Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data

Resolving chromatin remodeling-linked gene expression changes at cell type resolution is important for understanding disease states. We describe MAGICAL, a hierarchical Bayesian approach that leverages paired scRNA-seq and scATAC-seq data from different conditions to map disease-associated transcription factors, chromatin sites, and genes as regulatory circuits. By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference. We applied MAGICAL to study Staphylococcus aureus sepsis from peripheral blood mononuclear single-cell data that we generated from infected subjects with bloodstream infection and from uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be activated by bacterial sepsis. We addressed the challenging problem of distinguishing host regulatory circuit responses to methicillin-resistant- (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA) infections. While differential expression analysis failed to show predictive value, MAGICAL identified epigenetic circuit biomarkers that distinguished MRSA from MSSA.

The oral drug nitazoxanide restricts SARS-CoV-2 infection and attenuates disease pathogenesis in Syrian hamsters

A well-tolerated and cost-effective oral drug that blocks SARS-CoV-2 growth and dissemination would be a major advance in the global effort to reduce COVID-19 morbidity and mortality. Here, we show that the oral FDA-approved drug nitazoxanide (NTZ) significantly inhibits SARS-CoV-2 viral replication and infection in different primate and human cell models including stem cell-derived human alveolar epithelial type 2 cells. Furthermore, NTZ synergizes with remdesivir, and it broadly inhibits growth of SARS-CoV-2 variants B.1.351 (beta), P.1 (gamma), and B.1617.2 (delta) and viral syncytia formation driven by their spike proteins. Strikingly, oral NTZ treatment of Syrian hamsters significantly inhibits SARS-CoV-2-driven weight loss, inflammation, and viral dissemination and syncytia formation in the lungs. These studies show that NTZ is a novel host-directed therapeutic that broadly inhibits SARS-CoV-2 dissemination and pathogenesis in human and hamster physiological models, which supports further testing and optimization of NTZ-based therapy for SARS-CoV-2 infection alone and in combination with antiviral drugs.

Hybrid revascularization of chronic limb-threatening ischemia using popliteal below-knee and tibial trifurcation open endarterectomy distally plus inter-woven nitinol stenting proximally.

OBJECTIVES: Chronic limb-threatening ischemia (CLTI) is frequently due to multilevel, heavily calcified lesions, and it is often associated with desert foot. Effective revascularization currently presents an additional challenge due to the increasing age, comorbidities, and frailty related to these patients. Pure endovascular treatment often fails to achieve effective and durable revascularization and it is associated with still high amputation rates. We present a novel hybrid approach and discuss its usefulness for limb salvage in complex infrainguinal lesions. METHODS: Two no-option patients for both anatomical and medical-comorbidity reasons, were treated consecutively for CLTI. Both of them had prior failed percutaneous endovascular treatment, and bypass revascularization had been ruled out. We describe the technical details of an aggressive, but still less invasive hybrid approach, consisting of open distal popliteal artery (PA) and tibial trifurcation endarterectomy plus patch angioplasty, associated with proximal endovascular treatment with inter-woven nitinol stent from the superficial femoral artery (SFA) to the endarterectomized area. RESULTS: Technical success and salvage of the affected limb were achieved in both cases, presenting significant postoperative clinical and hemodynamic improvement and allowing early discharge hospital at home. There was no surgical wound infection or other complications. CONCLUSION: This hybrid approach through a single incision is safe and effective in the short term and can be used with excellent results for CLTI in high-risk and /or no-option patients.

mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge

The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.

