Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine.

INTRODUCTION: Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients.Current understanding of IBD pathogenesis implicates complex interactions between host genetics and the gut microbiome. Most cohorts studying the gut microbiota to date have been underpowered, examined single treatments and produced heterogeneous results. Lack of cross-treatment comparisons and well-powered independent replication cohorts hampers the ability to infer real-world utility of predictive signatures.IBD-RESPONSE will use multi-omic data to create a predictive tool for treatment response. Future patient benefit may include development of biomarker-based treatment stratification or manipulation of intestinal microbial targets. IBD-RESPONSE and downstream studies have the potential to improve quality of life, reduce patient risk and reduce expenditure on ineffective treatments. METHODS AND ANALYSIS: This prospective, multicentre, observational study will identify and validate a predictive model for response to advanced IBD therapies, incorporating gut microbiome, metabolome, single-cell transcriptome, human genome, dietary and clinical data. 1325 participants commencing advanced therapies will be recruited from ~40 UK sites. Data will be collected at baseline, week 14 and week 54. The primary outcome is week 14 clinical response. Secondary outcomes include clinical remission, loss of response in week 14 responders, corticosteroid-free response/remission, time to treatment escalation and change in patient-reported outcome measures. ETHICS AND DISSEMINATION: Ethical approval was obtained from the Wales Research Ethics Committee 5 (ref: 21/WA/0228). Recruitment is ongoing. Following study completion, results will be submitted for publication in peer-reviewed journals and presented at scientific meetings. Publications will be summarised at www.ibd-response.co.uk. TRIAL REGISTRATION NUMBER: ISRCTN96296121.

Virtual trauma patient simulation design using the McGill Simulation Complexity Score (MSCS): a breakthrough in trauma education.

BACKGROUND: Virtual patient simulations are interactive, computer-based cases. We designed scenarios based on the McGill Simulation Complexity Score (MSCS), a previously described objective complexity score. We aimed to establish validity of the MSCS and introduce a novel learning tool in trauma education at our institution. METHODS: After design of an easy and difficult patient scenario, we randomized medical students and residents to each perform 1 of the 2 scenarios. We conducted a 2-way analysis of variance of training level (medical student, resident) and scenario complexity (easy, difficult) to assess their effects on virtual time, the number of steps taken in the scenario, beneficial and harmful actions, and the ratio of beneficial over harmful actions. RESULTS: Virtual patient scenarios were successfully designed using the MSCS. Twenty-four medical students and 12 residents participated in the easy scenario (MSCS = 3), and 27 medical students and 12 residents did the difficult scenario (MSCS = 18). Though beneficial actions were similar between students and residents, sudents performed more harmful actions, particularly when the scenario was difficult. One virtual patient died in the easy scenario and 3 died in the difficult one (all medical students). Performance varied with level of complexity and there was significant interaction between level of training and number of steps, as well as with number of harmful actions. Decreasing performance with increasing level of complexity, as defined by the MSCS, suggests this score can accurately quantify difficulty. CONCLUSION: We established validity of the MSCS and showed its successful application on virtual patient scenario design.

The McGill Simulation Complexity Score (MSCS): a novel complexity scoring system for simulations in trauma.

