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. 2023 Apr 4;18(4):e0273202. doi: 10.1371/journal.pone.0273202

Anakinra in hospitalized COVID-19 patients guided by baseline soluble urokinase plasminogen receptor plasma levels: A real world, retrospective cohort study

Francesco Vladimiro Segala 1,*,#, Emanuele Rando 1,#, Federica Salvati 1, Marcantonio Negri 2, Francesca Catania 1, Flavia Sanmartin 1, Rita Murri 1,3, Evangelos J Giamarellos-Bourboulis 4, Massimo Fantoni 1,3
Editor: Cecilia Acuti Martellucci5
PMCID: PMC10072376  PMID: 37014833

Abstract

Background

In patients with COVID-19 and baseline soluble urokinase plasminogen receptor plasma (suPAR) levels ≥ 6ng/mL, early administration of anakinra, a recombinant interleukin-1 receptor antagonist, may prevent disease progression and death. In case of suPAR testing unavailability, the Severe COvid Prediction Estimate (SCOPE) score may be used as an alternative in guiding treatment decisions.

Methods

We conducted a monocenter, retrospective cohort study, including patients with SARS-CoV2 infection and respiratory failure. Patients treated with anakinra (anakinra group, AG) were compared to two control groups of patients who did not receive anakinra, respectively with ≥ 6 ng/mL (CG1) and < 6 ng/mL (CG2) baseline suPAR levels. Controls were manually paired by age, sex, date of admission and vaccination status and, for patients with high baseline suPAR, propensity score weighting for receiving anakinra was applied. Primary endpoint of the study was disease progression at day 14 from admission, as defined by patient distribution on a simplified version of the 11-point World Health Organization Clinical Progression Scale (WHO-CPS).

Results

Between July, 2021 and January, 2022, 153 patients were included, among which 56 were treated with off-label anakinra, 49 retrospectively fulfilled prescriptive criteria for anakinra and were assigned to CG1, and 48 presented with suPAR levels < 6ng/mL and were assigned to CG2. At day 14, when comparing to CG1, patients who received anakinra had significantly reduced odds of progressing towards worse clinical outcome both in ordinal regression analysis (OR 0.25, 95% CI 0.11–0.54, p<0.001) and in propensity-adjusted multiple logistic regression analysis (OR 0.32, 95% CI 0.12–0.82, p = 0.021) thus controlling for a wide number of covariates. Sensitivities of baseline suPAR and SCOPE score in predicting progression towards severe disease or death at day 14 were similar (83% vs 100%, p = 0.59).

Conclusion

This real-word, retrospective cohort study confirmed the safety and the efficacy of suPAR-guided, early use of anakinra in hospitalized COVID-19 patients with respiratory failure.

Background

Since it was first described in Wuhan, COVID-19 has resulted in an unprecedented health crisis, leading to 500 million reported cases [1] and to an estimated 18 million excess deaths [2]. Clinical presentation of SARS-CoV2 infection encompasses a large spectrum of manifestations, ranging from asymptomatic or mild, influenza-like symptoms, to pneumonia, severe respiratory failure and death [3]. Respiratory manifestations have often a sudden onset and are accompanied by systemic effects, indicating that SARS-CoV2 induces a major dysregulation of host response with a wide range of immuno-inflammatory alterations [4]. Thus, early identification of patients at risk and administration of timely, targeted treatments are crucial.

In a recent experimental study in mice, it was described that the injection of plasma from patients with severe COVID-19, enriched with danger-associated molecular patterns (DAMPs) like calprotectin (S100A8/A9), is inducing a compartmentalized inflammation in the host with the lungs and the intestine as the main sites of hyper-inflammation. Calprotectin was inducing the production of interleukin (IL)-1β. In the same model, the inhibition of murine interleukin (IL)-1α attenuated both pulmonary and intestinal inflammation [5]. Soluble urokinase plasminogen activator receptor was the biomarker which could predict the early increase of these DAMPs in the circulation release into its soluble form (suPAR) [6]. As a result, suPAR levels increase early in the disease process.

The potential role of suPAR in predicting severe respiratory failure (defined as partial oxygen pressure (PaO2) / fraction of inspired oxygen (FIO2) below 150 mmHg) and need for mechanical ventilation and death was suggested by Rovina et al. in 2020 [7] and, thereafter, two clinical trials were conducted to show the efficacy of early IL-1 targeting in COVID-19 patients presenting with suPAR levels above 6 ng/mL. The first is an open-label, non-randomized phase 2 clinical trial, the SAVE study, an interim analysis of which was published in March 2021 [8]. The second, the SAVE-MORE study, was a confirmatory, double-blind clinical trial, and they both showed significant efficacy of anakinra, a recombinant IL-1 receptor antagonist, in decreasing the risk of disease progression in patients with baseline suPAR levels ≥ 6 ng/mL [9]. In addition, to overcome the challenges posed by unavailability and low familiarity of physicians towards suPAR in clinical practice, the same authors developed and validated a clinical score based on baseline D-dimer, IL-6, CRP and ferritin levels, the SCOPE score [10]. The findings of SAVE and SAVE-MORE studies were then reviewed by the European Medicine Agency and led to the approval of biomarker-guided use of anakinra for the treatment of COVID-19 pneumonia [11]. However, to our knowledge, apart from the case of SCOPE score validation, the efficacy of anakinra guided by baseline plasma suPAR levels has not been further explored. Also, patients recruited in SAVE and SAVE-MORE clinical trials were largely non-vaccinated against SARS-CoV2.

