Defining critical illness using immunological endotypes in patients with and without sepsis: a cohort study

BACKGROUND

Sepsis is a heterogenous syndrome with limited therapeutic options. Identifying immunological endotypes through gene expression patterns in septic patients may lead to targeted interventions. We investigated whether patients admitted to a surgical intensive care unit (ICU) with sepsis and with high risk of mortality express similar endotypes to non-septic, but still critically ill patients using two multiplex transcriptomic metrics obtained both on admission to a surgical ICU and at set intervals.

METHODS

We analyzed transcriptomic data from 522 patients in two single-site, prospective, observational cohorts admitted to surgical ICUs over a 5-year period ending in July 2020. Using an FDA-cleared analytical platform (nCounter FLEX^®, NanoString, Inc.), we assessed a previously validated 29-messenger RNA transcriptomic classifier for likelihood of 30-day mortality (IMX-SEV-3) and a 33-messenger RNA transcriptomic endotype classifier. Clinical outcomes included all-cause mortality, development of chronic critical illness, and secondary infections. Univariate and multivariate analyses were performed to assess for true effect and confounding.

RESULTS

Sepsis was associated with a significantly higher predicted and actual hospital mortality. At enrollment, the predominant endotype for both septic and non-septic patients was adaptive, though with significantly different distributions. Inflammopathic and coagulopathic septic patients, as well as inflammopathic non-septic patients, showed significantly higher frequencies of secondary infections compared to those with adaptive endotypes (p < 0.01). Endotypes changed during ICU hospitalization in 57.5% of patients. Patients who remained adaptive had overall better prognosis, while those who remained inflammopathic or coagulopathic had worse overall outcomes. For severity metrics, patients admitted with sepsis and a high predicted likelihood of mortality showed an inflammopathic (49.6%) endotype and had higher rates of cumulative adverse outcomes (67.4%). Patients at low mortality risk, whether septic or non-septic, almost uniformly presented with an adaptive endotype (100% and 93.4%, respectively).

CONCLUSION

Critically ill surgical patients express different and evolving immunological endotypes depending upon both their sepsis status and severity of their clinical course. Future studies will elucidate whether endotyping critically ill, septic patients can identify individuals for targeted therapeutic interventions to improve patient management and outcomes.

Defining critical illness using immunological endotypes in patients with and without of sepsis: A cohort study

Background: Sepsis is a heterogenous syndrome with limited therapeutic options. Identifying characteristic gene expression patterns, or endotypes, in septic patients may lead to targeted interventions. We investigated whether patients admitted to a surgical ICU with sepsis and with high risk of mortality express similar endotypes to non-septic, but still critically ill patients using two multiplex transcriptomic metrics obtained both on admission to a surgical intensive care unit (ICU) and at set intervals. Methods: We analyzed transcriptomic data from 522 patients in two single-site, prospective, observational cohorts admitted to surgical ICUs over a 5-year period ending in July 2020 . Using an FDA-cleared analytical platform (nCounter FLEX ^® , NanoString, Inc.), we assessed a previously validated 29-messenger RNA transcriptomic classifier for likelihood of 30-day mortality (IMX-SEV-3) and a 33-messenger RNA transcriptomic endotype classifier. Clinical outcomes included all-cause (in-hospital, 30-, 90-day) mortality, development of chronic critical illness (CCI), and secondary infections. Univariate and multivariate analyses were performed to assess for true effect and confounding. Results: Sepsis was associated with a significantly higher predicted and actual hospital mortality. At enrollment, the predominant endotype for both septic and non-septic patients was adaptive , though with significantly different distributions. Inflammopathic and coagulopathic septic patients, as well as inflammopathic non-septic patients, showed significantly higher frequencies of secondary infections compared to those with adaptive endotypes (p<0.01). Endotypes changed during ICU hospitalization in 57.5% of patients. Patients who remained adaptive had overall better prognosis, while those who remained inflammopathic or coagulopathic had worse overall outcomes. For severity metrics, patients admitted with sepsis and a high predicted likelihood of mortality showed an inflammopathic (49.6%) endotype and had higher rates of cumulative adverse outcomes (67.4%). Patients at low mortality risk, whether septic or non-septic, almost uniformly presented with an adaptive endotype (100% and 93.4%, respectively). Conclusion : Critically ill surgical patients express different and evolving immunological endotypes depending upon both their sepsis status and severity of their clinical course. Future studies will elucidate whether endotyping critically ill, septic patients can identify individuals for targeted therapeutic interventions to improve patient management and outcomes.

