Supervised learning of enhancer-promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning.

MOTIVATION: Understanding the rules that govern enhancer-driven transcription remains a central unsolved problem in genomics. Now with multiple massively parallel enhancer perturbation assays published, there are enough data that we can utilize to learn to predict enhancer-promoter (EP) relationships in a data-driven manner. RESULTS: We applied machine learning to one of the largest enhancer perturbation studies integrated with transcription factor (TF) and histone modification ChIP-seq. The results uncovered a discrepancy in the prediction of genome-wide data compared to data from targeted experiments. Relative strength of contact was important for prediction, confirming the basic principle of EP regulation. Novel features such as the density of the enhancers/promoters in the genomic region was found to be important, highlighting our lack of understanding on how other elements in the region contribute to the regulation. Several TF peaks were identified that improved the prediction by identifying the negatives and reducing False Positives. In summary, integrating genomic assays with enhancer perturbation studies increased the accuracy of the model, and provided novel insights into the understanding of enhancer-driven transcription. AVAILABILITY AND IMPLEMENTATION: The trained models, data, and the source code are available at http://doi.org/10.5281/zenodo.11290386 and https://github.com/HanLabUNLV/sleps.

Gilteritinib clinical activity in relapsed/refractory FLT3 mutated acute myeloid leukemia previously treated with FLT3 inhibitors.

Gilteritinib is approved for the treatment of relapsed/refractory (R/R) acute myeloid leukemia (AML) with an FLT3-mutation (FLT3mut+ ). However, the gilteritinib phase 3 ADMIRAL study (Perl et al NEJM 2019) was conducted prior to widespread adoption of either midostaurin as a component of standard intensive induction and consolidation or posttransplant FLT3 inhibitor maintenance. We performed a retrospective analysis using data from 11 US centers and where we identified 113 patients who received gilteritinib alone or as combination therapy for the treatment of R/R FLT3mut+ AML. The composite complete remission (CR) rate (CRc, defined as CR + CRi + CR with incomplete platelet recovery [CRp]) was 48.7% (n = 55). The CRc rate after treatment with gilteritinib in patients who were treated with only prior 7+3 and midostaurin with or without consolidation was 58% with a median survival of 7.8 months. Survival was longest in patients who obtained a CR, particularly a cMRD (clinical minimal or measurable residual disease) negative response; this remained significant after censoring at the time of stem cell transplant. The mitogen-activated protein kinase pathway activating mutations that are known for gilteritinib resistance (NRAS, KRAS, and PTPN11) had lower CRc (35% vs. 60.5%) and lower median overall survival than patients' whose leukemia did not express these mutations (4.9 months vs. 7.8 months) (HR 2.4; 95% CI 1. 5.4) p value <.01.

Linezolid and fentanyl: An underrecognized drug-to-drug interaction.

WHAT IS KNOWN AND OBJECTIVE: Despite its frequent use in clinical practice, fentanyl's pro-serotonergic effects are underrecognized, especially in combination with linezolid. Life-threatening reactions can occur. CASE SUMMARY: We report a case of serotonin syndrome developed shortly after the initiation of linezolid in a 63-year-old patient in whom selective serotonin reuptake inhibitor therapy was discontinued for the duration of antibiotic therapy. However, fentanyl transdermal patch treatment was inadvertently continued. Noteworthy, 24 hours following discontinuation of linezolid, the patient experienced complete resolution of symptoms. WHAT IS NEW AND CONCLUSION: Fentanyl can increase the intrasynaptic release of serotonin through their effects on y-amino butyric acid and its phenylpiperidine chemical structure. We illustrate the importance of thorough medication reconciliation and review of all potential drug-to-drug interactions when indicating linezolid therapy to ensure patient safety. We believe that our case provides novel observations and insight that could help recognize similar cases in clinical practice.

Effect of distance to health facility on the maintenance of INR therapeutic ranges in rheumatic heart disease patients from Cape Town: no evidence for an association.