Aim of this study is to explore suPAR guided-use and efficacy of anakinra for the treatment of COVID-19 (100mg subcutaneously once daily for up to 10 days) and compare the performances of suPAR and the SCOPE score in a real world setting in a large University Hospital in Rome, between June 2021 and January 2022.

Methods

Study population and design

We conducted a retrospective cohort study at the University Hospital “Policlinico Agostino Gemelli IRCCS”, Rome. All adult patients hospitalized for COVID-19 and treated with subcutaneous anakinra between the 1st July, 2021 and the 31rd January, 2022 were included. All patients were diagnosed with COVID-19 pneumonia using both real time-PCR and chest CT-scan.

As per institutional protocol, patients were eligible to receive anakinra if they presented with baseline suPAR levels ≥ 6 ng/mL, had respiratory failure (defined as PaO2/FiO2 ratio below 300 mmHg) requiring low-flow oxygen therapy (namely Venturi mask and nasal cannula), and did not show signs of neutropenia or severe bacterial co-infection. Baseline was defined as the date of hospital admission. Then, for each patient treated with anakinra (“anakinra group”), two controls were selected. The first control group (CG1) consisted of patients who retrospectively fulfilled the prescriptive criteria for anakinra but did not receive it at the discretion of the attending physicians, while the second control group (CG2) consisted of patients who developed COVID-related pneumonia but presented with baseline suPAR < 6ng/mL, and therefore did not fulfill the prescriptive criteria. Patients included into both control groups were manually matched to a given patient of the anakinra group according to the following criteria: date of admission (± 1 week), age (± 5 years), vaccine status against COVID-19 (whether they were fully vaccinated or not), and gender. Data collection, group allocation and matching were fully retrospective. A patient was defined to be fully vaccinated two weeks after receiving all recommended doses in the primary series of their COVID-19 vaccination [12]. We excluded, from all groups, patients diagnosed with moderate to severe immunodeficiency as defined by the CDC [13], subjects who presented with severe respiratory failure requiring high-flow oxygen therapy or the intensive care unit (ICU) on admission, patients included in clinical trials and individuals who received anti-IL6 treatment, namely tocilizumab or sarilumab.

All patients provided written informed consent to participate in the study and, in the period between study start and the approval of anakinra by the Italian Medicine Agency for the treatment of COVID-19 (23rd September, 2021), written informed consent for off-label use of anakinra was obtained to all individuals who received the study drug. The study was approved by “Fondazione Policlinico Gemelli IRCCS” ethical committee (protocol number 0010006/22, study ID 4770).

Procedures and outcomes

All patients included in the study received standard of care for COVID-19 as per NIH guidelines [14]. Anakinra was administered subcutaneously at the dose of 100mg once a day, and the treatment was continued for up to ten days, according to patient response. Onset of significant adverse events, such as severe bacterial infection, granulocytopenia or acute elevation of liver enzymes was also considered as an indication for treatment discontinuation. As part of routine laboratory exams requested for all COVID-19 patients, D-dimer, IL-6, Ferritin and CRP levels were measured, along with suPAR, on the day of hospitalization, and SCOPE score was calculated. Bacterial co-infection was defined as infection being diagnosed within the first 48 hours of hospital admission for COVID-19. When diagnosis occurred ≥ 48 hours after admission for COVID-19, these infections were defined as bacterial superinfections.

The main outcome of the study was disease progression at day 14 from admission. This was assessed using a simplified version of the WHO Clinical Progression Scale (WHO-CPS) [15]: a score of 1 was given for uninfected/ambulatory disease (WHO-CPS score 0–3), 2 for moderate disease (WHO-CPS score 4–5), 3 for severe disease (WHO-CPS score 6–9) and a score of 4 in case of death (WHO-CPS score 10). The same score was used by SAVE and SAVE-MORE studies, making the results of this real-world retrospective study more comparable to the ones of clinical trials.

Secondary outcomes were crude in-hospital mortality rate, length of hospitalization, development of severe respiratory failure with PaO2/FiO2 below 100 and 150 mmHg, and incidence of anakinra-related adverse events.

Statistical analysis

The analysis aimed to investigate clinical and laboratory characteristics by comparing patients included in the anakinra group with patients belonging to the two control groups, as follows: patients treated with anakinra vs. patients with suPAR levels ≥ 6 ng/mL who were not treated with anakinra (CG1), and patients treated with anakinra vs. patients with suPAR levels < 6 ng/mL (CG2). Continuous variables were described using median and interquartile ranges, and categorical variables using frequencies and percentages. Wilcoxon rank-sum test was used to compare continuous variables and Pearson’s χ2 test for categorical variables. A p-value of <0.05 was used to consider differences statistically significant. Since the p-value was potentially affected by small sample sizes, standardized differences (SD) were calculated by dividing the difference between the groups by the pooled standard deviation of the two groups (see S3 Table). An SD > 0.1 was interpreted as a meaningful difference. A propensity score (PS) of receiving anakinra was estimated through the use of a generalized boosted model. Covariates to include in the PS were identified by selecting variables with an SD > 0.1 in the comparison between patients with suPAR ≥ 6 ng/mL who were treated with anakinra, and patients not treated with anakinra (CG1). Variables with SD > 0.1 included in the PS were: age, smoker status, coronary artery disease, cerebrovascular disease, chronic kidney disease, PaO2/FiO2 ratio, C-reactive protein levels, white blood cells count, ferritin levels, D-dimer levels, use of dexamethasone, use of remdesivir, and the co-presence of a bacterial infection. A patient who was treated with anakinra was weighted by the inverse of the probability that he or she would be treated with anakinra, and a patient who did not receive anakinra was weighted by the inverse of the probability that he or she would not receive anakinra, equivalent to 1 minus his or her propensity score. The balance of the propensity model was later evaluated by verifying the obtained balance of PS covariates if they had an SD < 0.1 (see S1 Fig) and by comparing the baseline characteristics of the two exposure groups after applying the inverse probability of treatment weighting (IPTW). After that, crude and propensity-weighted single and multiple logistic regression models were performed to evaluate risk factors independently associated with the modified-WHO progression scale. Variables in the multiple logistic regression were restricted to only three due to respect the numerosity of outcomes and they were included if they had an influence on the primary outcome based on clinical importance by investigators’ consensus. Variables included in the model were: anakinra use, age, and PaO2/FiO2 ratio. Odds ratios and 95% confidence intervals (CI) were calculated. Multicollinearity was assessed by computing the variance inflation factor. Model predictive performances were assessed by calculating the ROC curve and the R2.