Calpain activity is negatively regulated by a KCTD7-Cullin-3 complex via non-degradative ubiquitination

Calpains are a class of non-lysosomal cysteine proteases that exert their regulatory functions via limited proteolysis of their substrates. Similar to the lysosomal and proteasomal systems, calpain dysregulation is implicated in the pathogenesis of neurodegenerative disease and cancer. Despite intensive efforts placed on the identification of mechanisms that regulate calpains, however, calpain protein modifications that regulate calpain activity are incompletely understood. Here we show that calpains are regulated by KCTD7, a cytosolic protein of previously uncharacterized function whose pathogenic mutations result in epilepsy, progressive ataxia, and severe neurocognitive deterioration. We show that KCTD7 works in complex with Cullin-3 and Rbx1 to execute atypical, non-degradative ubiquitination of calpains at specific sites (K398 of calpain 1, and K280 and K674 of calpain 2). Experiments based on single-lysine mutants of ubiquitin determined that KCTD7 mediates ubiquitination of calpain 1 via K6-, K27-, K29-, and K63-linked chains, whereas it uses K6-mediated ubiquitination to modify calpain 2. Loss of KCTD7-mediated ubiquitination of calpains led to calpain hyperactivation, aberrant cleavage of downstream targets, and caspase-3 activation. CRISPR/Cas9-mediated knockout of Kctd7 in mice phenotypically recapitulated human KCTD7 deficiency and resulted in calpain hyperactivation, behavioral impairments, and neurodegeneration. These phenotypes were largely prevented by pharmacological inhibition of calpains, thus demonstrating a major role of calpain dysregulation in KCTD7-associated disease. Finally, we determined that Cullin-3-KCTD7 mediates ubiquitination of all ubiquitous calpains. These results unveil a novel mechanism and potential target to restrain calpain activity in human disease and shed light on the molecular pathogenesis of KCTD7-associated disease.

Multisite validation of a host response signature for predicting likelihood of bacterial and viral infections in patients with suspected influenza

BACKGROUND

Indiscriminate use of antimicrobials and antimicrobial resistance is a public health threat. IMX-BVN-1, a 29-host mRNA classifier, provides two separate scores that predict likelihoods of bacterial and viral infections in patients with suspected acute infections. We validated the performance of IMX-BVN-1 in adults attending acute health care settings with suspected influenza.

METHOD

We amplified 29-host response genes in RNA extracted from blood by NanoString nCounter. IMX-BVN-1 calculated two scores to predict probabilities of bacterial and viral infections. Results were compared against the infection status (no infection; highly probable/possible infection; confirmed infection) determined by clinical adjudication.

RESULTS

Amongst 602 adult patients (74.9% ED, 16.9% ICU, 8.1% outpatients), 7.6% showed in-hospital mortality and 15.5% immunosuppression. Median IMX-BVN-1 bacterial and viral scores were higher in patients with confirmed bacterial (0.27) and viral (0.62) infections than in those without bacterial (0.08) or viral (0.21) infection, respectively. The AUROC distinguishing bacterial from nonbacterial illness was 0.81 and 0.87 when distinguishing viral from nonviral illness. The bacterial top quartile's positive likelihood ratio (LR) was 4.38 with a rule-in specificity of 88%; the bacterial bottom quartile's negative LR was 0.13 with a rule-out sensitivity of 96%. Similarly, the viral top quartile showed an infinite LR with rule-in specificity of 100%; the viral bottom quartile had a LR of 0.22 and a rule-out sensitivity of 85%.

CONCLUSION

IMX-BVN-1 showed high accuracy for differentiating bacterial and viral infections from noninfectious illness in patients with suspected influenza. Clinical utility of IMX-BVN will be validated following integration into a point of care system.

1723 Diagnostic accuracy of a novel transcriptomic classifier for bacterial and viral infections – an individual patient data meta-analysis

Aims, Objectives and Background

Arising from demographic differences between healthcare systems, patients in the emergency department (ED) present with a broad range of diagnoses and clinical severities. Independent validation of a novel diagnostic tool is critical to ensure reliable and reproducible clinical performance. So far, three independent cohort studies have validated the performance of the machine-learning classifier IMX-Bacterial/Viral/Non-infected (IMX-BVN) to diagnose bacterial and viral infections; those have been combined to facilitate an individual patient data meta-analysis of performance.

Method and Design

ED patients (n=1,277) with suspected infection from three international, observational studies (USA/Germany/Greece) were included. Of those, 661 had a unanimous (‘consensus’) ground truth of infection status established by panel adjudication. Quantitative expression of 29-signature mRNAs was measured on a NanoString nCounter® SPRINT system. The classifier BVN version 3 (IMX-BVN-3) was applied to generate scores, which fall into four discrete interpretation bands (very unlikely, unlikely, possible, very likely). Sensitivity, specificity, and corresponding nominal likelihood ratios were calculated with 95% confidence intervals for each interpretation band.