BACKGROUND: In medical education, simulation can be defined as an activity in which an individual demonstrates skills, procedures and critical thinking using interactive mannequins in a setting closely resembling the clinical environment. To our knowledge, the complexity of trauma simulations has not previously been assessed. We aimed to develop an objective trauma simulation complexity score and assess its interrater reliability. METHODS: The McGill Simulation Complexity Score (MSCS) was designed to address the need for objective evaluation of the complexity of trauma scenarios. Components of the score reflected the Advanced Trauma Life Support approach to trauma. The score was developed to take into account the severity of trauma injuries and the complexity of their management. We assessed interrater reliability at 5 high-fidelity simulation events. Interrater reliability was calculated using the Pearson correlation coefficient (PCC) and the intraclass correlation coefficient (ICC). RESULTS: The MSCS has 5 categories: airway, breathing, circulation, disability, and extremities or exposure. The scale has 5 levels for each category, from 0 to 4; level increases with complexity, with 0 corresponding to normal or absent. Cases designed to lead to cardiac arrest, regardless of whether or not the trainee has the ability to resuscitate the simulated patient and regardless of the level of each category, are automatically assigned the maximum score. Between 3 and 9 raters used the MSCS to grade the level of complexity of 26 scenarios at the 5 events. The mean MSCS was 10.2 (range 3.0-20.0). Mean PCC and ICC values were both above 0.7 and therefore statistically significant. CONCLUSION: The MSCS for trauma is an innovative scoring system with high interrater reliability.

Penn State equation versus indirect calorimetry for nutritional assessment in patients with traumatic brain injury.

BACKGROUND: Nutritional assessment can be challenging in patients with traumatic brain injury (TBI), and indirect calorimetry may be a more suitable method than predictive equations. We compared the Penn State equation versus the gold standard of indirect calorimetry for the nutritional assessment of patients with TBI, and quantified the difference between nutritional requirements and actual patient intake. METHODS: This single-centre, prospective cohort study included patients with moderate (Glasgow Coma Scale score 9-12) and severe (Glasgow Coma Scale score 3-8) TBI admitted to the Montreal General Hospital intensive care unit (ICU) between June 2018 and March 2019. Penn State equation estimates and indirect calorimetry measurements were collected, and actual intake was drawn from medical records. We compared the 2 assessment methods using a Spearman correlation coefficient. RESULTS: Twenty-three patients with TBI (moderate in 7 and severe in 16) were included in the study. Overall, there was a moderate positive correlation between the Penn State equation estimate and indirect calorimetry readings (correlation coefficient 0.457, p = 0.03); however, the correlation was weaker in severe TBI (correlation coefficient 0.174, p = 0.5) than in moderate TBI (correlation coefficient 0.929, p = 0.003). When compared to indirect calorimetry assessment, patients received 5.4% (p = 0.5) of required intake on the first day and 43.9% (p = 0.8) of required daily intake throughout their ICU stay. CONCLUSION: Patients with moderate or severe TBI in the ICU received less than 50% of their nutritional requirements. The difference between the Penn State equation and indirect calorimetry assessments was most noticeable for patients with severe TBI, which indicates that indirect calorimetry may be a more suitable tool for assessment of nutritional needs in this population.

The genomic landscape of teenage and young adult T-cell acute lymphoblastic leukemia.

BACKGROUND: Treatment on risk adapted intensive pediatric protocols has improved outcome for teenagers and young adults (TYA) with T-cell acute lymphoblastic leukemia (T-ALL). Understanding the biology of disease in this age group and the genetic basis of relapse is a key goal as patients with relapsed/refractory disease have poor outcomes with conventional chemotherapy and novel molecular targets are required. This study examines the question of whether TYA T-ALL has a specific biological-molecular profile distinct from pediatric or adult T-ALL. METHODS: Genomic characterization was undertaken of a retrospective discovery cohort of 80 patients aged 15-26 years with primary or relapsed T-ALL, using a combination of Genome-Wide Human SNP Array 6.0, targeted gene mutation and promoter methylation analyses. Findings were confirmed by MLPA, real-time quantitative PCR, and FISH. Whole Exome Sequencing was performed in 4 patients with matched presentation and relapse to model clonal evolution. A prevalence analysis was performed on a final data set of 1,792 individual cases to identify genetic lesions with age specific frequency patterns, including 972 pediatric (1-14 years), 439 TYA (15-24 years) and 381 adult (≥25 years) cases. These cases were extracted from 19 publications with comparable genomic data identified through a PubMed search. RESULTS: Genomic characterization of this large cohort of TYA T-ALL patients identified recurrent isochromosome 7q i(7q) in our discovery cohort (n = 3). Prevalence analysis did not identify any age specific genetic abnormalities. Genomic analysis of 6 pairs of matched presentation - relapsed T-ALL established that all relapses were clonally related to the initial leukemia. Whole exome sequencing analysis revealed recurrent, targetable, mutations disrupting NOTCH, PI3K/AKT/mTOR, FLT3, NRAS as well as drug metabolism pathways. CONCLUSIONS: All genetic aberrations in TYA T-ALL occurred with an incidence similar or intermediate to that reported in the pediatric and adult literature, demonstrating that overall TYA T-ALL exhibits a transitional genomic profile. Analysis of matched presentation - relapse supported the hypothesis that relapse is driven by the Darwinian evolution of sub-clones associated with drug resistance (NT5C2 and TP53 mutations) and re-iterative mutation of known key T-ALL drivers, including NOTCH1.

