Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality

BACKGROUNDPatients hospitalized for COVID-19 exhibit diverse clinical outcomes, with outcomes for some individuals diverging over time even though their initial disease severity appears similar to that of other patients. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity.METHODSWe performed deep immunophenotyping and conducted longitudinal multiomics modeling, integrating 10 assays for 1,152 Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study participants and identifying several immune cascades that were significant drivers of differential clinical outcomes.RESULTSIncreasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, formation of neutrophil extracellular traps, and T cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma Igs and B cells and dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to failure of viral clearance in patients with fatal illness.CONCLUSIONOur longitudinal multiomics profiling study revealed temporal coordination across diverse omics that potentially explain the disease progression, providing insights that can inform the targeted development of therapies for patients hospitalized with COVID-19, especially those who are critically ill.TRIAL REGISTRATIONClinicalTrials.gov NCT04378777.FUNDINGNIH (5R01AI135803-03, 5U19AI118608-04, 5U19AI128910-04, 4U19AI090023-11, 4U19AI118610-06, R01AI145835-01A1S1, 5U19AI062629-17, 5U19AI057229-17, 5U19AI125357-05, 5U19AI128913-03, 3U19AI077439-13, 5U54AI142766-03, 5R01AI104870-07, 3U19AI089992-09, 3U19AI128913-03, and 5T32DA018926-18); NIAID, NIH (3U19AI1289130, U19AI128913-04S1, and R01AI122220); and National Science Foundation (DMS2310836).

Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology

Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.

Respiratory Infection- and Asthma-prone, Low Vaccine Responder Children Demonstrate Distinct Mononuclear Cell DNA Methylation Pathways

Background

Infants with frequent viral and bacterial respiratory infections exhibit compromised immunity to routine immunisations. They are also more likely to develop chronic respiratory diseases in later childhood. This study investigated the feasibility of epigenetic profiling to reveal endotype-specific molecular pathways with potential for early identification and immuno-modulation. Peripharal immune cells from respiratory infection allergy/asthma prone (IAP) infants were retrospectively selected for genome-wide DNA methylation and single nucleotide polymorphism analysis. The IAP infants were enriched for the low vaccine responsiveness (LVR) phenotype (Fishers Exact p-value = 0.01).

Results

An endotype signature of 813 differentially methylated regions (DMRs) comprising 238 lead CpG associations (FDR < 0.05) emerged, implicating pathways related to asthma, mucin production, antigen presentation and inflammasome activation. Allelic variation explained only a minor portion of this signature. Stimulation of mononuclear cells with monophosphoryl lipid A (MPLA), a TLR agonist, partially reversing this signature at a subset of CpGs, suggesting the potential for epigenetic remodelling.

Conclusions

This proof-of-concept study establishes a foundation for precision endotyping of IAP children and highlights the potential for immune modulation strategies using adjuvants for furture investigation.

Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology

Age is a major risk factor for severe coronavirus disease-2019 (COVID-19), yet the mechanisms responsible for this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host and viral dynamics in a prospective, multicenter cohort of 1,031 patients hospitalized for COVID-19, ranging from 18 to 96 years of age. We performed blood transcriptomics and nasal metatranscriptomics, and measured peripheral blood immune cell populations, inflammatory protein expression, anti-SARS-CoV-2 antibodies, and anti-interferon (IFN) autoantibodies. We found that older age correlated with an increased SARS-CoV-2 viral load at the time of admission, and with delayed viral clearance over 28 days. This contributed to an age-dependent increase in type I IFN gene expression in both the respiratory tract and blood. We also observed age-dependent transcriptional increases in peripheral blood IFN-γ, neutrophil degranulation, and Toll like receptor (TLR) signaling pathways, and decreases in T cell receptor (TCR) and B cell receptor signaling pathways. Over time, older adults exhibited a remarkably sustained induction of proinflammatory genes (e.g., CXCL6) and serum chemokines (e.g., CXCL9) compared to younger individuals, highlighting a striking age-dependent impairment in inflammation resolution. Augmented inflammatory signaling also involved the upper airway, where aging was associated with upregulation of TLR, IL17, type I IFN and IL1 pathways, and downregulation TCR and PD-1 signaling pathways. Metatranscriptomics revealed that the oldest adults exhibited disproportionate reactivation of herpes simplex virus and cytomegalovirus in the upper airway following hospitalization. Mass cytometry demonstrated that aging correlated with reduced naïve T and B cell populations, and increased monocytes and exhausted natural killer cells. Transcriptional and protein biomarkers of disease severity markedly differed with age, with the oldest adults exhibiting greater expression of TLR and inflammasome signaling genes, as well as proinflammatory proteins (e.g., IL6, CXCL8), in severe COVID-19 compared to mild/moderate disease. Anti-IFN autoantibody prevalence correlated with both age and disease severity. Taken together, this work profiles both host and microbe in the blood and airway to provide fresh insights into aging-related immune changes in a large cohort of vaccine-naïve COVID-19 patients. We observed age-dependent immune dysregulation at the transcriptional, protein and cellular levels, manifesting in an imbalance of inflammatory responses over the course of hospitalization, and suggesting potential new therapeutic targets.

Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients

Coronavirus disease 2019 (COVID-19) poses significant risks for solid organ transplant (SOT) recipients, who have atypical but poorly characterized immune responses to SARS-CoV-2 infection. We sought to understand and the host immunologic and microbial features of COVID-19 in SOT recipients by leveraging a prospective multicenter cohort of 1164 hospitalized patients. Using multi-omic immuoprofiling, we studied 86 SOT recipients in this cohort, who were age- and sex-matched 2:1 with 172 non-SOT controls. PBMC and nasal transcriptional profiling unexpectedly demonstrated upregulation of innate immune pathways related to interferon (IFN) and Toll-like receptor signaling, and complement activation, in SOT recipients. Longitudinal analyses across the first 30-days post-hospitalization demonstrated persistent upregulation of these innate immunity pathways in SOT recipients. The levels of several proinflammatory serum chemokines, such as CX3CL1 and KITLG, were also higher in SOT recipients at the time of hospitalization, although IFN-gamma levels were lower. We observed differential dynamics of CXCL11, which remained persistently elevated in SOT recipients over the course of hospitalization. Nasal microbiome alpha diversity was higher in SOT recipients versus controls, but no differences in taxonomic abundance beyond SARS-CoV-2 were observed. SOT recipients had higher nasal SARS-CoV-2 viral loads and impaired viral clearance compared to controls. Antibody analysis demonstrated lower anti-SARS-CoV-2 spike IgG levels in SOT recipients upon hospitalization, but no distinctions over time compared to controls. Mass cytometry demonstrated marked differences in blood immune cell populations, with SOT recipients exhibiting decreased plasmablasts and transitional B cells, and increased senescent T cells. Severe disease in SOT recipients was characterized by a less robust induction of inflammatory chemokines, such as IL-6 and CCL7, and a more subtle proinflammatory transcriptional response in the blood and airway. Together, our study reveals distinct immune features and altered viral dynamics in SOT recipients compared to non-SOT controls. We unexpectedly find that SOT recipients exhibit an augmented, predominantly innate immune response in both the blood and upper respiratory tract that remains relatively stable across disease severity, in contrast to non-SOT controls. These findings may relate to the paradoxical observation that SOT recipients have similar COVID-19 mortality rates versus the general population, despite being more susceptible to SARS-CoV-2 infection, remaining infectious longer, and having higher rates of hospitalization. In summary, we find that COVID-19 in SOT recipients is characterized by a biologically distinct immune state, suggesting the potential for unique prognostic biomarkers and therapeutic approaches in this vulnerable population.

The Implication of Sphingolipids in Viral Infections

Sphingolipids are involved in cell signaling and metabolic pathways, and their metabolites play a critical role in host defense against intracellular pathogens. Here, we review the known mechanisms of sphingolipids in viral infections and discuss the potential implication of the study of sphingolipid metabolism in vaccine and therapeutic development.

Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants

Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity. In this study, we carried out deep immunophenotyping and conducted longitudinal multi-omics modeling integrating ten distinct assays on a total of 1,152 IMPACC participants and identified several immune cascades that were significant drivers of differential clinical outcomes. Increasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, NETosis, and T-cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma immunoglobulins and B cells, as well as dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to the failure of viral clearance in patients with fatal illness. Our longitudinal multi-omics profiling study revealed novel temporal coordination across diverse omics that potentially explain disease progression, providing insights that inform the targeted development of therapies for hospitalized COVID-19 patients, especially those critically ill.

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients

The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.

Intention to obtain a COVID-19 vaccine among Brazilian immigrant women in the U.S

Background

COVID-19 has disproportionately impacted low-income immigrant communities. There is concern that the current uptake of COVID-19 vaccines is suboptimal and that this may be contributing to COVID-19 inequities. However, little is known about the acceptability of COVID-19 vaccines among immigrants in the U.S. Our goal was to gauge COVID-19 vaccine intentions among Brazilian immigrant women living in the U.S.