In the population of patients not treated with anakinra (CG1 and CG2), baseline suPAR and SCOPE score performances in predicting progression to severe disease and death were analyzed. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated by a 2 x 2 table. Diagnostic odds ratio and positive and negative likelihood ratios (LR+, LR−) were also estimated. Pearson’s χ2 tests was run to assess heterogeneity of sensitivities and specificities between the two predictors, the null hypothesis being in both cases that all are equal.

Statistical analyses were performed with R software version 4.0.5 and RStudio version 1.4.1106 [16].

Results

Between July 1, 2021 and January 31, 2022, 153 patients were included. Among them, 56 were treated with off-label anakinra, 49 retrospectively fulfilled prescriptive criteria for anakinra and were assigned to CG1, and 48 presented with suPAR levels < 6ng/mL and were assigned to CG2. Baseline characteristics of the overall population and of the three study groups and are reported in Table 1, while outcomes are reported in Table 2.

Table 1. Patient’s characteristics.

Overall (n = 153) suPAR < 6ng/mL suPAR ≥ 6 ng/mL
Control Group 2b (n = 48) Control Group 1a (n = 49) Anakinra group (n = 56)
p-valuec
Age, years, median (quartiles) 67 (55–77) 63 (50–74) 68 (60–79) 67 (57–78) 0.54
Male sex, n (%) 99/153 (64.7) 28/48 (58) 32/49 (65) 39/56 (70) 0.64
Fully vaccinated, n (%) 62/146 (42.8) 20/45 (44) 20/45 (44) 22/55 (40) 0.65
BMI, median (quartiles) 26.6 (24.1, 30.3) 27.2 (22.6–31.7) 26.8 (24.5–30.3) 26.2 (24.7–28.7) 0.91
Comorbidities, n (%)
    Smoking 12/153 (7.8)  3/48 (6.2) 2/49 (4.1) 7/56 (12) 0.17
    COPD 13/153 (8.5)  4/48 (8.3) 4/49 (8.2) 5/56 (8.9) >0.99
    High blood pressure 72/153 (47.1)  21/48 (44) 24/49 (49) 27/56 (48) 0.94
    Coronary artery disease 24/153 (15.8)  1/48 (2.1) 9/48 (19) 14/56 (25) 0.44
    Congestive heart failure 7/153 (4.6)  1/48 (2.1) 3/49 (6.1) 3/56 (5.4) >0.99
    Atrial fibrillation 12/153 (7.8)  2/48 (4.2) 4/49 (8.2) 6/56 (11) 0.75
    Stroke 7/153 (4.6)  3/48 (6.2) 4/49 (8.2) 0/56 (0) 0.044
    Diabetes mellitus 29/153 (18.9) 6/48 (12) 10/49 (20) 12/56 (21) >0.99
    Chronic kidney disease 10 (6.5) 3/48 (6.2) 2/49 (4.1) 5/56 (8.9) 0.44
Symptom onset-admission, days, median (quartiles) 6.0 (3.0, 9.0) 6.5 (5.0, 9.0) 5.0 (2.0, 8.0) 7.0 (3.8, 9.0) 0.18
Bacterial co-infection, n (%) 7/153 (4.6)  1/48 (2.1) 5/49 (10) 1/56 (1.8) 0.10
Bacterial supernfection, n (%) 21 (13.7) 5/48 (10) 7/49 (14) 9/56 (16) 0.80
PaO2/FiO2 ratio at baseline, mmHg, median (IQR) 250 (206–283) 274 (241–295) 240 (196–269) 240 (198–272) 0.81
Laboratory values at baseline, median (quartiles)
    Lymphocytes, cells/mm3 1010 (750–1395) 1165 (880–1480) 940 (740–1460) 910 (730–1200) 0.77
    WBC, cells/mm3 6440 (4735–8585) 6335 (4195–9612) 7030 (5045–8808) 6200 (5005–8110) 0.72
    IL-6, ng/L 18 (8–46) 13 (7–29) 20 (8–59) 32 (8–60) 0.89
    Ferritin, ng/mL 637 (276–1379) 530 (253–1080) 964 (375–1570) 515 (246–1321) 0.12
    D-dimer, ng/mL 757 (534–1317) 580 (367–1293) 854 (618–1394) 790 (575–1300) 0.66
    CRP, mg/L 71 (36–116) 60 (20–94) 106 (39–156) 68 (39–124) 0.26
    SCOPE score 8 (6–9) 6 (5–8) 8 (6.3–10) 8 (6.3–9) 0.47
    suPAR, ng/mL 6.9 (5.3–9.2) 4.8 (4.1–5.3) 9 (7–11.6) 8 (6.8–9.8) 0.14
In-hospital therapy, n (%)
    Anakinra duration (days)   - - 6 (5, 8) -
    Dexamethasone 143/153 (94.1)  41/47 (87) 46/49 (94) 56/56 (100) 0.10
    Remdesivir 49/153 (32) 19/47 (40) 12/49 (24) 17/56 (30) 0.58
    Tocilizumab 11/153 (7.2)  2/47 (4.3) 9/49 (18) 0/56 (0) <0.001
    Monoclonal antibodies 9/153 (5.9)  6/47 (13) 2/49 (4.1) 1/56 (1.8) 0.60