KDM5 inhibition offers a novel therapeutic strategy for the treatment of KMT2D mutant lymphomas.

Loss-of-function mutations in KMT2D are a striking feature of germinal center (GC) lymphomas, resulting in decreased histone 3 lysine 4 (H3K4) methylation and altered gene expression. We hypothesized that inhibition of the KDM5 family, which demethylates H3K4me3/me2, would reestablish H3K4 methylation and restore the expression of genes repressed on loss of KMT2D. KDM5 inhibition increased H3K4me3 levels and caused an antiproliferative response in vitro, which was markedly greater in both endogenous and gene-edited KMT2D mutant diffuse large B-cell lymphoma cell lines, whereas tumor growth was inhibited in KMT2D mutant xenografts in vivo. KDM5 inhibition reactivated both KMT2D-dependent and -independent genes, resulting in diminished B-cell signaling and altered expression of B-cell lymphoma 2 (BCL2) family members, including BCL2 itself. KDM5 inhibition may offer an effective therapeutic strategy for ameliorating KMT2D loss-of-function mutations in GC lymphomas.

Identifying risk factors for development of nephrolithiasis in end-stage renal disease patients.

INTRODUCTION: We sought to assess the incidence and risk factors for stone development in patients with end-stage renal disease (ESRD) on hemodialysis (HD). METHODS: Medical records of patients receiving HD between 2007 and 2017 were retrospectively reviewed. Patients who had been on HD for at least three months and had imaging studies (computed tomography [CT] scans or ultrasound [US]) pre- and post-initiation of HD were included. Exclusion criterion was presence of stones pre-HD. De novo stones were defined as renal stones found on followup imaging. Demographics, laboratory data, comorbidities, and dialysis characteristics were compared between non-stone-formers and stone-formers using propensity score matching. RESULTS: A total of 133 patients met the inclusion criteria. Their median age was 68.5 years, median body mass index 28.7 kg/m2, and median dialysis duration 59.5 months. After HD, 14 (10.5%) patients developed de novo stones and their median dialysis-to-stone duration was 23.5 months. When compared with non-stone-formers, stone-formers had significantly lower incidence of hypertension (48.2% vs. 14.3%; p=0.03), lower serum ionized calcium (1.16 vs. 1.07 mmol/L; p=0.01) and magnesium (0.95 vs. 0.81 mmol/L; p=0.01), and significantly higher serum uric acid (281.5 vs. 319.0 µmol/L; p=0.03). Multivariate analysis demonstrated that lower serum ionized calcium (adjusted odds ratio [OR] 0.00001; 95% confidence interval [CI] 0-0.18) and magnesium (adjusted OR 0.0003; 95% CI 0-0.59) were significantly associated with stone-formation. CONCLUSIONS: The incidence of de novo nephrolithiasis in ESRD patients on HD was 10.5%. Increased serum uric acid, decreased serum magnesium and ionized calcium, and absence of hypertension were associated with increased stone-formation in ESRD patients on HD.

Correction: Genomic profiling reveals spatial intra-tumor heterogeneity in follicular lymphoma.