Gastrointestinal involvement attenuates COVID-19 severity and mortality

Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of coronavirus disease 2019 (COVID-19), we investigated the impact of GI infection on disease pathogenesis in three large cohorts of patients in the United States and Europe. Unexpectedly, we observed that GI involvement was associated with a significant reduction in disease severity and mortality, with an accompanying reduction in key inflammatory proteins including IL-6, CXCL8, IL-17A and CCL28 in circulation. In a fourth cohort of COVID-19 patients in which GI biopsies were obtained, we identified severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) within small intestinal enterocytes for the first time in vivo but failed to obtain culturable virus. High dimensional analyses of GI tissues confirmed low levels of cellular inflammation in the GI lamina propria and an active downregulation of key inflammatory genes including IFNG, CXCL8, CXCL2 and IL1B among others. These data draw attention to organ-level heterogeneity in disease pathogenesis and highlight the role of the GI tract in attenuating SARS-CoV-2-associated inflammation with related mortality benefit.

Prospective Molecular Profiling of Circulating Tumor Cells from Patients with Melanoma Receiving Combinatorial Immunotherapy.

BACKGROUND: Blood molecular profiling of circulating tumor cells (CTCs) can enable monitoring of patients with metastatic melanoma during checkpoint inhibitor immunotherapy (CII) and in combination with targeted therapies. We developed a microfluidics-based CTC platform to explore CTC profiling utility in CII-treated patients with melanoma using a melanoma messenger RNA (mRNA)/DNA biomarker panel. METHODS: Blood samples (n = 213) were collected prospectively from 75 American Joint Committee on Cancer-staged III/IV melanoma patients during CII treatment and those enriched for CTCs. CTC profiling was performed using 5 known melanoma mRNA biomarkers and BRAF V600E DNA mutation. CTC biomarker status associations with clinical outcomes were assessed. RESULTS: CTCs were detected in 88% of blood samples from patients with melanoma. CTC-derived biomarkers and clinical variables analyzed using classification and regression tree analysis revealed that a combination of lactate dehydrogenase, CTC-mRNA biomarkers, and tumor BRAF-mutation status was indicative of clinical outcomes for patients with stage IV melanoma (n = 52). The panel stratified low-risk and high-risk patients, whereby the latter had poor disease-free (P = 0.03) and overall survival (P = 0.02). Incorporation of a DNA biomarker with mRNA profiling increased overall CTC-detection capability by 57% compared to mRNA profiling only. RNA sequencing of isolated CTCs identified significant catenin beta 1 (CTNNB1) overexpression (P <0.01) compared to nondisease donor blood. CTC-CTNNB1 was associated with progressive disease/stable disease compared to complete-responder patient status (P = 0.02). Serial CTC profiling identified subclinical disease in patients who developed progressive disease during treatment/follow-up. CONCLUSIONS: CTC-derived mRNA/DNA biomarkers have utility for monitoring CII, targeted, and combinatorial therapies in metastatic melanoma patients.

Do you know this syndrome?

Goltz syndrome is a rare genetic disease of X-linked dominant inheritance. It is more common in female patients and, in most cases, results in miscarriage of male fetuses. It has a broad scope of possible clinical manifestations. Its diagnosis consists of the sum of the many clinical, radiological and histopathological findings. The treatment options are genetic counseling, reconstructive surgery and multidisciplinary approach, aiming to improve quality of life and ensure a normal and productive life.

Você conhece esta síndrome? / Do you know this syndrome?

A síndrome de Goltz é uma doença genética rara, de herança dominante ligada ao X, mais comum em doentes do sexo feminino e, na maioria das vezes, resulta no aborto dos fetos do sexo masculino. Tem um amplo espectro de manifestações clínicas possíveis. O diagnóstico consiste no somatório dos numerosos achados clínicos, radiológicos e histopatológicos. O tratamento é o aconselhamento genético, cirurgias reconstrutivas e abordagem multidisciplinar, com objetivo de melhorar a qualidade de vida e garantir uma vida normal e produtiva.

Goltz syndrome is a rare genetic disease of X-linked dominant inheritance. It is more common in female patients and, in most cases, results in miscarriage of male fetuses. It has a broad scope of possible clinical manifestations. Its diagnosis consists of the sum of the many clinical, radiological and histopathological findings. The treatment options are genetic counseling, reconstructive surgery and multidisciplinary approach, aiming to improve quality of life and ensure a normal and productive life.