Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases shows aberrant immune responses to infection

In COVID-19, hyperinflammatory and dysregulated immune responses contribute to severity. Patients with pre-existing autoimmune conditions can therefore be at increased risk of severe COVID-19 and/or associated sequelae, yet SARS-CoV-2 infection in this group has been little studied. Here, we performed single-cell analysis of peripheral blood mononuclear cells from patients with three major autoimmune diseases (rheumatoid arthritis, psoriasis, or multiple sclerosis) during SARS-CoV-2 infection. We observed compositional differences between the autoimmune disease groups coupled with altered patterns of gene expression, transcription factor activity, and cell-cell communication that substantially shape the immune response under SARS-CoV-2 infection. While enrichment of HLA-DRlow CD14+ monocytes was observed in all three autoimmune disease groups, type-I interferon signaling as well as inflammatory T cell and monocyte responses varied widely between the three groups of patients. Our results reveal disturbed immune responses to SARS-CoV-2 in patients with pre-existing autoimmunity, highlighting important considerations for disease treatment and follow-up.

Vitamin C deficiency in critically ill COVID-19 patients admitted to intensive care unit

Objectives

To determine vitamin C plasma kinetics, through the measurement of vitamin C plasma concentrations, in critically ill Coronavirus infectious disease 2019 (COVID-19) patients, identifying eventually the onset of vitamin C deficiency.

Design

Prospective, observational, single-center study.

Setting

Intensive Care Unit (ICU), Vall d'Hebron University Hospital, Barcelona. Study period from November 12th, 2020, to February 24th, 2021.

Patients

Patients who had a severe hypoxemic acute respiratory failure due to COVID-19 were included.

Interventions

Plasma vitamin C concentrations were measured on days 1, 5, and 10 of ICU admission. There were no vitamin C enteral nor parenteral supplementation. The supportive treatment was performed following the standard of care or acute respiratory distress syndrome (ARDS) patients.

Measurement

Plasma vitamin C concentrations were analyzed using an ultra-performance liquid chromatography (UPLC) system with a photodiode array detector (wavelength set to 245 nm). We categorized plasmatic levels of vitamin C as follows: undetectable: < 1,5 mg/L, deficiency: <2 mg/L. Low plasma concentrations: 2-5 mg/L; (normal plasma concentration: > 5 mg/L).

Main results

Forty-three patients were included (65% men; mean age 62 ± 10 years). The median Sequential Organ Failure Assessment (SOFA) score was 3 (1-4), and the Acute Physiology and Chronic Health disease Classification System (APACHE II) score was 13 (10-22). Five patients had shock. Bacterial coinfection was documented in 7 patients (16%). Initially all patients required high-flow oxygen therapy, and 23 (53%) further needed invasive mechanical ventilation during 21 (± 10) days. The worst PaO2/FIO2 registered was 93 (± 29). ICU and hospital survival were 77 and 74%, respectively. Low or undetectable levels remained constant throughout the study period in the vast majority of patients.

Conclusion

This observational study showed vitamin C plasma levels were undetectable on ICU admission in 86% of patients with acute respiratory failure due to COVID-19 pneumonia requiring respiratory support. This finding remained consistent throughout the study period.

Endotoxin activity trend and multi-organ dysfunction in critically ill patients with septic shock, who received Polymyxin-B hemadsorption: A multicenter, prospective, observational study

BACKGROUND

The baseline endotoxin activity (EAT0) may predict the outcome of critically ill septic patients who receive Polymyxin-B hemadsorption (PMX-HA), however, the clinical implications of specific EA trends remain unknown.

METHODS

Subgroup analysis of the prospective, multicenter, observational study EUPHAS2. We included 50 critically ill patients with septic shock and EAT0 ≥ 0.6, who received PMX-HA. The primary outcome of the study was the EA and SOFA score progression from T0 to 120 h afterwards (T120). Secondary outcomes included the EA and SOFA score progression in whom had EA at 48 h (EAT48) < 0.6 (EA responders, EA-R) versus who had not (EA non-responders, EA-NR).

RESULTS

Septic shock was mainly caused by 27 abdominal (54%) and 17 pulmonary (34%) infections, predominantly due to Gram negative bacteria (39 patients, 78%). The SAPS II score was 67.5 [52.8-82.3] and predicted a mortality rate of 75%. Between T0 and T120, the EA decreased (p < 0.001), while the SOFA score and the Inotropic Score (IS) improved (p < 0.001). In comparison with EA-NR (18 patients, 47%), the EA-R group (23 patients, 53%) showed faster IS improvement and lower requirement of continuous renal replacement therapy (CRRT) during the ICU stay. Overall hospital mortality occurred in 18 patients (36%).