BACKGROUND: Lack of adherence to international normalised ratio (INR) monitoring in rheumatic heart disease (RHD) patients is a contributor to cardio-embolic complications. This population-based observational study investigated whether the distance between home and an INR clinic affects the maintenance of therapeutic INR in RHD patients on warfarin. METHODS: Residential addresses, INR clinics, and INR results of patients with RHD were extracted from the Cape Town component of the Global Rheumatic Heart Disease Registry (REMEDY) database. Addresses of homes and INR clinics were converted to geographical coordinates and verified in ArcGIS 10®. ArcGIS 10® and Google Maps® were used for spatial mapping and obtaining shortest road distances respectively. The travel distance between the home and INR clinic was correlated with time within therapeutic range (TTR) using the Rosendaal linear interpolation method, and with the fraction of INR within range, based on an average of three INR readings of patients and compared with recommended therapeutic ranges. RESULTS: RHD patients (n = 133) resided between 0.2 km and 50.8 km (median distance, 3.60 km) from one of 33 INR clinics. There was no significant difference in the achievement of the therapeutic INR between patients who travelled a shorter distance compared to those who travelled a longer distance (in range = 3.50 km versus out of range = 3.75 km, p = 0.78). This finding was the same for patients with mechanical valve replacement (n = 105) (3.50 km versus 3.90 km, p = 0.81), and native valves (3.45 km versus 2.75 km, p = 0.84). CONCLUSIONS: There is no association between the maintenance of INR within therapeutic range amongst RHD patients in Cape Town and distance from patients' residence to the INR clinic.

Genome wide clustering on integrated chromatin states and Micro-C contacts reveals chromatin interaction signatures.

We can now analyze 3D physical interactions of chromatin regions with chromatin conformation capture technologies, in addition to the 1D chromatin state annotations, but methods to integrate this information are lacking. We propose a method to integrate the chromatin state of interacting regions into a vector representation through the contact-weighted sum of chromatin states. Unsupervised clustering on integrated chromatin states and Micro-C contacts reveals common patterns of chromatin interaction signatures. This provides an integrated view of the complex dynamics of concurrent change occurring in chromatin state and in chromatin interaction, adding another layer of annotation beyond chromatin state or Hi-C contact separately.

A pilot study to develop assessment tools for Group A Streptococcus surveillance studies.

Introduction: Group A Streptococcus (GAS) causes pharyngitis (sore throat) and impetigo (skin sores) GAS pharyngitis triggers rheumatic fever (RF) with epidemiological evidence supporting that GAS impetigo may also trigger RF in Australian Aboriginal children. Understanding the concurrent burden of these superficial GAS infections is critical to RF prevention. This pilot study aimed to trial tools for concurrent surveillance of sore throats and skins sore for contemporary studies of RF pathogenesis including development of a sore throat checklist for Aboriginal families and pharynx photography. Methods: Yarning circle conversations and semi-structured interviews were performed with Aboriginal caregivers and used to develop the language and composition of a sore throat checklist. The sore throat story checklist was combined with established methods of GAS pharyngitis and impetigo surveillance (examination, bacteriological culture, rapid antigen detection and serological tests) and new technologies (photography) and used for a pilot cross-sectional surveillance study of Aboriginal children attending their health clinic for a routine appointment. Feasibility, acceptability, and study costs were compiled. Results: Ten Aboriginal caregivers participated in the sore-throat yarning circles; a checklist was derived from predominant symptoms and their common descriptors. Over two days, 21 Aboriginal children were approached for the pilot surveillance study, of whom 17 were recruited; median age was 9 years [IQR 5.5-13.5], 65% were female. One child declined throat swabbing and three declined finger pricks; all other surveillance elements were completed by each child indicating high acceptability of surveillance assessments. Mean time for screening assessment was 19 minutes per child. Transport of clinical specimens enabled gold standard microbiological and serological testing for GAS. Retrospective examination of sore throat photography concorded with assessments performed on the day. Conclusion: Yarning circle conversations were effective in deriving culturally appropriate sore throat questionnaires for GAS pharyngitis surveillance. New and established tools were feasible, practical and acceptable to participants and enable surveillance to determine the burden of superficial GAS infections in communities at high risk of RF. Surveillance of GAS pharyngitis and impetgio in remote Australia informs primary RF prevention with potential global translation.

Multicenter evaluation of the addition of eltrombopag to immunosuppressive therapy for adults with severe aplastic anemia.