Methods

We conducted an online survey between July and August 2020 offered in Portuguese and English languages among a convenience sample of Brazilian immigrant women ages 18 years and older. Women were recruited through online advertisements by community-based organizations and social media groups to complete a survey that assessed intention to get a COVID-19 vaccine, attitudes toward vaccines, and perceptions about the pandemic.

Results

Of the total sample (N = 353), most (70.8%) indicated they intended to get a COVID-19 vaccine. In bivariate analyses, vaccine intentions were significantly associated with perceptions about the severity of the pandemic, trusted sources of health information, and the number of years lived in the U.S. Multinomial logistic regression models revealed that those who did not intend to be vaccinated had lived a longer time in the U.S. (OR: -0.12 95% CI: -0.19, -0.05), perceived the pandemic to be a minor issue (OR: 1.52, 95% CI: 0.62, 2.42), and trusted information from social networks (OR: -1.94, 95% CI: -3.25, -0.63) or private news sources (OR: -1.71, 95% CI: -2.78, -0.63).

Conclusions

While most women reported they would get a COVID-19 vaccine, efforts to reach those who may be hesitant should target those who have lived in the U.S. for longer periods of time and do not perceive the pandemic to be a major crisis. Healthcare providers may be particularly suited to deliver this information given high levels of trust.

Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study

BACKGROUND

Better understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management.

METHODS

Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed.

FINDINGS

The median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age ≥ 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63- 4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC.

INTERPRETATION

Integration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19.

FUNDING

NIH.

Increased femoral antetorsion correlates with higher degrees of lateral retropatellar cartilage degeneration, further accentuated in genu valgum

PURPOSE

The role of increased femoral antetorsion (femAT) as a contributor to patellofemoral (PF) osteoarthritis (OA) is unknown. The purpose of this study was to investigate whether increased femAT was associated with advanced cartilage degeneration in the lateral PF joint.

METHODS

Patients who underwent complete radiographic workup for surgical intervention due to OA in any knee joint compartment were included. Cartilage morphology according to the International Cartilage Repair Society (ICRS) cartilage lesion classification system in the PF joint, femoral and tibial torsion, frontal leg axis, and tibial tuberosity-trochlear groove (TT-TG) distance were assessed. Increased femAT was defined as  > 20° according to previous reports.

RESULTS

A total of 144 patients were included. Ninety-seven patients had a femAT of  < 20° and 45 of  > 20°. A significant odds ratio (OR) was found for lateral retropatellar (OR 3.5; p = 0.02) ICRS grade 3 and 4 cartilage degeneration and increased femAT  ≥ 20°. In the medial PF compartment, increased femAT had an inverse effect (OR 0.16; p = 0.01). No significant ORs were found for TT-TG distance, tibial torsion, or leg axis. The lateral retropatellar ICRS grade showed a linear correlation to increased femAT values. In valgus knees, isolated lateral PF OA had an even more pronounced correlation to increased femAT (p = 0.004).

CONCLUSION

Increased femAT showed higher grades of lateral retropatellar cartilage degeneration, which was even more pronounced in valgus knees.

LEVEL OF EVIDENCE

Cohort study: Level III.

Linear influence of distal femur osteotomy on the Q-angle: one degree of varization alters the Q-angle by one degree

PURPOSE

The effect of a distal femur varization osteotomy on patellofemoral biomechanics in genu valgum is unknown. The purpose of this study was to quantify the influence of frontal leg axis correction on the Q-angle with a novel three-dimensional (3-D) measurement method.

METHODS

3-D surface models of ten lower extremities were generated using patient computed tomography (CT) data. The preoperative 3-D Q-angle was measured using a novel defined and validated 3-D measurement method. Biplanar supracondylar osteotomies were simulated with different degrees of varus correction (from 1° to 15°) in one-degree steps beginning from the preoperative valgus deformity, resulting in a total of 150 simulations. Additionally, mechanical leg axis and 3-D Q-angle measurements were performed on 3-D surface models of the postoperative CT scans of the same individuals. Further, pre- and postoperative TT-TG distance was measured.

RESULTS

Mean preoperative Q-angle was 15.8 ± 3.9° (range 10°-21.4°) with a mean preoperative mechanical leg axis of 6.5° ± 2.4 valgus (range 3.8°-11.6° valgus). The Q-angle changed linearly 0.9 ± 0° per 1° of varization. No difference was detected between simulated 3-D Q-angles and effectively corrected postoperative values (n.s.). TT-TG distance changed irregularly and minimally, and with no correlation to the degree of varization.