CONCLUSIONS

In critically ill patients with septic shock and EAT0 ≥ 0.6 who received PMX-HA, EA decreased and SOFA score improved over 120 h. In whom high EA resolved within 48 h, IS improvement was faster and CRRT requirement was lower compared with patients with EAT48 ≥ 0.6.

Planning for the assistance of critically ill patients in a Pandemic Situation: The experience of Vall d'Hebron University Hospital

INTRODUCTION

In the context of community transmission of the virus, the impact of the pandemic on health-care systems, mainly on intensive care units (ICU), was expected to be devastating. Vall d'Hebron University Hospital (HUVH) implemented an unprecedented critical patient-care planning and management of resources.

METHODS

We describe a cohort of critically ill patients during the first two months of the pandemic (from March 3, 2020, to May 2, 2020) in HUVH, Barcelona. In this manuscript, we report our previsions, strategies implemented, and the outcomes obtained.

RESULTS

Three-thousand and thirty-three patients were admitted to the HUVH Critical Care Units. Throughout the study period, the proportion of patients on IMV or IMV and ECMO remained above 78%. Most patients were men (65%); the most common age group was 60-70 years. Twenty-three patients received ECMO, and eighteen were cannulated at another center and transferred to HUVH. At the end of the study, fourteen patients were successfully decannulated, three patients died, and the rest of the patients were still on ECMO. Eight pregnant women have been treated in the ICU, with a survival rate of 100%. The ICU mortality of patients younger than 60 years was 3.2%. The mean ICU stay of both survivors and nonsurvivors was 14 days.

CONCLUSION

The adequate preparation for resource expansion for critically ill patients care, main challenges, and overall positive results can serve as a precedent for similar future scenarios.

Precision medicine in sepsis and septic shock: From omics to clinical tools

Sepsis is a heterogeneous disease with variable clinical course and several clinical phenotypes. As it is associated with an increased risk of death, patients with this condition are candidates for receipt of a very well-structured and protocolized treatment. All patients should receive the fundamental pillars of sepsis management, which are infection control, initial resuscitation, and multiorgan support. However, specific subgroups of patients may benefit from a personalized approach with interventions targeted towards specific pathophysiological mechanisms. Herein, we will review the framework for identifying subpopulations of patients with sepsis, septic shock, and multiorgan dysfunction who may benefit from specific therapies. Some of these approaches are still in the early stages of research, while others are already in routine use in clinical practice, but together will help in the effective generation and safe implementation of precision medicine in sepsis.

Label-Free Plasmonic Biosensor for Rapid, Quantitative, and Highly Sensitive COVID-19 Serology: Implementation and Clinical Validation

Serological tests are essential for the control and management of COVID-19 pandemic (diagnostics and surveillance, and epidemiological and immunity studies). We introduce a direct serological biosensor assay employing proprietary technology based on plasmonics, which offers rapid (<15 min) identification and quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in clinical samples, without signal amplification. The portable plasmonic device employs a custom-designed multiantigen (RBD peptide and N protein) sensor biochip and reaches detection limits in the low ng mL^–1 range employing polyclonal antibodies. It has also been implemented employing the WHO-approved anti-SARS-CoV-2 immunoglobulin standard. A clinical validation with COVID-19 positive and negative samples (n = 120) demonstrates its excellent diagnostic sensitivity (99%) and specificity (100%). This positions our biosensor as an accurate and easy-to-use diagnostics tool for rapid and reliable COVID-19 serology to be employed both at laboratory and decentralized settings for the disease management and for the evaluation of immunological status during vaccination or treatment.

JAK2-STAT Epigenetically Regulates Tolerized Genes in Monocytes in the First Encounter With Gram-Negative Bacterial Endotoxins in Sepsis

Microbial challenges, such as widespread bacterial infection in sepsis, induce endotoxin tolerance, a state of hyporesponsiveness to subsequent infections. The participation of DNA methylation in this process is poorly known. In this study, we perform integrated analysis of DNA methylation and transcriptional changes following in vitro exposure to gram-negative bacterial lipopolysaccharide, together with analysis of ex vivo monocytes from septic patients. We identify TET2-mediated demethylation and transcriptional activation of inflammation-related genes that is specific to toll-like receptor stimulation. Changes also involve phosphorylation of STAT1, STAT3 and STAT5, elements of the JAK2 pathway. JAK2 pathway inhibition impairs the activation of tolerized genes on the first encounter with lipopolysaccharide. We then confirm the implication of the JAK2-STAT pathway in the aberrant DNA methylome of patients with sepsis caused by gram-negative bacteria. Finally, JAK2 inhibition in monocytes partially recapitulates the expression changes produced in the immunosuppressive cellular state acquired by monocytes from gram-negative sepsis, as described by single cell-RNA-sequencing. Our study evidences both the crucial role the JAK2-STAT pathway in epigenetic regulation and initial response of the tolerized genes to gram-negative bacterial endotoxins and provides a pharmacological target to prevent exacerbated responses.