Results and Conclusion

360 patients (54.4%) were consensus adjudicated to have a bacterial infection (range: 37.9–81.2%) and 153 (23.1%) to have a viral infection (range: 15.3–44.1%). Pooled likelihood ratios of the interpretation bands for bacterial infections were (from ‘very unlikely bacterial’ to ‘very likely bacterial’) 0.082 (0.039–0.176)/0.333 (0.264–0.419)/2.244 (1.598–3.152)/9.459 (5.808–15.404), associated with a rule-in specificity of 0.947 (0.915–0.967) and a rule-out sensitivity of 0.981 (0.960–0.991) in the outer interpretation bands. Pooled likelihood ratios of the interpretation bands for viral infections were (from ‘very unlikely viral’ to ‘very likely viral’) 0.182 (0.102–0.324)/0.292 (0.181–0.471)/0.956 (0.593–1.540)/6.021 (4.636–7.821), associated with a rule-in specificity of 0.884 (0.853–0.909) and rule-out sensitivity of 0.928 (0.876–0.959).

The IMX-BVN-3 classifier exhibits strong performance in a combined cohort of patients from different geographies and settings to rule-in and rule-out patients presenting to EDs with suspected bacterial and viral infections.

Evaluation of a Multivalent Transcriptomic Metric for Diagnosing Surgical Sepsis and Estimating Mortality Among Critically Ill Patients

Importance

Rapid and accurate discrimination of sepsis and its potential severity currently require multiple assays with slow processing times that are often inconclusive in discerning sepsis from sterile inflammation.

Objective

To analyze a whole-blood, multivalent, host-messenger RNA expression metric for estimating the likelihood of bacterial infection and 30-day mortality and compare performance of the metric with that of other diagnostic and prognostic biomarkers and clinical parameters.

Design, Setting, and Participants

This prospective diagnostic and prognostic study was performed in the surgical intensive care unit (ICU) of a single, academic health science center. The analysis included 200 critically ill adult patients admitted with suspected sepsis (cohort A) or those at high risk for developing sepsis (cohort B) between July 1, 2020, and July 30, 2021.

Exposures

Whole-blood sample measurements of a custom 29-messenger RNA transcriptomic metric classifier for likelihood of bacterial infection (IMX-BVN-3) or 30-day mortality (severity) (IMX-SEV-3) in a clinical-diagnostic laboratory setting using an analysis platform (510[k]-cleared nCounter FLEX; NanoString, Inc), compared with measurement of procalcitonin and interleukin 6 (IL-6) plasma levels, and maximum 24-hour sequential organ failure assessment (SOFA) scores.

Main Outcomes and Measures

Estimated sepsis and 30-day mortality performance.

Results

Among the 200 patients included (124 men [62.0%] and 76 women [38.0%]; median age, 62.5 [IQR, 47.0-72.0] years), the IMX-BVN-3 bacterial infection classifier had an area under the receiver operating characteristics curve (AUROC) of 0.84 (95% CI, 0.77-0.90) for discriminating bacterial infection at ICU admission, similar to procalcitonin (0.85 [95% CI, 0.79-0.90]; P = .79) and significantly better than IL-6 (0.67 [95% CI, 0.58-0.75]; P < .001). For estimating 30-day mortality, the IMX-SEV-3 metric had an AUROC of 0.81 (95% CI, 0.66-0.95), which was significantly better than IL-6 levels (0.57 [95% CI, 0.37-0.77]; P = .006), marginally better than procalcitonin levels (0.65 [95% CI, 0.50-0.79]; P = .06), and similar to the SOFA score (0.76 [95% CI, 0.62-0.91]; P = .48). Combining IMX-BVN-3 and IMX-SEV-3 with procalcitonin or IL-6 levels or SOFA scores did not significantly improve performance. Among patients with sepsis, IMX-BVN-3 scores decreased over time, reflecting the resolution of sepsis. In 11 individuals at high risk (cohort B) who subsequently developed sepsis during their hospital course, IMX-BVN-3 bacterial infection scores did not decline over time and peaked on the day of documented infection.

Conclusions and Relevance

In this diagnostic and prognostic study, a novel, multivalent, transcriptomic metric accurately estimated the presence of bacterial infection and risk for 30-day mortality in patients admitted to a surgical ICU. The performance of this single transcriptomic metric was equivalent to or better than multiple alternative diagnostic and prognostic metrics when measured at admission and provided additional information when measured over time.