In the original version of this article the authors noted an omission in the author affiliations where the university details: Queen Mary University of London was not included in the original affiliation for the majority of the authors. The correct affiliations are as follows1. Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK3. Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK6. Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK.

The Impact of Intradialytic Pedaling Exercise on Arterial Stiffness: A Pilot Randomized Controlled Trial in a Hemodialysis Population.

OBJECTIVES: Regular exercise is known to reduce arterial stiffness (AS) in hemodialysis patients. However, the impact of a more realistic intradialytic form of exercise, such as pedaling, is unclear. We aimed to examine (i) the effect of intradialytic pedaling exercise on AS over 4 months and (ii) the longer term effect of pedaling on AS 4 months after exercise cessation. METHODS: Patients on stable in-center hemodialysis (3 x/week) were randomly assigned 1:1 to either intradialytic pedaling exercise (EX) or to a control group receiving usual hemodialysis (nonEX) for 4 months. At baseline and 4 months, peripheral and central blood pressure (BP) indices, heart rate (HR), augmentation index HR corrected (AIx75), and carotid-femoral pulse wave velocity (cfPWV) were assessed (applanation tonometry). Measurements were repeated in the EX group 4 months postexercise cessation. RESULTS: As per protocol analysis was completed in 10 EX group participants (58 ± 17 years, body mass index 26 ± 4 kg/m2) and 10 nonEX group participants (53 ± 15 years, body mass index 27 ± 6 kg/m2). Peripheral and central BP was unchanged in both groups. AIx75 was unchanged in the EX group, however, a significant median increase of 3.5% [interquartile range, IQR 1.0, 8.5] was noted in the nonEX group (P = 0.009). We noted a significantly greater absolute decrease in cfPWV in the EX group compared to controls: -1.00 [IQR -1.95, 0.05] vs. 0.20 [IQR -0.10, 0.90] (P = 0.033). Interestingly, the decrease in cfPWV observed in the EX group was partially reversed 4 months after exercise cessation. CONCLUSION: Intradialytic pedaling exercise has a beneficial impact on AS. This relationship warrants further investigation. CLINICAL TRIALS REGISTRATION: Trial Number #NCT03027778 (clinicaltrials.gov).

TNFRSF14 aberrations in follicular lymphoma increase clinically significant allogeneic T-cell responses.

Donor T-cell immune responses can eradicate lymphomas after allogeneic hematopoietic stem cell transplantation (AHSCT), but can also damage healthy tissues resulting in harmful graft-versus-host disease (GVHD). Next-generation sequencing has recently identified many new genetic lesions in follicular lymphoma (FL). One such gene, tumor necrosis factor receptor superfamily 14 (TNFRSF14), abnormal in 40% of FL patients, encodes the herpes virus entry mediator (HVEM) which limits T-cell activation via ligation of the B- and T-lymphocyte attenuator. As lymphoma B cells can act as antigen-presenting cells, we hypothesized that TNFRSF14 aberrations that reduce HVEM expression could alter the capacity of FL B cells to stimulate allogeneic T-cell responses and impact the outcome of AHSCT. In an in vitro model of alloreactivity, human lymphoma B cells with TNFRSF14 aberrations had reduced HVEM expression and greater alloantigen-presenting capacity than wild-type lymphoma B cells. The increased immune-stimulatory capacity of lymphoma B cells with TNFRSF14 aberrations had clinical relevance, associating with higher incidence of acute GVHD in patients undergoing AHSCT. FL patients with TNFRSF14 aberrations may benefit from more aggressive immunosuppression to reduce harmful GVHD after transplantation. Importantly, this study is the first to demonstrate the impact of an acquired genetic lesion on the capacity of tumor cells to stimulate allogeneic T-cell immune responses which may have wider consequences for adoptive immunotherapy strategies.

Outcomes of post-cardiac surgery patients with persistent hyperlactatemia in the intensive care unit: a matched cohort study.

