritis (RA) treatment mean an increasing number of patients now achieve disease remission. However, long-term treatments can carry side effects and associated financial costs. In addition, some patients still experience painful and debilitating disease flares, the mechanisms of which are poorly understood. High rates of flare and a lack of effective prediction tools can limit attempts at treatment withdrawal. The BIOlogical Factors that Limit sustAined Remission in rhEumatoid arthritis (BIO-FLARE) experimental medicine study was designed to study flare and remission immunobiology. Here, we present the clinical outcomes and predictors of drug-free remission and flare, and develop a prediction model to estimate flare risk. DESIGN, SETTING AND PARTICIPANTS: BIO-FLARE was a multicentre, prospective, single-arm, open-label experimental medicine study conducted across seven National Health Service Trusts in the UK. Participants had established RA in clinical remission (disease activity score in 28 joints with C reactive protein (DAS28-CRP)<2.4) and were receiving methotrexate, sulfasalazine or hydroxychloroquine (monotherapy or combination). INTERVENTIONS: The intervention was disease-modifying anti-rheumatic drug cessation, followed by observation for 24 weeks or until flare, with clinical and immune monitoring. OUTCOME MEASURES: The primary outcome measure was the proportion of participants experiencing a confirmed flare, defined as DAS28-CRP≥3.2 or DAS28-CRP≥2.4 twice within 2 weeks, and time to flare. Exploratory predictive modelling was also performed using multivariable Cox regression to understand risk factors for flare. RESULTS: 121 participants were recruited between September 2018 and December 2020. Flare rate by week 24 was 52.3% (95% CI 43.0 to 61.7), with a median (IQR) time to flare of 63 (41-96) days. Female sex, baseline methotrexate use, anti-citrullinated peptide antibody level and rheumatoid factor level were associated with flare. An exploratory prediction model incorporating these variables allowed estimation of flare risk, with acceptable classification (C index 0.709) and good calibration performance. CONCLUSION: The rate of flare was approximately 50%. Several baseline clinical parameters were associated with flare. The BIO-FLARE study design provides a robust experimental medicine model for studying flare and remission immunobiology. TRIAL REGISTRATION NUMBER: ISRCTN registry 16371380.
Permissive central tolerance plus defective peripheral checkpoints license pathogenic memory B cells in CASPR2-antibody encephalitis.
Autoantibody-mediated diseases targeting one autoantigen provide a unique opportunity to comprehensively understand the development of disease-causing B cells and autoantibodies. Convention suggests that such autoreactivities are generated during germinal center reactions. Here, we explore earlier immune checkpoints, focusing on patients with contactin-associated protein-like 2 (CASPR2)-autoantibody encephalitis. In both disease and health, high (~0.5%) frequencies of unmutated CASPR2-reactive naïve B cells were identified. By contrast, CASPR2-reactive memory B cells were exclusive to patients, and their B cell receptors demonstrated affinity-enhancing somatic mutations with pathogenic effects in neuronal cultures and mice. The unmutated, precursor memory B cell receptors showed a distinctive balance between strong CASPR2 reactivity and very limited binding across the remaining human proteome. Our results identify permissive central tolerance, defective peripheral tolerance, and autoantigen-specific tolerance thresholds in humans as sequential steps that license CASPR2-directed pathology. By leveraging the basic immunobiology, we rationally direct tolerance-restoring approaches, with an experimental paradigm applicable across autoimmunity.
Biallelic PI4KA variants cause neurological, intestinal and immunological disease.
Phosphatidylinositol 4-kinase IIIα (PI4KIIIα/PI4KA/OMIM:600286) is a lipid kinase generating phosphatidylinositol 4-phosphate (PI4P), a membrane phospholipid with critical roles in the physiology of multiple cell types. PI4KIIIα's role in PI4P generation requires its assembly into a heterotetrameric complex with EFR3, TTC7 and FAM126. Sequence alterations in two of these molecular partners, TTC7 (encoded by TTC7A or TCC7B) and FAM126, have been associated with a heterogeneous group of either neurological (FAM126A) or intestinal and immunological (TTC7A) conditions. Here we show that biallelic PI4KA sequence alterations in humans are associated with neurological disease, in particular hypomyelinating leukodystrophy. In addition, affected individuals may present with inflammatory bowel disease, multiple intestinal atresia and combined immunodeficiency. Our cellular, biochemical and structural modelling studies indicate that PI4KA-associated phenotypical outcomes probably stem from impairment of PI4KIIIα-TTC7-FAM126's organ-specific functions, due to defective catalytic activity or altered intra-complex functional interactions. Together, these data define PI4KA gene alteration as a cause of a variable phenotypical spectrum and provide fundamental new insight into the combinatorial biology of the PI4KIIIα-FAM126-TTC7-EFR3 molecular complex.