Planning for the assistance of critically ill patients in a Pandemic Situation: The experience of Vall d'Hebron University Hospital

INTRODUCTION

In the context of community transmission of the virus, the impact of the pandemic on health-care systems, mainly on intensive care units (ICU), was expected to be devastating. Vall d́Hebron University Hospital (HUVH) implemented an unprecedented critical patient-care planning and management of resources.

METHODS

We describe a cohort of critically ill patients during the first two months of the pandemic (from March 3, 2020, to May 2, 2020) in HUVH, Barcelona. In this manuscript, we report our previsions, strategies implemented, and the outcomes obtained.

RESULTS

Three-thousand and thirty-three patients were admitted to the HUVH Critical Care Units. Throughout the study period, the proportion of patients on IMV or IMV and ECMO remained above 78%. Most patients were men (65%); the most common age group was 60-70 years. Twenty-three patients received ECMO, and eighteen were cannulated at another center and transferred to HUVH. At the end of the study, fourteen patients were successfully decannulated, three patients died, and the rest of the patients were still on ECMO. Eight pregnant women have been treated in the ICU, with a survival rate of 100%. The ICU mortality of patients younger than 60 years was 3.2%. The mean ICU stay of both survivors and nonsurvivors was 14 days.

CONCLUSION

The adequate preparation for resource expansion for critically ill patients care, main challenges, and overall positive results can serve as a precedent for similar future scenarios.

Inflammatory cytokines and organ dysfunction associate with the aberrant DNA methylome of monocytes in sepsis

BACKGROUND

Sepsis, a life-threatening organ dysfunction caused by a dysregulated systemic immune response to infection, associates with reduced responsiveness to subsequent infections. How such tolerance is acquired is not well understood but is known to involve epigenetic and transcriptional dysregulation.

METHODS

Bead arrays were used to compare global DNA methylation changes in patients with sepsis, non-infectious systemic inflammatory response syndrome, and healthy controls. Bioinformatic analyses were performed to dissect functional reprogramming and signaling pathways related to the acquisition of these specific DNA methylation alterations. Finally, in vitro experiments using human monocytes were performed to test the induction of similar DNA methylation reprogramming.

RESULTS

Here, we focused on DNA methylation changes associated with sepsis, given their potential role in stabilizing altered phenotypes. Tolerized monocytes from patients with sepsis display changes in their DNA methylomes with respect to those from healthy controls, affecting critical monocyte-related genes. DNA methylation profiles correlate with IL-10 and IL-6 levels, significantly increased in monocytes in sepsis, as well as with the Sequential Organ Failure Assessment score; the observed changes associate with TFs and pathways downstream to toll-like receptors and inflammatory cytokines. In fact, in vitro stimulation of toll-like receptors in monocytes results in similar gains and losses of methylation together with the acquisition of tolerance.

CONCLUSION

We have identified a DNA methylation signature associated with sepsis that is downstream to the response of monocytes to inflammatory signals associated with the acquisition of a tolerized phenotype and organic dysfunction.

Label-free Bacteria Quantification in Blood Plasma by a Bioprinted Microarray Based Interferometric Point-of-Care Device

Existing clinical methods for bacteria detection lack speed, sensitivity, and, importantly, point-of-care (PoC) applicability. Thus, finding ways to push the sensitivity of clinical PoC biosensing technologies is crucial. Here we report a portable PoC device based on lens-free interferometric microscopy (LIM). The device employs high performance nanoplasmonics and custom bioprinted microarrays and is capable of direct label-free bacteria ( E. coli) quantification. With only one-step sample handling we offer a sample-to-data turnaround time of 40 min. Our technology features detection sensitivity of a single bacterial cell both in buffer and in diluted blood plasma and is intrinsically limited by the number of cells present in the detection volume. When employed in a hospital setting, the device has enabled accurate categorization of sepsis patients (infectious SIRS) from control groups (healthy individuals and noninfectious SIRS patients) without false positives/negatives. User-friendly on-site bacterial clinical diagnosis can thus become a reality.