Eltrombopag has been shown to improve response rates when added to standard therapy in adults with severe aplastic anemia in controlled trial settings. However, outcomes in real-world populations have mostly been examined in small retrospective studies. This robust, multicenter, retrospective cohort study across six academic health systems compared outcomes in patients who received immunosuppressive therapy with or without eltrombopag. The study included 82 patients who received front-line therapy from January 2014 to August 2021. Overall response rates at 6 months did not differ significantly for patients receiving eltrombopag versus immunosuppressive therapy alone (58% v. 65%, p = 0.56). However, complete response rates at 6 and 12 months were over two times higher in the eltrombopag arm (29% v. 12%, p = 0.06 and 48% v. 18%, p = 0.005). Rates of hepatotoxicity were similar across both arms. Eltrombopag addition did not impact overall survival (median not reached in either arm at 2 years, p = 0.86) or disease-free survival (median not reached v. 13.3 months at 2 years, p = 0.20). Eltrombopag may not produce as large of a benefit in real-world settings compared to controlled trial settings but may offer patients deeper responses with similar rates of toxicity to immunosuppressive therapy alone.

Age Adjusted Comorbidity Risk Index Does Not Predict Outcomes in an Autologous Hematopoietic Stem Cell Transplant Population.

The hematopoietic comorbidity risk index (HCT-CI) is a pre-transplant risk assessment tool used to prognosticate morbidity and mortality of patients undergoing allogeneic hematopoietic stem cell transplantation. Recently, the HCT-CI was updated to include an age component (HCT-CI-age). Although other studies have validated this tool in allogeneic stem cell transplant recipients, it has never been studied in an autologous transplant patient population. We retrospectively reviewed 181 patients who underwent their first autologous hematopoietic stem cell transplant. We aimed (1) to assess whether an HCT-CI score of 3 or greater is associated with greater mean transplant hospital days, greater total hospital days, or greater risk of intensive care unit (ICU) utilization and (2) whether age influences any of these responses independent of HCT-CI. There were 136 patients with an HCT-CI score of 3 or higher and 45 with a score less than 3. The length of initial transplant hospitalization in days was not statistically significant (15.6 v 16.4 days, P = 0.38). Utilizing spline modeling prediction curves, transplant hospital days were estimated to increase from a mean of 15.5 days for a patient with 4 comorbidities to a mean of 22.7 days for a patient with 8 comorbidities. Age made no significant impact on any of the outcomes. The HCT-CI, with or without age, in an autologous stem cell transplantation did not predict length of hospitalization or utilization of the ICU. Patients with higher-HCT-CI scores at baseline may incrementally utilize more resources, and this should be explored in a larger cohort population.

Use of Cystatin C to Assess Immunotherapy Toxicity in a Patient With Melanoma.

The advent of immunotherapy has improved outcomes of patients in a number of cancers.1 While immunotherapy helps the immune system recognize malignant cells, it also can lead to adverse effects that mimic autoimmune diseases including, but not limited to, rash, colitis, pneumonitis, and nephritis. Diagnosis of immunotherapy related nephritis is based on serum creatinine trends, which can be falsely elevated in the setting of high muscle mass. Cystatin C is an adjunctive kidney biomarker that can estimate glomerular filtration rate independent of muscle mass. We present a case where the use of cystatin C avoided unnecessary therapy interruption in a young, athletic man being treated with nivolumab for melanoma. Further research is needed to define the role cystatin C in monitoring kidney function during immunotherapy.

Missing Piece Study protocol: prospective surveillance to determine the epidemiology of group A streptococcal pharyngitis and impetigo in remote Western Australia.