COPD: chronic obstructive pulmonary disease; ICU: intensive-care unit; HFNC: high-flow nasal cannula

a patients who retrospectively fulfilled the prescriptive criteria for anakinra but did not receive the drug.

b patients admitted for COVID-19 pneumonia but who presented with baseline suPAR < 6 ng/mL.

c p-values from the comparison between anakinra group and CG1.

Table 2. Outcomes.

Overall (n = 153) suPAR < 6ng/mL suPAR ≥ 6 ng/mL
Control Group 2b (n = 48) Control Group 1a (n = 49) Anakinra group (n = 56)
p-valuec
    Supplementary oxygen, days, median (quartiles) 10 (7, 17) 7 (5, 11) 14 (9, 20) 10 (8, 15) 0.032
    Length of stay, days, median (quartiles) 11 (8, 19) 10 (7, 14) 15 (10, 23) 11 (8, 18) 0.008
    Need of high flow oxygen between days 1 and 14 n (%) 42/153 (27.5)  6/48 (12) 20/49 (41) 16/56 (29) 0.19
    PaO2/FiO2 < 100, n (%) 17/153 (11.1)  1/48 (2.1) 9/49 (18) 7/56 (12) 0.40
    PaO2/FiO2 < 150, n (%) 40/153 (26.1)  4/48 (8.3) 23/49 (47) 13/56 (23) 0.011
    Admission to ICU, n (%) 4/153 (2.6)  0/48 (0) 2/49 (4.1) 2/56 (3.6) >0.99
    Non-invasive ventilation, n (%) 3/153 (2)  0/48 (0) 2/49 (4.1) 1/56 (1.8) 0.60
    Mechanical ventilation, n (%) 1 (0.7)  0/48 (0) 0/49 (0) 1/56 (1.8) >0.99
Allocation to strata of the WHO Clinical Progression Scale at day 14, n (%) Odds ratio 0.25 (0.11–0.54) p<0.0001 d
    0–3 87/149 (58.4) 36/47 (77) 17/49 (35) 34/54 (64)  
    4–5 47/149 (3.5) 9/47 (19) 22/49 (45) 16/54 (30)  
    6–9 9/149 (6) 2/47 (4.3) 5/49 (10) 2/54 (3.8)  
    10 6/149 (4) 0/47 (0) 5/49 (10) 2/54 (1.9)  
In-hospital death, n (%) 11/153 (7.2) 1/48 (2.1) 6/49 (12) 4/56 (7.1) 0.51

a patients who retrospectively fulfilled the prescriptive criteria for anakinra but did not receive the drug.

b patients admitted for COVID-19 pneumonia but who presented with baseline suPAR < 6 ng/mL.

c p-values from the comparison between anakinra group and CG1.

d Ordinal regression analysis comparing anakinra group and CG1.

Overall, median age was 67 years (interquartile range, IQR, 55–77), 65% of enrolled subjects were males and median BMI was 26.6 (IQR, 24–30). Forty-three percent of included subjects were fully vaccinated. Patients belonging to the three group presented no significant differences in age, BMI, sex, vaccine status, time since symptom onset or comorbidities (with the exception of stroke). Median PaO2/FiO2 ratio at baseline was 250 mmHg (IQR 206–283). When comparing anakinra group with CG1, there was no significant difference in baseline levels of CRP, ferritin, IL-6, white blood cell count and SCOPE score. Also, even though severe bacterial co-infection was a contraindication to receive anakinra, no significant difference was noted between the two groups. P-values from the comparison between anakinra group and the CG1 are reported in Tables 1 and 2, while direct comparison between anakinra group and CG2 is reported in the appendix (pp 2–3). Median duration of oxygen therapy and hospital stay were, respectively, 10 (IQR, 7–17) and 11 days (IQR, 8–19).

Overall, 94% of study patients received dexamethasone, 32% received remdesivir, 7% tocilizumab and 6% received monoclonal antibodies against COVID-19. Median duration of anakinra was 6 days (IQR, 5–8). The drug was discontinued due to adverse event in two cases, once for liver enzymes elevation and once for development of pancytopenia. Incidence of bacterial co-infection was similar among the three groups.

When compared to CG1, patients in the anakinra group experienced less days of supplementary oxygen (10 vs 14 days, p-value = 0.032), had shorter hospital stay (11 vs 15 days, p-value = 0.008), and were less likely to progress to severe respiratory failure with PaO2/FiO2 < 150mmHg (23% vs. 47%, p-value = 0.011) during hospitalization. The results of the crude logistic regression model are reported in Table 3. As further shown in Table 4, receiving anakinra was associated with significantly reduced odds for progressing towards severe disease or death in the propensity-adjusted multiple logistic regression analysis (OR 0.32, p-value = 0.021), along with age (OR 1.09, p-value<0.001). However, no differences were recorded in HFNC use (29% vs. 41%, p-value = 0.19), ICU admission (3.6% vs. 4.1%, p-value>0.99) and death (7.1% vs. 12%, p-value = 0.51). Length of hospital stay and time to progression towards ARDS (defines as PF < 150 and use of HFNC) are shown in Fig 1, while day 14 allocation in the WHO-CPS are shown in Fig 2.