BACKGROUND: Higher morbidity and mortality rates are seen amongst patients presenting with hyperlactatemia in the postoperative period. The purpose of this study was to determine the relationship between persistent elevations in lactate and poor ICU outcome in post-cardiac surgery patients. METHODS: This was a retrospective matched cohort analysis of cardiac surgery patients undergoing bypass and/or valve surgery in a university hospital centre. Selection criteria were: cardiac bypass and/or valve surgery; admission to the ICU for > 24 h postoperatively; and peak lactate ≥ 3.0 mmol/L. Hyperlactatemic patients were matched to 2 normolactatemic patients. Multivariable conditional logistic regression was used to determine predictors of hyperlactatemia and mortality. RESULTS: Four hundred sixty-nine post-cardiac surgery patients were admitted to the ICU for > 24 h. 144 of these patients had an arterial blood lactate ≥ 3.0 mmol/L. Amongst the mortalities, 78.9 % presented with hyperlactatemia. Independent risk factors predictive of a lactate ≥ 3.0 mmol/L were preoperative IABP insertion (RR 2.8, CI 1.1-7.2) and postoperative acute kidney injury (RR 3.2, CI 2.1-5.4). Patients whose lactate concentrations continued to increase >30 h postoperatively were more likely to die (RR 8.44 CI 2.50-28.53). CONCLUSIONS: The persistence of hyperlactatemia is a more important determinant of postoperative outcome than the absolute value of the peak lactate concentration. A simple postoperative lactate washout does not sufficiently explain this lactate accumulation. Mortality is proposed to be secondary to a state of ongoing hypoperfusion.

Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma.

Follicular lymphoma is an incurable B cell malignancy characterized by the t(14;18) translocation and mutations affecting the epigenome. Although frequent gene mutations in key signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlaps with that in the closely related diffuse large B cell lymphoma (DLBCL). Using a combination of discovery exome and extended targeted sequencing, we identified recurrent somatic mutations in RRAGC uniquely enriched in patients with follicular lymphoma (17%). More than half of the mutations preferentially co-occurred with mutations in ATP6V1B2 and ATP6AP1, which encode components of the vacuolar H(+)-ATP ATPase (V-ATPase) known to be necessary for amino acid-induced activation of mTORC1. The RagC variants increased raptor binding while rendering mTORC1 signaling resistant to amino acid deprivation. The activating nature of the RRAGC mutations, their existence in the dominant clone and their stability during disease progression support their potential as an excellent candidate for therapeutic targeting.

Renoprotective effects of continuous positive airway pressure in chronic kidney disease patients with sleep apnea.

PURPOSE: Chronic kidney disease (CKD) is associated with a high incidence of obstructive sleep apnea (OSA). We assessed the effect of continuous positive airway pressure (CPAP) on renal function in patients with CKD and OSA. METHODS: In this retrospective cohort study, 42 patients with Stage 3-5 CKD and OSA were stratified into two groups: patients who use CPAP more (average >4 h/night on >70 % of nights) and patients who use CPAP less (average ≤4 h/night on ≤70 % of nights). Median follow-up time was 2.3 (1.6-2.9) years for greater and 2.0 (0.6-3.5) years for lesser CPAP users. Chart reviews were carried out to record clinical characteristics, proteinuria measurements by urine dipstick, and eGFR values calculated by CKD-EPI equations. Univariate analyses were performed using Wilcoxon rank-sum and Kruskal-Wallis tests. Multivariate logistic regression models were applied to assess eGFR decline after CPAP prescription. RESULTS: Twelve (29 %) of the 42 subjects used CPAP more. Groups were similar with respect to age, body mass index, blood pressure, Charlson Comorbidity Index, and baseline eGFR and proteinuria. The median rate of decline of eGFR was significantly slower at -0.07 mL/min/1.73 m(2)/year (range -30 to 13) in those who used more CPAP compared to those who used it less at -3.15 mL/min/1.73 m(2)/year (range -27 to 7) (p = 0.027).Greater use of CPAP was also associated with a significantly reduced level of proteinuria at 0.15 (range 0.0-3.0) versus 0.70 g/L (range 0.0-3.0) (p = 0.046). Less compliant CPAP users were more likely to have progressive decline of eGFR (decline >3 mL/min/1.73 m(2)/year), with unadjusted OR 5.0 (95 % CI 0.93-26.8) and adjusted OR 8.9 (95 % CI 1.1-72.8), adjusting for CCI and baseline eGFR. CONCLUSIONS: Compliance to CPAP therapy is associated with a slower rate of progression of CKD in patients with CKD and OSA.