INTRODUCTION: Group A ß-haemolytic Streptococcus (GAS), a Gram-positive bacterium, causes skin, mucosal and systemic infections. Repeated GAS infections can lead to autoimmune diseases acute rheumatic fever (ARF) and rheumatic heart disease (RHD). Aboriginal and Torres Strait Islander peoples in Australia have the highest rates of ARF and RHD in the world. Despite this, the contemporaneous prevalence and incidence of GAS pharyngitis and impetigo in remote Australia remains unknown. To address this, we have designed a prospective surveillance study of GAS pharyngitis and impetigo to collect coincident contemporary evidence to inform and enhance primary prevention strategies for ARF. METHODS AND ANALYSIS: The Missing Piece Study aims to document the epidemiology of GAS pharyngitis and impetigo through collection of clinical, serological, microbiological and bacterial genomic data among remote-living Australian children. The study comprises two components: (1) screening of all children at school for GAS pharyngitis and impetigo up to three times a year and (2) weekly active surveillance visits to detect new cases of pharyngitis and impetigo. Environmental swabbing in remote schools will be included, to inform environmental health interventions. In addition, the application of new diagnostic technologies, microbiome analysis and bacterial genomic evaluations will enhance primary prevention strategies, having direct bearing on clinical care, vaccine development and surveillance for vaccine clinical trials. ETHICS AND DISSEMINATION: Ethical approval has been obtained from the Western Australian Aboriginal Health Ethics Committee (Ref: 892) and Human Research Ethics Committee of the University of Western Australia (Ref: RA/4/20/5101). Study findings will be shared with community members, teachers and children at participating schools, together with academic and medical services. Sharing findings in an appropriate manner is important and will be done in a suitable way which includes plain language summaries and presentations. Finally, findings and updates will also be disseminated to collaborators, researchers and health planners through peer-reviewed journal publications.

Standardization of Epidemiological Surveillance of Group A Streptococcal Impetigo.

Impetigo is a highly contagious bacterial infection of the superficial layer of skin. Impetigo is caused by group A Streptococcus (Strep A) and Staphylococcus aureus, alone or in combination, with the former predominating in many tropical climates. Strep A impetigo occurs mainly in early childhood, and the burden varies worldwide. It is an acute, self-limited disease, but many children experience frequent recurrences that make it a chronic illness in some endemic settings. We present a standardized surveillance protocol including case definitions for impetigo including both active (purulent, crusted) and resolving (flat, dry) phases and discuss the current tests used to detect Strep A among persons with impetigo. Case classifications that can be applied are detailed, including differentiating between incident (new) and prevalent (existing) cases of Strep A impetigo. The type of surveillance methodology depends on the burden of impetigo in the community. Active surveillance and laboratory confirmation is the preferred method for case detection, particularly in endemic settings. Participant eligibility, surveillance population and additional considerations for surveillance of impetigo, including examination of lesions, use of photographs to document lesions, and staff training requirements (including cultural awareness), are addressed. Finally, the core elements of case report forms for impetigo are presented and guidance for recording the course and severity of impetigo provided.

Spatial codistribution of HIV, tuberculosis and malaria in Ethiopia.

BACKGROUND: HIV, tuberculosis (TB) and malaria are the three most important infectious diseases in Ethiopia, and sub-Saharan Africa. Understanding the spatial codistribution of these diseases is critical for designing geographically targeted and integrated disease control programmes. This study investigated the spatial overlap and drivers of HIV, TB and malaria prevalence in Ethiopia. METHODS: HIV, TB and malaria data were obtained from different nationwide prevalence surveys, and geospatial covariates were obtained from publicly available sources. A Bayesian model-based geostatistical framework was applied to each survey leveraging the strength of high-resolution spatial covariates to predict continuous disease-specific prevalence surfaces and their codistribution. RESULTS: The national prevalence was 1.54% (95% CI 1.40 to 1.70) for HIV, 0.39% (95% CI 0.34 to 0.45) for TB and 1.1% (95%CI 0.95 to 1.32) for malaria. Substantial subnational variation was predicted with the highest HIV prevalence estimated in Gambela (4.52%), Addis Ababa (3.52%) and Dire Dawa (2.67%) regions. TB prevalence was highest in Dire Dawa (0.96%) and Gambela (0.88%), while malaria was highest in Gambela (6.1%) and Benishangul-Gumuz (3.8%). Spatial overlap of their prevalence was observed in some parts of the country, mainly Gambela region. Spatial distribution of the diseases was significantly associated with healthcare access, demographic, and climatic factors. CONCLUSIONS: The national distribution of HIV, TB and malaria was highly focal in Ethiopia, with substantial variation at subnational and local levels. Spatial distribution of the diseases was significantly associated with healthcare access, demographic and climatic factors. Spatial overlap of HIV, TB and malaria prevalence was observed in some parts of the country. Integrated control programmes for these diseases should be targeted to these areas with high levels of co-endemicity.