Table 3. Crude multiple logistic regression for risk factors associated with progression towards severe disease or death at day 14.

Population: patients with baseline suPAR ≥ 6ng/mL who fulfilled the prescriptive criteria for anakinra (n = 105)
Variable Univariable Multivariable
OR1 95% CI1 p-value OR1 95% CI1 p-value
Age (years) 1.07 1.03, 1.13 0.005 1.09 1.03, 1.15 0.004
Anakinra 0.31 0.08, 1.01 0.064 0.32 0.08, 1.12 0.087
PaO2/FiO2 ratio 1.00 0.99, 1.01 0.371 0.99 0.98, 1.00 0.154

OR: Odds Ratio; CI: Confidence Interval.

Severe disease is defined according to the WHO Clinical Progression Scale (WHO-CPS score 6–10).

Table 4. Propensity-adjusted multiple logistic regression for risk factors associated with progression towards severe disease or death at day 14.

Population: patients with baseline suPAR ≥ 6ng/mL who fulfilled the prescriptive criteria for anakinra (n = 105)
  Variable Univariable Multivariable
OR1 95% CI1 p-value OR1 95% CI1 p-value
    Age (years) 1.07 1.04, 1.12 < 0.001 1.09 1.05, 1.14 < 0.001
    Anakinra 0.34 0.13, 0.79 0.016 0.32 0.12, 0.82 0.021
    PaO2/FiO2 ratio 1.00 0.99, 1.00 0.243 0.99 0.98, 1.00 0.051

OR: Odds Ratio; CI: Confidence Interval.

Severe disease is defined according to the WHO Clinical Progression Scale (WHO-CPS score 6–10).

Fig 1. Time to progression towards ARDS and length of hospital stay of patients with baseline SuPAR ≥ 6 ng/mL who received and did not receive anakinra.

Fig 1

Time to progression to ARDS (A) and length of hospital stay (B) of patients admitted for COVID-19 with baseline SuPAR ≥ 6 ng/mL and non-severe respiratory failure who received and did not receive anakinra. ARDS was defined as PaO2/FiO2 < 150 mmHg and use of high-flow oxygen therapy/NIV or MV. COVID-19 = coronavirus disease 2019. ARDS = acute respiratory distress syndrome. SuPAR = soluble urokinase plasminogen activator receptor. HR = hazard ratio.

Fig 2. Disease progression at day 14 from hospital admission.

Fig 2

Distribution of the WHO-CPS scores at day 28 of patients admitted for COVID-19 with baseline SuPAR ≥ 6 ng/mL and non-severe respiratory failure who received and did not receive anakinra (Control Group 1). Comparison is done by unadjusted ordinal regression analysis; the ORs of the 95% CIs are provided. COVID-19 = coronavirus disease 2019. SuPAR = soluble urokinase plasminogen activator receptor. OR = odds ratio.

When ordinal regression analysis was done comparing the allocation of the WHO-CPS strata by day 14 (Table 2), it was found that anakinra treatment was associated with 0.25 odds for less worse outcome than comparators (p-value <0.0001). This is fully corroborating the analysis of anakinra efficacy of the SAVE-MORE trial [8].

Performances of baseline suPAR and SCOPE score in predicting progression towards severe disease or death at day 14 from admission are reported in Fig 3. Overall, sensitivities were similar (83% vs 100%, p-value = 0.59) but suPAR was more specific (54% vs 29%, p-value = 0.003). In this study, SCOPE score negative predictive value was 100%.

Fig 3. suPAR vs SCOPE score performances in predicting progression to severe disease or death at day 14.

Fig 3

Severe disease is defined according to the WHO Clinical Progression Scale (WHO-CPS score 6–10). CI = Confidence Interval; LR = likelihood ratio.

Discussion

Our study confirmed the clinical benefit of administration of subcutaneous anakinra in preventing disease progression in patients hospitalized for COVID-19 pneumonia with elevated suPAR levels at the time of admission. To our knowledge, this is the first study exploring performances of suPAR in identifying candidates to receive anakinra outside of a clinical trial. Here, patients treated with anakinra were compared to two control groups of patients who did not receive anakinra, respectively with ≥ 6 ng/mL and < 6 ng/mL baseline suPAR. This was done to further explore the role of this biomarker in early patient identification.

Among the 105 subjects with elevated suPAR levels at admission, 56 patients were treated with off-label anakinra and showed significantly lower odds of worsening to severe disease and death by day 14, and these results were confirmed even when controlling for age and PaO2/FiO2 ratio. Disease severity was defined in accordance with the WHO clinical progression scale, a composite outcome that defines “severe disease” as progression towards respiratory failure requiring high-flow oxygen therapy and/or non-invasive and/or invasive mechanical ventilation at a certain time point [15]. In addition, individuals who received anakinra experienced a 4-day shorter median hospital stay and were less likely to evolve towards severe respiratory failure with PaO2 / FiO2 below 150mmHg during hospitalization. Importantly, patients belonging to both control groups were paired for date of admission and were selected to have similar age, sex and rate of vaccination against SARS-CoV2 to patients treated with anakinra (Table 1). Coupling for date of admission was done to avoid differences in standard of care (SoC) and circulating COVID variants, since Delta and Omicron variants were associated with varying disease severity [17] and published data from clinical trials were obtained from patients hospitalized before both variants became dominant in Europe [18, 19]. Also, data from clinical trials did not control the benefit of anakinra for patients fully vaccinated against SARS-CoV2, as mass vaccination campaigns initiated few months before the end of SAVE-MORE enrollment.