Multiomic features associated with mucosal healing and inflammation in paediatric Crohn’s disease
SummaryBackgroundThe gastrointestinal microbiota has an important role in mucosal immune homoeostasis and may contribute to maintaining mucosal healing in Crohn's disease (CD).AimTo identify changes in the microbiota, metabolome and protease activity associated with mucosal healing in established paediatric CDMethodsTwenty‐five participants aged 3‐18 years with CD, disease duration of over 6 months, and maintenance treatment with biological therapy were recruited. They were divided into a low calprotectin group (faecal calprotectin <100 μg/g, “mucosal healing,” n = 11), and a high calprotectin group (faecal calprotectin >100 μg/g, “mucosal inflammation,” n = 11). 16S gene‐based metataxonomics, 1H‐NMR spectroscopy‐based metabolic profiling and protease activity assays were performed on stool samples.ResultsRelative abundance of Dialister species was six‐times greater in the low calprotectin group (q = 0.00999). Alpha and beta diversity, total protease activity and inferred metagenomic profiles did not differ between groups. Pentanoate (valerate) and lysine were principal discriminators in a machine‐learning model which differentiated high and low calprotectin samples using NMR spectra (R2 0.87, Q2 0.41). Mean relative concentration of pentanoate was 1.35‐times greater in the low calprotectin group (95% CI 1.03‐1.68, P = 0.036) and was positively correlated with Dialister. Mean relative concentration of lysine was 1.54‐times greater in the high calprotectin group (95% CI 1.05‐2.03, P = 0.028).ConclusionsThis multiomic study identified an increase in Dialister species and pentanoate, and a decrease in lysine, in patients with “mucosal healing.” It supports further investigation of these as potential novel therapeutic targets in CD.
The Role of PTEN in Innate and Adaptive Immunity.
The lipid and protein phosphatase and tensin homolog (PTEN) controls the differentiation and activation of multiple immune cells. PTEN acts downstream from T- and B-cell receptors, costimulatory molecules, cytokine receptors, integrins, and also growth factor receptors. Loss of PTEN activity in human and mice is associated with cellular and humoral immune dysfunction, lymphoid hyperplasia, and autoimmunity. Although most patients with PTEN hamartoma tumor syndrome (PHTS) have no immunological symptoms, a subclinical immune dysfunction is present in many, and clinical immunodeficiency in few. Comparison of the immune phenotype caused by PTEN haploinsufficiency in PHTS, phosphoinositide 3-kinase (PI3K) gain-of-function in activated PI3K syndrome, and mice with conditional biallelic Pten deletion suggests a threshold model in which coordinated activity of several phosphatases control the PI3K signaling in a cell-type-specific manner. Emerging evidence highlights the role of PTEN in polygenic autoimmune disorders, infection, and the immunological response to cancer. Targeting the PI3K axis is an emerging therapeutic avenue.
A systematic review of sudden unexpected death in epilepsy (SUDEP) in childhood.
BACKGROUND: Sudden Unexpected Death in Epilepsy (SUDEP) is a significant cause of death in childhood epilepsy, and causes considerable concern to patients and their families. Despite this, the condition remains poorly understood. This systematic review investigates the risk factors, pathophysiology, and circumstances associated with childhood SUDEP. It aimed to explore the etiology of SUDEP and inform clinicians approaching SUDEP risk disclosure. METHODS: A structured electronic database search of MEDLINE, CENTRAL, EMBASE, and ISI web of science was conducted. Studies were included if they described clinical details of one or more patients, aged 18 years of age and below, who had SUDEP. Two reviewers independently reviewed each article for data extraction and quality assessment. RESULTS: Information on 108 cases of pediatric SUDEP was extracted from 22 included studies. These comprised five cohort studies, four retrospective case control studies, seven case series, and five case reports. Factors that appeared to be linked to pediatric SUDEP included those associated with severe epilepsy (early age of onset, high seizure frequency, intellectual impairment and developmental delay, multiple antiepileptic drug therapy, and structural abnormalities). The majority of included studies was noncomparative and had significant risk of bias. CONCLUSIONS: There is currently insufficient evidence to determine the etiology of pediatric SUDEP. Current best practice to prevent pediatric SUDEP is to optimize the management of epilepsy. A national SUDEP registry would provide invaluable high-quality data and insights into modifiable risk factors, genetic predispositions, and novel prevention strategies.
Neonatal outcomes of waterbirth: a systematic review and meta-analysis.
INTRODUCTION: In 2015, 9% of babies born in the UK were delivered underwater. Waterbirth is increasing in popularity, despite uncertainty regarding its safety for neonates. This systematic review and meta-analysis appraises the existing evidence for neonatal outcomes following waterbirth. METHODS: A structured electronic database search was performed with no language restrictions. All comparative studies which reported neonatal outcomes following waterbirth, and that were published since 1995, were included. Quality appraisal was performed using a modified Critical Appraisal Skills Programme scoring system. The primary outcome was neonatal mortality. Data for each neonatal outcome were tabulated and analysed. Meta-analysis was performed for comparable studies which reported sufficient data. RESULTS: The majority of the 29 included studies were small, with limited follow-up and methodological flaws. They were mostly conducted in Europe and high-income countries. Reporting of data was heterogeneous. No significant difference in neonatal mortality, neonatal intensive care unit/special care baby unit admission rate, Apgar scores, umbilical cord gases or infection rates was found between babies delivered into water and on land. CONCLUSIONS: This systematic review and meta-analysis did not identify definitive evidence that waterbirth causes harm to neonates compared with land birth. However, there is currently insufficient evidence to conclude that there are no additional risks or benefits for neonates when comparing waterbirth and conventional delivery on land.