Standardization of Epidemiological Surveillance of Invasive Group A Streptococcal Infections.

Invasive group A streptococcal (Strep A) infections occur when Streptococcus pyogenes, also known as beta-hemolytic group A Streptococcus, invades a normally sterile site in the body. This article provides guidelines for establishing surveillance for invasive Strep A infections. The primary objective of invasive Strep A surveillance is to monitor trends in rates of infection and determine the demographic and clinical characteristics of patients with laboratory-confirmed invasive Strep A infection, the age- and sex-specific incidence in the population of a defined geographic area, trends in risk factors, and the mortality rates and rates of nonfatal sequelae caused by invasive Strep A infections. This article includes clinical descriptions followed by case definitions, based on clinical and laboratory evidence, and case classifications (confirmed or probable, if applicable) for invasive Strep A infections and for 3 Strep A syndromes: streptococcal toxic shock syndrome, necrotizing fasciitis, and pregnancy-associated Strep A infection. Considerations of the type of surveillance are also presented, noting that most people who have invasive Strep A infections will present to hospital and that invasive Strep A is a notifiable disease in some countries. Minimal surveillance necessary for invasive Strep A infection is facility-based, passive surveillance. A resource-intensive but more informative approach is active case finding of laboratory-confirmed Strep A invasive infections among a large (eg, state-wide) and well defined population. Participant eligibility, surveillance population, and additional surveillance components such as the use of International Classification of Disease diagnosis codes, follow-up, period of surveillance, seasonality, and sample size are discussed. Finally, the core data elements to be collected on case report forms are presented.

Modes of transmission and attack rates of group A Streptococcal infection: a protocol for a systematic review and meta-analysis.

BACKGROUND: Group A Streptococcus (Strep A) is an important cause of mortality and morbidity globally. This bacterium is responsible for a range of different infections and post-infectious sequelae. Summarising the current knowledge of Strep A transmission to humans will address gaps in the evidence and inform prevention and control strategies. The objective of this study is to evaluate the modes of transmission and attack rates of group A streptococcal infection in human populations. METHODS: This systematic review protocol was prepared according to the Preferred Reporting Items for Systematic reviews and Meta-analysis Protocols (PRISMA-P) 2015 Statement. Using a comprehensive search strategy to identify any transmission studies that have been published in English since 1980, full-text articles will be identified and considered for inclusion against predefined criteria. We will include all studies reporting on Strep A transmission, who have identified a mode of transmission, and who reported attack rates. Risk of bias will be appraised using an appropriate tool. Our results will be described narratively and where feasible and appropriate, a meta-analysis utilizing the random-effects model will be used to aggregate the incidence proportions (attack rates) for each mode of transmission. In addition, we will also evaluate the emm genotype variants of the M protein causing Strep A infection and the association with transmission routes and attack rates, if any, by setting, socioeconomic background and geographical regions. DISCUSSION: We anticipate that this review will contribute to elucidating Strep A modes of transmission which in turn, will serve to inform evidence-based strategies including environmental health activities to reduce the transmission of Strep A in populations at risk of severe disease. TRIAL REGISTRATION: Systematic review registration: PROSPERO ( CRD42019138472 ).

Performance and Practicality of a Rapid Molecular Test for the Diagnosis of Strep A Pharyngitis in a Remote Australian Setting.

Over 5 days, 120 schoolchildren from two schools in the remote Kimberley region of Australia were screened for Strep A pharyngitis. Molecular point-of-care testing identified Strep A pharyngitis in 13/18 (72.2%) symptomatic children. The portability and feasibility of molecular point-of-care testing was highly practical for remote settings.

Prevalence of group A Streptococcal infection in Africa to inform GAS vaccines for rheumatic heart disease: A systematic review and meta-analysis.