In this study, there were no significant differences in the rate of vaccinated and non-vaccinated individuals and, among patients with elevated suPAR, the magnitude of the efficacy of anakinra in preventing disease progression was maintained regardless to vaccine status. Being vaccinated was in fact associated with a trend towards higher odds of disease progression, but this may be biased by the fact that vaccinated people were older and generally presented more risk factors for disease progression than non-vaccinated people (appendix, pg 4). Interestingly, along decreased odds for disease progression, non-vaccinated people presented with a lower baseline PaO2/FiO2 and increased inflammatory markers, thus suggesting that anakinra benefit may be more pronounced in this population.

Furthermore, among patients with elevated suPAR baseline levels, there was no statistical difference in terms of prescription of dexamethasone, remdesivir, and anti-SARS-CoV2 monoclonal antibodies. By contrast, when compared to patients treated with anakinra, individuals with low baseline suPAR showed a more favorable baseline profile and evolved towards less severe infections (appendix, pp 2–3).

A peculiar finding of the present study is that median duration of anakinra was 6 days (IQR, 5–8), in contrast with SAVE-MORE study protocol, which called for a treatment duration of 10 days and in any case not inferior to 7 days [20]. Being a retrospective, real-world study, a minimum treatment duration was not defined, leaving the decision whether to keep treating or discontinue to the attending clinician. Therefore, apart from two cases (3.6%), in which potentially drug-related adverse events occurred, anakinra was interrupted due to clinical benefit, namely the resolution of respiratory failure and withdrawal of oxygen supplementation.

The prescriptive heterogeneity reported here is a consequence of the fact that some of the prescribers in charge for the patients participated to SAVE-MORE clinical trial, and the clinical experience gained during trial recruitment influenced their familiarity with both suPAR predictive accuracy and anakinra safety profile. Thus, it is likely that this experience led to the acquisition of the confidence necessary to keep prescribing anakinra also in their daily practice, outside of the clinical trial, as an off-label medication. Indeed, only clinicians who participated to the SAVE-MORE trial became familiar with suPAR interpretation, since the measurement of this biomarker was implemented in our center only at the beginning of the study period. Thus, at the time of prescription, there was no intent to allocate patients to any “intervention” or “control” group. There were no specific clinical reasons why CG1 patients did not receive the study drug and data collection, group allocation and matching were entirely retrospective. Written informed consent for administration of any off-label medication was required by our institution.

These findings support the assumption that a biomarker-guided, early prescriptive strategy of an immunomodulatory drug for the treatment of an acute infection is still challenging to be implemented, even in a setting where the biomarker is readily available. However, recognition of the importance of the role of biomarkers in early patient identification is critical in guiding IL-1 blockade, since several studies, both randomized [21, 22] and observational [23, 24], reported conflicting results–as well as a Cochrane systematic review [25]–likely as a consequence of the fact that IL-1 antagonists prescribed at a disease stage that was already too advanced for the drug to provide substantial benefit. Yet, poor availability of suPAR assays is a major limitation for this approach, as non-widespread suPAR availability was cited by NIH guidelines to be the key factor preventing anakinra to enter among the Panel recommended drugs [26]. In this respect, this study provides further evidence to support the role of the SCOPE score as an alternative to baseline suPAR. This was done in line with the assumption, consistent with the work of Giamarellos-Bourboulis et al. [10], that SCOPE score may serve as an alternative marker of early activation of the pathological processes that foster COVID-19 disease progression, namely the inflammatory, endothelial and coagulation pathways. Indeed, our retrospective analysis confirmed that suPAR and SCOPE score have similar sensitivities in predicting severe disease and death at day 14. Importantly, in individuals who were not treated with anakinra, SCOPE score showed a negative predictive value of 100%, thus supporting its potential value in guiding prescriptive decision making.

Our study has obvious limitations. First, being retrospective and observational in nature, its results may be biased by confounding factors that could have affected clinical progression apart from the study drug. However, baseline characteristics among the three groups, and especially among anakinra group and patients with baseline suPAR ≥ 6ng/mL (CG1), were similar. Furthermore, as discussed above, this risk was minimized by selecting controls according to age, vaccine status and gender. Second, observational studies carry the risk of immortal time bias [27], but this bias has been minimized by the fact that we excluded patients admitted or considered for admission in ICU. Also, even if they have intrinsic limitations, observational studies have the advantage to provide data from real-world scenario, without the selection bias that may affect perspective studies. Third, it is important to acknowledge that the results may have been biased by a low sample size, even if the results are consistent with the findings of clinical trials. Fourth, the main study outcome did not differentiate between asymptomatic and mildly symptomatic disease, as well as, among patients categorized as developing “severe disease”, between the ones treated with HFNC, mechanical ventilation, vasopressors, dialysis and ECMO (WHO-CPS score 6 to 9).

Conclusions

In conclusion, this real-word, retrospective cohort study confirmed the safety and the efficacy of suPAR-guided, early use of anakinra in hospitalized COVID-19 patients with respiratory failure. Our results support the indication that all COVID patients with suPAR levels ≥ 6ng/ml at time of hospitalization should receive anakinra, including the ones belonging to the control group of this study.

Also, it provides further evidence in support of the utilization of SCOPE score in guiding clinical decision-making as an alternative to suPAR. However, despite its approval by drug regulatory agencies, further evidence is needed for the widespread dissemination of this personalized, biomarker-guided therapeutic approach to COVID-19.

Supporting information

S1 Fig. Covariates balance after applying the generalized boosted model to estimate the propensity score of receiving anakinra.