Non-oncotic properties of albumin. A multidisciplinary vision about the implications for critically ill patients

INTRODUCTION

Effective resuscitation with human albumin solutions is achieved with less fluid than with crystalloid solutions. However, the role of albumin in today's critical care unit is also linked to its multiple pharmacological effects. Areas covered: The potential clinical benefits of albumin in select populations of critically ill patients like sepsis seem related to immunomodulatory and anti-inflammatory effects, antibiotic transportation and endothelial stabilization. Albumin transports many drugs used in critically ill patients. Such binding to albumin is frequently lessened in critically ill patients with hypoalbuminemia. These changes could result in sub-optimal treatment. Albumin has immunomodulatory capacity by binding several bacterial products. Albumin also influences vascular integrity, contributing to the maintenance of the normal capillary permeability. Moreover, the albumin molecule encompasses several antioxidant properties, thereby significantly reducing re-oxygenation injury, which is especially important in sepsis. In fact, most studies of albumin administration are a combination of a degree of resuscitation with a degree of maintenance or supplementation of albumin. Expert commentary: The potential clinical benefits of the use of albumin in selected critically ill patients such as sepsis seem related to its immunomodulatory and anti-inflammatory effects, antioxidant properties, antibiotic transportation and endothelial stabilization. Additional studies are warranted to further elucidate the underlying physiologic and molecular rationale.

Epidemiology of sepsis in Catalonia: analysis of incidence and outcomes in a European setting

BACKGROUND

Up-to-date identification of local trends in sepsis incidence and outcomes is of considerable public health importance. The aim of our study was to estimate annual incidence rates and in-hospital mortality trends for hospitalized patients with sepsis in a European setting, while avoiding selection bias in relation to different complexity hospitals.

METHODS

A large retrospective analysis of a 5-year period (2008-2012) was conducted of hospital discharge records obtained from the Catalan Health System (CatSalut) Minimum Basic Data Set for Acute-Care Hospitals (a mandatory population-based register of admissions to all public and private acute-care hospitals in Catalonia). Patients hospitalized with sepsis were detected on the basis of ICD-9-CM codes used to identify acute organ dysfunction and infectious processes.

RESULTS

Of 4,761,726 discharges from all acute-care hospitals in Catalonia, 82,300 cases (1.72%) had sepsis diagnoses. Annual incidence was 212.7 per 100,000 inhabitants/year, rising from 167.2 in 2008 to 261.8 in 2012. Length of hospital stay fell from 18.4 to 15.3 days (p < .00001), representing a relative reduction of 17%. Hospital mortality fell from 23.7 to 19.7% (p < .0001), representing a relative reduction of 16.9%. These differences were confirmed in the multivariate analysis (adjusted for age group, sex, comorbidities, ICU admission, emergency admission, organ dysfunction, number of organ failures, sepsis source and bacteraemia).

CONCLUSIONS

Sepsis incidence has risen in recent years, whereas mortality has fallen. Our findings confirm reports for other parts of the world, in the context of scarce administrative data on sepsis in Europe.

The sounds of cardiac arrest: innovating to obtain an accurate record during in-hospital cardiac arrest

BACKGROUND

To obtain an accurate audit during in-hospital cardiac arrest, following recommendations of the Utstein style and measuring time intervals between the different interventions, is difficult.

OBJECTIVE

To assess whether the use of an audio recording system during in-hospital cardiac arrest resuscitation allows the register of more items during cardiopulmonary resuscitation.

MATERIAL AND METHODS

Prospective observational study between January 2008 and December 2009. The population that were included, were hospitalized patients and non-hospitalized patients assisted by a cardiac arrest team, except for critical areas. An audio recording system with a timer was turned on when cardiac arrest team was alerted. Recordings were reviewed to fill in the items recommended by the Utstein style. Time intervals were calculated. Mean number of completed items per patient were compared between recorded and non-recorded cardiac arrest.

RESULTS

119 CA team alerts took place. 64 (53.7%) cases were real CA and 37 (57.8%) of them were properly recorded. A mean number of items per patient in recorded cardiac arrest cases were 18.18 (±3.2) vs. 15.96 (±4.1) in non-recorded cardiac arrest cases (p<0.05). In the recorded cases, mean times were: alert - arrival: 1.23 (±0.95)min; arrival - cardiopulmonary resuscitation initiation: 0.63 (±0.38)min; arrival - first defibrillation: 2.06 (±1.33)min; arrival - intubation: 8.42 (±4.64)min; arrival - first adrenaline: 3.30 (±1.98)min.

CONCLUSIONS

The audio recording system permits the register of a larger number of items per patient during in-hospital cardiac arrest and allows measurement of time intervals between the different interventions during cardiopulmonary resuscitation.