High Throughput Sequencing Analysis of the Immunoglobulin Heavy Chain Gene from Flow-Sorted B Cell Sub-Populations Define the Dynamics of Follicular Lymphoma Clonal Evolution.

Understanding the dynamics of evolution of Follicular Lymphoma (FL) clones during disease progression is important for monitoring and targeting this tumor effectively. Genetic profiling of serial FL biopsies and examples of FL transmission following bone marrow transplant suggest that this disease may evolve by divergent evolution from a common ancestor cell. However where this ancestor cell resides and how it evolves is still unclear. The analysis of the pattern of somatic hypermutation of the immunoglobulin gene (Ig) is traditionally used for tracking the physiological clonal evolution of B cells within the germinal center and allows to discriminate those cells that have just entered the germinal center and display features of ancestor cells from those B cells that keep re-circulating across different lymphoid organs. Here we investigated the pattern of somatic hypermutation of the heavy chain of the immunoglobulin gene (IgH-VH) in 4 flow-sorted B cells subpopulations belonging to different stages of differentiation, from sequential lymph node biopsies of cases displaying diverse patterns of evolution, using the GS-FLX Titanium sequencing platform. We observed an unexpectedly high level of clonality, with hundreds of distinct tumor subclones in the different subpopulations from the same sample, the majority detected at a frequency <10-2. By using a lineage trees analysis we observed in all our FL and t-FL cases that the oligoclonal FL population was trapped in a narrow intermediate stage of maturation that maintains the capacity to undergo SHM, but was unable to further differentiate. The presence of such a complex architecture highlights challenges currently encountered in finding a cure for this disease.

Disease evolution and outcomes in familial AML with germline CEBPA mutations.

In-depth molecular investigation of familial leukemia has been limited by the rarity of recognized cases. This study examines the genetic events initiating leukemia and details the clinical progression of disease across multiple families harboring germ-line CEBPA mutations. Clinical data were collected from 10 CEBPA-mutated families, representing 24 members with acute myeloid leukemia (AML). Whole-exome (WES) and deep sequencing were performed to genetically profile tumors and define patterns of clonal evolution. Germline CEBPA mutations clustered within the N-terminal and were highly penetrant, with AML presenting at a median age of 24.5 years (range, 1.75-46 years). In all diagnostic tumors tested (n = 18), double CEBPA mutations (CEBPAdm) were detected, with acquired (somatic) mutations preferentially targeting the C-terminal. Somatic CEBPA mutations were unstable throughout the disease course, with different mutations identified at recurrence. Deep sequencing of diagnostic and relapse paired samples confirmed that relapse-associated CEBPA mutations were absent at diagnosis, suggesting recurrence was triggered by novel, independent clones. Integrated WES and deep sequencing subsequently revealed an entirely new complement of mutations at relapse, verifying the presentation of a de novo leukemic episode. The cumulative incidence of relapse in familial AML was 56% at 10 years (n = 11), and 3 patients experienced ≥3 disease episodes over a period of 17 to 20 years. Durable responses to secondary therapies were observed, with prolonged median survival after relapse (8 years) and long-term overall survival (10-year overall survival, 67%). Our data reveal that familial CEBPA-mutated AML exhibits a unique model of disease progression, associated with favorable long-term outcomes.