(DOCX)

S1 Table. Patients with suPAR < 6 ng/mL vs patients treated with anakinra.

(DOCX)

S2 Table. Fully vaccinated vs non vaccinated individuals, descriptive statistics.

(DOCX)

S3 Table. Standardized mean differences (SMD) comparing patients with suPAR≥ 6 ng/mL treated with anakinra (1) and not treated with anakinra (0).

(DOCX)

S1 Dataset

(XLSX)

Acknowledgments

We thank Francesca Schinzari, Annalisa Potenza (Policlinico “A. Gemelli” IRCCS, Malattie Infettive Columbus) and all the other fellow first-line colleagues of the “COVID Columbus” hospital who, despite working incessantly and passionately to contain COVID-19 pandemic, also found time to provide support for the development of this report.

Data Availability

Minimal data set has been added as Supporting Information file. Some data cannot be shared publicly because of Ethical Committee requirements. Data are available from the Policlinico Gemelli Institutional Data Access (contact via Silvia Lamonica, silvia.lamonica@policlinicogemelli.it) for researchers who meet the criteria for access to confidential data.

Funding Statement

The author(s) received no specific funding for this work.

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Decision Letter 0

Cecilia Acuti Martellucci

18 Oct 2022

PONE-D-22-21590Anakinra in hospitalized COVID-19 patients guided by baseline soluble urokinase plasminogen receptor plasma levels: a real world, retrospective cohort studyPLOS ONE

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Reviewer #1: REVIEW PONE

The Authors present a retrospective study evaluating the real-life use of subcutaneous anakinra (ANK) in patients with COVID-19 pneumonia. In the paper, three groups are described: patients with suPAR > 6ng/mL who received ANK, patients with suPAR <6ng/mL who did not receive ANK and patients with suPAR <6ng/mL. The Authors show that the use of ANK reduced the odds of progression toward worse clinical outcomes and hospital length of stay. The paper is well written and provides an interesting real-life experience on the use of ANK.

However, a few major points should be addressed:

- Line 97: the Authors should explain their definition of “severe” when defining bacterial co-infections;

- Line 110-111: it is not clear if patients who received anti-IL6 treatments were excluded or not, as in the paper 7% received tocilizumab; given that patients with immunosuppression were excluded, it does not seem that the Authors refer to previous treatment with anti-IL6 molecules for other condition; this issue should be clarified;

- Line 136: why did the Authors analyze two different cut-offs for severe respiratory failure (100 and 150)? Given the endpoints and the definition of ARDS I would use only the 150 cut-off;

- Was suPAR requested for all patients admitted with COVID-19 during the study period? If not, what are the characteristics of the patients for whom suPAR was and was not requested?

- The selection of patients in the control groups does not appear to be clear. Were all patients with suPAR >6ng/mL included in the study, or were only patients used for the matching procedure considered? If so, how many patients presented with suPAR>6ng/mL, were not treated with ANK and were not included in the study? And what were the characteristics of these patients?

- In the statistical analysis section, more information should be provided regarding the matching procedure and the associated analysis (i.e., use of conditional logistic regression analysis, which is suggested for this kind of studies).

- The time from admission to administration of ANK should be described;

- The main outcome is disease progression at day 14, using a simplified version of the WHO-CPS; however, in Figure 1 the Authors evaluated progression to ARDS; I believe it would be more coherent with the main outcome to describe time to progression towards severe disease (which was defined as WHO-CPS 6-9), and possibly leave progression to ARDS as a secondary outcome; moreover, the definition of ARDS should be coherent throughout the text (Line 203-204: PF<150 and use of HFNC; line 216-217 PF <150 and use of HFNC/NIV or MV).

- Results and table 3: where are the results of the matching cohort described? It seems from table 3 that 105 patients are included, i.e. 49+56. If a 1:1 matching was performed, the number of patients should be different.

- Line 269-275: the association between vaccine status and outcome is not statistically significant at univariate and multivariate analysis, so I would delete the phrase “Being vaccinated was in fact associated with a trend towards higher odds of disease progression, but this may be biased by the fact that vaccinated people were older and generally presented more risk factors for disease progression than non-vaccinated people (appendix, pg 4).”, while I would keep the following one (Line 272-275).

- Line 324: how did you exclude patients considered for admission to ICU?

- Figure 1: The difference between the two groups appears more significant in the first 24-48h. It seems that about 30% of patients in the control group progressed to ARDS in the first 24h, compared to 10% of patients in the ANK group, so it would be important to know the time of administration of ANK (see also the previous comment)

Minor comments:

- Line 92: 31rd should be changed to 31st

- Line 194: “co-infections” should probably be changed to “superinfections”

- Line 203: “defines” should be “defined”;

- Secondary outcomes are “crude in-hospital mortality rate, length of hospitalization, development of severe respiratory failure with PaO2/FiO2 below 100 and 150 mmHg, and incidence of anakinra-related adverse events”; however, in the results section, supplementary oxygen and ICU admissions are also described. This should be added in the methods section.

- Line 230-233: I would specify that patients analyzed did not receive anakinra (i.e: “performances of baseline suPAR and SCOPE score in predicting progression towards severe disease or death at day 14 from admission in patients non receiving ANK…”)

- Line 320-321: baseline characteristics were not very similar between patients with suPAR >6 and <6, so I would just say that patients with suPAR >6 had similar characteristics.

Reviewer #2: This is a small retrospective real-world study about supar guided anakinra treatment in COVID-19. This is the first study of real-world data. My concerns are as follows:

-As the study was retrospective, please make clear how written informed consent was received from participants. This is not clearly described and easy to follow.

-Please describe in more detail the matching statistical procedure.