Factors Associated With COVID-19 Death in the United States: Cohort Study

BACKGROUND

Since the initial COVID-19 cases were identified in the United States in February 2020, the United States has experienced a high incidence of the disease. Understanding the risk factors for severe outcomes identifies the most vulnerable populations and helps in decision-making.

OBJECTIVE

This study aims to assess the factors associated with COVID-19-related deaths from a large, national, individual-level data set.

METHODS

A cohort study was conducted using data from the Optum de-identified COVID-19 electronic health record (EHR) data set; 1,271,033 adult participants were observed from February 1, 2020, to August 31, 2020, until their deaths due to COVID-19, deaths due to other reasons, or the end of the study. Cox proportional hazards models were constructed to evaluate the risks for each patient characteristic.

RESULTS

A total of 1,271,033 participants (age: mean 52.6, SD 17.9 years; male: 507,574/1,271,033, 39.93%) were included in the study, and 3315 (0.26%) deaths were attributed to COVID-19. Factors associated with COVID-19-related death included older age (80 vs 50-59 years old: hazard ratio [HR] 13.28, 95% CI 11.46-15.39), male sex (HR 1.68, 95% CI 1.57-1.80), obesity (BMI 40 vs <30 kg/m2: HR 1.71, 95% CI 1.50-1.96), race (Hispanic White, African American, Asian vs non-Hispanic White: HR 2.46, 95% CI 2.01-3.02; HR 2.27, 95% CI 2.06-2.50; HR 2.06, 95% CI 1.65-2.57), region (South, Northeast, Midwest vs West: HR 1.62, 95% CI 1.33-1.98; HR 2.50, 95% CI 2.06-3.03; HR 1.35, 95% CI 1.11-1.64), chronic respiratory disease (HR 1.21, 95% CI 1.12-1.32), cardiac disease (HR 1.10, 95% CI 1.01-1.19), diabetes (HR 1.92, 95% CI 1.75-2.10), recent diagnosis of lung cancer (HR 1.70, 95% CI 1.14-2.55), severely reduced kidney function (HR 1.92, 95% CI 1.69-2.19), stroke or dementia (HR 1.25, 95% CI 1.15-1.36), other neurological diseases (HR 1.77, 95% CI 1.59-1.98), organ transplant (HR 1.35, 95% CI 1.09-1.67), and other immunosuppressive conditions (HR 1.21, 95% CI 1.01-1.46).

CONCLUSIONS

This is one of the largest national cohort studies in the United States; we identified several patient characteristics associated with COVID-19-related deaths, and the results can serve as the basis for policy making. The study also offered directions for future studies, including the effect of other socioeconomic factors on the increased risk for minority groups.

Transcriptional Repression of SIRT3 Potentiates Mitochondrial Aconitase Activation to Drive Aggressive Prostate Cancer to the Bone

Metabolic dysregulation is a known hallmark of cancer progression, yet the oncogenic signals that promote metabolic adaptations to drive metastatic cancer remain unclear. Here, we show that transcriptional repression of mitochondrial deacetylase sirtuin 3 (SIRT3) by androgen receptor (AR) and its coregulator steroid receptor coactivator-2 (SRC-2) enhances mitochondrial aconitase (ACO2) activity to favor aggressive prostate cancer. ACO2 promoted mitochondrial citrate synthesis to facilitate de novo lipogenesis, and genetic ablation of ACO2 reduced total lipid content and severely repressed in vivo prostate cancer progression. A single acetylation mark lysine258 on ACO2 functioned as a regulatory motif, and the acetylation-deficient Lys258Arg mutant was enzymatically inactive and failed to rescue growth of ACO2-deficient cells. Acetylation of ACO2 was reversibly regulated by SIRT3, which was predominantly repressed in many tumors including prostate cancer. Mechanistically, SRC-2-bound AR formed a repressive complex by recruiting histone deacetylase 2 to the SIRT3 promoter, and depletion of SRC-2 enhanced SIRT3 expression and simultaneously reduced acetylated ACO2. In human prostate tumors, ACO2 activity was significantly elevated, and increased expression of SRC-2 with concomitant reduction of SIRT3 was found to be a genetic hallmark enriched in prostate cancer metastatic lesions. In a mouse model of spontaneous bone metastasis, suppression of SRC-2 reactivated SIRT3 expression and was sufficient to abolish prostate cancer colonization in the bone microenvironment, implying this nuclear-mitochondrial regulatory axis is a determining factor for metastatic competence. SIGNIFICANCE: This study highlights the importance of mitochondrial aconitase activity in the development of advanced metastatic prostate cancer and suggests that blocking SRC-2 to enhance SIRT3 expression may be therapeutically valuable. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/1/50/F1.large.jpg.