CONCLUSION

Distal femur varization osteotomy has a linear effect on the Q-angle with a change of 1° per 1° of varization. The difference in TT-TG distance was mainly due to an unintentional rotational component implemented during surgery.

Quantifying (12/13)CH(4) migration and fate following sub-surface release to an agricultural soil

Following gas generation in a Geological Disposal Facility (GDF), (14)C-containing gases could migrate through the geosphere, eventually diffusing into soils at the Earth's surface. This paper reports summary results from laboratory and field experiments to obtain information on the probable rates of a) diffusive transport and b) oxidation of (12/13)CH(4) (as a surrogate for (14)CH4) in a typical agricultural soil in the UK. Rates of CH(4) oxidation were generally low in the field and undisturbed soil columns, though a re-packed column of homogenised topsoil oxidised ambient atmospheric CH(4) 20× faster than an undisturbed soil column. In contrast to low observed rates of CH(4) oxidation, the effective diffusion of CH(4) through the soil was rapid. Isotopically labelled CH(4) injected at a depth of 45 cm in the field diffused to the surface and exited the soil over a time period ranging from 8 to 24 h. The rate of CH(4) diffusion through the soil was increased by the presence of ryegrass roots which increased soil porosity and decreased water content. δ(13)C values for laboratory column soils after labelled CH(4) injection experiments showed no sign of residual (13)C, despite the extremely high δ(13)C values of the injected (12/13)CH(4). If laboratory observations are confirmed by measurements in field samples it can be concluded that the majority of (14)CH(4) from a GDF which enters a soil with low methanotrophic activity will be lost to the free atmosphere after diffusing rapidly through the soil column.

A Modelling and Experimental Study for Long-Term Prediction of Localised Corrosion in Carbon Steel Overpacks for High-Level Radioactive Waste

This paper describes a joint modelling and experimental study for investigation of pit growth in carbon steel High-Level Radioactive Waste overpacks under consideration in Japan. A mathematical model of the growth of corrosion pits in metals has been developed. This model is implemented in the computer program CAMLE, and includes representation of the chemical, electrochemical and migration processes that control pit-growth rates. Experiments to provide key input data for the model are described, in addition to experiments to measure ‘short-term’ pit growth. Predictions from the model are compared with these data. Overall, the comparisons are encouraging and the model shows good potential as a tool for assessment of the long-term corrosion behaviour of overpacks under repository conditions. Future developments of the model to improve agreement are discussed.

Concomitant renal cell carcinoma with pituitary adenoma

Renal cell carcinoma has a complex and variable natural history. We report a case underlining this who presented concomitant renal cell carcinoma metastasis with pituitary and adrenocortical adenomas. A 62-year-old woman presented with visual loss. Imaging revealed a large sellar mass with suprasellar extension. Four years before, nephrectomy and adrenalectomy had been performed for a renal cell carcinoma with metastasis in a coexistent adrenocortical adenoma. Faced with progressive visual loss and the questionable pituitary pathology, the patient underwent trans-sphenoidal surgery. Due to profuse tumor bleeding, only a biopsy was possible. In a second operation, the patient underwent craniotomy with subtotal resection of the tumor. Histological examination of the specimen revealed a metastasis of the renal cell carcinoma and a pituitary adenoma. The case presented here and a review of the reports suggest that there are some differences between the clinical features and outcomes of metastases of renal cell carcinoma and those of pituitary gland metastases from other primary sites.

[Spontaneous intraspinal epidural hematoma secondary to use of platelet aggregation inhibitors]

HISTORY AND ADMISSION FINDINGS

A 64-year-old woman previously in good health experienced an acute onset of severe neck pain and weakness of the left arm that had developed within minutes. Neurological examination revealed paresis of the left arm. There was a previous history of cardiovascular disease and she had been treated with 100 mg of aspirin per day.

INVESTIGATIONS

MRI revealed a left posterolateral intraspinal mass extending from C3 to C7. The hemostatic evaluation showed no abnormalities (platelet count, prothrombin time, partial thromboplastin time).

TREATMENT AND COURSE

A laminectomy with evacuation of the epidural hematoma was performed. The postoperative course was uneventful, with complete disappearance of the neurological deficit.

CONCLUSION

We report a rare condition of spontaneous spinal epidural hematoma that was associated with aspirin intake. A short time interval from onset of symptoms to diagnosis (MRI) and surgery is crucial for the outcome.