Concurrent perforated Meckel's diverticulum and intestinal malrotation in an 8-year-old boy.
An 8-year-old boy with a history of recurrent abdominal pain presented with a 12 h history of severe periumbilical pain, nausea and vomiting. On examination, he was found to have a tender, erythematous, paraumbilical mass. At operative exploration, an abscess cavity was identified and followed to reveal a gangrenous Meckel's diverticulum, perforated at its tip to create the abscess. Around this Meckel's diverticulum, the small bowel had torted to produce a significant small bowel volvulus on a shortened mesentery. The caecum and ascending colon were found to be in the left upper quadrant and an intraoperative diagnosis of malrotation was made. Following resection of the Meckel's diverticulum and surgical correction of the malrotation, the child made an excellent recovery. His abdominal pain has not recurred in 6 months of follow-up since the operation.
Validity of self-reported hysterectomy: a prospective cohort study within the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS).
OBJECTIVE: To evaluate the validity of self-reported hysterectomy against the gold standard of uterine visualisation using pelvic ultrasound. DESIGN: Prospective cohort study. SETTING: UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) based in 13 National Health Service (NHS) Trusts in England, Wales and Northern Ireland. PARTICIPANTS: Between April 2001 and October 2005, 48 215 postmenopausal women aged 50-74 randomised to the ultrasound screening arm of UKCTOCS underwent the first (initial) scan on the trial. INTERVENTIONS: At recruitment, the women completed a recruitment questionnaire (RQ) which included previous hysterectomy. The sonographer asked each woman regarding previous hysterectomy (interview format, IF) prior to the scan. At the scan, in addition to ovarian morphology, endometrial thickness (ET)/endometrial abnormality were captured if the uterus was visualised at the scan. OUTCOME MEASURES: Self-reported hysterectomy at RQ or IF was compared to ultrasound data on ET/endometrial abnormality (as surrogate uterine visualisation markers) on the first (initial) scan. RESULTS: Of 48 215 women, 3 had congenital uterine agenesis and 218 inconclusive results. The uterus was visualised in 39 121 women. 8871 self-reported hysterectomy at RQ, 8641 at IF and 8487 at both. The uterus was visualised in 39 123, 39 353 and 38 969 women not self-reporting hysterectomy at RQ, IF or both. Validity, sensitivity, specificity, positive predictive value and negative predictive value of using RQ alone, IF or both RQ/IF were 99.6%, 98.9%, 99.7%, 98.9% and 99.7%; 98.9%, 98.4%, 99.1%, 95.9% and 99.7%; 99.8%, 99.6%, 99.9%, 99.4% and 99.9%, respectively. CONCLUSIONS: Self-reported hysterectomy is a highly accurate and valid source for studying long-term associations of hysterectomy with disease onset. TRIAL REGISTRATION: International Standard Randomised Controlled Trial Number (ISRCTN)-22488978.
Animal models of intestinal inflammation: clues to the pathogenesis of inflammatory bowel disease
In the last decade a number of models of chronic intestinal inflammation have been described that resemble aspects of the pathology found in patients with inflammatory bowel disease. Several themes have emerged from these studies that are of relevance to the pathogenesis of inflammatory bowel disease. Firstly, intestinal inflammation is a consequence of an aberrant chronic immune response triggered by enteric bacteria. Both innate and adaptive immune mechanisms can cause colitis and in many models there is evidence of differential activation of T helper 1 (Th1)-type cells. Targeting the Th1 pathway prevents experimental colitis and there is also evidence that this may be useful in Crohn's disease. Secondly, specialized populations of regulatory T cells have been shown to prevent colitis and in some systems cure it, suggesting immune responses in the intestine are subject to dominant T cell-mediated control. Here we focus on new insights into the pathogenesis and regulation of intestinal inflammation as revealed by model systems and how these may be harnessed for the treatment of IBD.
Homing of intestinal immune cells
The homing of immune cells into the intestinal mucosa, the gut-associated lymphoid tissue or the mesenteric lymph nodes involves a complex process of molecular events that is dependent on cell type and cell maturation. Key factors that collectively determine the homing of leukocytes and their interaction with resident endothelial, epithelial, stromal and immune cells are interactions between integrins or selectins with their tissue adhesion molecules as well as chemokine receptors and their ligands. The organization of the small and large intestinal tissue and the mucosa associated lymphoid tissue as well as the presence or absence of inflammatory stimuli influence the homing of intestinal immune cells. The homing pattern of intestinal dendritic cells and CD4+ T cells and its role for the pathogenesis and regulation of inflammatory bowel disease are discussed.