BACKGROUND: The prevalence of group A streptococcal (GAS) disease is estimated at >18.1 million cases with an incidence of >1.78 million cases per year. While a significant cause of mortality and morbidity on the global scale, the burden of GAS disease in Africa is unknown. We conducted a systematic review on the prevalence of GAS disease among children and adults in Africa and the frequency and distribution of emm types among isolates. METHODS: We performed a comprehensive literature search in a number of databases, using an African search filter. Two reviewers independently selected articles meeting pre-specified criteria and extracted relevant data as per a data extraction form. We applied the random-effects meta-analysis model to aggregate GAS prevalence estimates with 95% CI for GAS prevalence, incorporating the Freeman-Tukey transformation to account for between-study variability. RESULTS: Twenty-five studies were included. Invasive GAS disease prevalence ranged from 0.6% to 10.8% in samples from normally-sterile sites including blood, CSF and soft tissue. A single study reported a prevalence of 74% in skin infections. Prevalence of emm types varied with up to 88 different strains reported, corresponding to a vaccine coverage of 28% to 65%. The pooled prevalence of GAS in persons presenting with pharyngitis was 21% (95% CI, 17% to 26%). CONCLUSIONS: The prevalence of GAS remains high among symptomatic individuals residing in Africa. Data on molecular strain characterisation of GAS in Africa is largely non-existent, thus the need for further studies is warranted to inform current prevention efforts including vaccine development.

The incidence of sore throat and group A streptococcal pharyngitis in children at high risk of developing acute rheumatic fever: A systematic review and meta-analysis.

BACKGROUND: Group A streptococcal (GAS) pharyngitis has traditionally been considered the sole precursor of acute rheumatic fever (ARF). Evidence from Australia, however, suggests that GAS skin infections may contribute to the pathogenesis of ARF. A missing piece of evidence is the incidence of sore throat and GAS pharyngitis in this setting. We conducted a systematic review and meta-analysis of the incidence of sore throat and GAS pharyngitis in all children at risk of developing ARF. METHODS: Databases were systematically searched for studies reporting on the incidence of pharyngitis among children from low to upper-middle income countries, and Indigenous children living in high-income countries. Studies were subjected to data extraction by two independent reviewers. Following an assessment of the methodological quality of the studies, we extracted incidence rates (IRs) and conducted a meta-analysis. This systematic review is registered on PROSPERO (CRD42019113019). RESULTS: From 607 titles identified by the search, 11 articles met the predetermined inclusion criteria; ten studies reported IRs while for the remaining study, the incidence was calculated. The pooled incidence estimated for sore throat was 82.5 per 100 child-years (95% confidence interval [CI], 6.5 to 1044.4 per 100 child-years, I2 = 100%) and GAS pharyngitis was 10.8 per 100 child-years (95% CI, 2.3 to 50.0 per 100 child-years, I2 = 99.9%). CONCLUSIONS: The pooled IRs for sore throat in children at risk of developing ARF were higher than rates reported in developed nations (32.70-40 per 100 child-years) and similar for GAS pharyngitis (12.8-14 per 100 years). The limited Australian data lend support to the need for further studies to inform the role of GAS pharyngitis in the development of ARF in Australian Indigenous children, so as to inform local primary prevention strategies for ARF and Rheumatic Heart Disease (RHD).

Clinical outcomes of adults with hemophagocytic lymphohistiocytosis treated with the HLH-04 protocol: a retrospective analysis.

Hemophagocytic lymphohistiocytosis (HLH) is a rare syndrome of pathologic immune activation in children that is increasingly being recognized in adults. Efficacy data for the HLH-04 protocol in adults is lacking. This study retrospectively analyzed 31 adult patients, median age 46 years, who received HLH-04 from 1/1/2004 to 5/1/2018. HLH etiology included malignancy (n = 9), autoimmune (n = 8), infection (n = 8), and idiopathic (n = 6). Eighteen patients were evaluable for response at week 4 with 7 having no response, 11 reaching partial response, and 0 reaching complete response (CR). Six patients eventually achieved CR at a median 195 days. The 1-year overall survival (OS) was 35% and median OS was 3.2 months. Univariate analysis showed shorter survival for hemoglobin <9 g/dL (HR 4.29, p = 0.003), platelets <100 × 109/L (HR 4.06, p = 0.027), ANC <1 × 109/L (HR 5.24, p = 0.001), and total bilirubin >1.2 mg/dL (HR 3.30, p = 0.022). Outcomes of adults treated with HLH-04 remain dismal and newer treatment modalities are needed.