-In the manuscript the authors describe that tocilizumab was an exclusion criterion but in Table 1 some participants have received tocilizumab. Please explain

-Table 1 and 2: it would be easier for the reader to provide here also p values of comparison with CG2 instead of supplement

- Incidence of bacterial co-infection was similar: it would be very interesting to provide these data

-Lines 288-299: here the authors discuss something very important, namely the Hawthorne effect. It is very important to have real world data and see how a strategy developed in the context of a clinical trial finds applicability and is easily implemented in everyday routine. This is of great value in real world data studies such as this one, which is the first after the two clinical trials for suPAR guided anakinra.

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Reviewer #1: No

Reviewer #2: Yes: Evdoxia Kyriazopoulou

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PLoS One. 2023 Apr 4;18(4):e0273202. doi: 10.1371/journal.pone.0273202.r003

Author response to Decision Letter 0


26 Nov 2022

Dear PLOS-One Editor,

please find attached a point-by-point response to Journal Requirements and to Reviewers.

Response to Journal Requirements

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming.

R: Style requirements have been checked on the provided links. Supplementary information have been renamed and title page has been reformatted.

2. In the Methods section of your revised manuscript, please amend lines 112-116 to match the description in lines 298-299 (Written informed consent for administration of any off-label medication was required by our institution).

R: To avoid redundancy and misunderstanding, the sentence “Written informed consent for administration of any off-label medication was required by our institution” has been removed.

3. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found.

R: Thank you for the remark. Minimal data set has been added as Supporting Information file.

4. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly.

R: File naming and in-text citations have been modified as per journal requirements.

Response to Reviewer #1

Major comments:

1. The Authors should explain their definition of “severe” when defining bacterial co-infections

R: Bacterial co-infection was considered “severe” when associated with life-threatening organ dysfunction (Singer et al. JAMA, 2016). Definition has been added in the text (Lines 105-106).

2. It is not clear if patients who received anti-IL6 treatments were excluded or not, as in the paper 7% received tocilizumab; given that patients with immunosuppression were excluded, it does not seem that the Authors refer to previous treatment with anti-IL6 molecules for other condition; this issue should be clarified

R: We thank the reviewer for the observation. Anti-IL6 treatment has been considered as an exclusion criterion for study enrollment as in our institutional protocol it was listed among the contraindications to anakinra administration. However, 18% (9/49) patients included in CG1 and 4.3% (2/47) patients included in CG2 received later during hospitalization, as part of the standard of treatment for COVID-19, accounting for 7.2% of the total population. In contrast, as shown in Table 1, patients who received anakinra did not receive anti-IL6 during the whole course of the hospitalization. The issue has been clarified in the text (Lines 121-124)

3. Why did the Authors analyze two different cut-offs for severe respiratory failure (100 and 150)? Given the endpoints and the definition of ARDS I would use only the 150 cut-off.

R: Thank you for the observation. We agree with the Reviewer, and we removed the 100mmHg cut-off.

4. Was suPAR requested for all patients admitted with COVID-19 during the study period? If not, what are the characteristics of the patients for whom suPAR was and was not requested?

R: Yes, once our laboratory implemented the suPAR assay, it was requested for every new COVID patient as part of the routine laboratory exams requested at admission.

5. The selection of patients in the control groups does not appear to be clear. Were all patients with suPAR >6ng/mL included in the study, or were only patients used for the matching procedure considered? If so, how many patients presented with suPAR>6ng/mL, were not treated with ANK and were not included in the study? And what were the characteristics of these patients?

R: Thank you for the observation. Matching was done by the authors of this study by directly looking for a suitable patient on the internal informatic system. For every patient treated with anakinra, all collectors followed the same matching procedure:

1. Searched for patients admitted for COVID-19 in the same time period (± 1 week).

2. Among patients admitted in the same time period, data collectors identified the ones with similar age (± 5 years), gender and vaccinal status. Those patients were then considered eligible for the study.

3. Screened for inclusion criteria.

4. Screened for exclusion criteria.

Hence, we did not collect data of all the other patients with baseline suPAR ≥ 6ng/ml, since the description of this population felt outside the scope of the present study.

More details about the matching procedure have been added in the text (Lines 112-120)

6. In the statistical analysis section, more information should be provided regarding the matching procedure and the associated analysis (i.e., use of conditional logistic regression analysis, which is suggested for this kind of studies).

R: As reported in the previous response, matching was done entirely by the authors of the study (E.R., F.S., F.C, F.S. and F.V.S.), actively looking for eligible patients within the hospital informatic system and, therefore, statistical analysis was introduced only upon data collection completion.

7. The time from admission to administration of ANK should be described.

R: We thank the Reviewer for the observation. Median time from admission to ANK administration was 1day (IQR: 1-2). We added this data to Table 1.

8. The main outcome is disease progression at day 14, using a simplified version of the WHO-CPS; however, in Figure 1 the Authors evaluated progression to ARDS; I believe it would be more coherent with the main outcome to describe time to progression towards severe disease (which was defined as WHO-CPS 6-9), and possibly leave progression to ARDS as a secondary outcome; moreover, the definition of ARDS should be coherent throughout the text (Line 203-204: PF<150 and use of HFNC; line 216-217 PF <150 and use of HFNC/NIV or MV).

R: We agree with the Reviewer: progression towards severe disease is indeed the main outcome, and progression towards ARDS is one the secondary outcomes. We clarified this in the Methods section (Lines 161-164) and, to avoid confusion, we inverted the naming of Figure 1 and Figure 2. As suggested by the reviewer, ARDS definition has been uniformed throughout the text.

9. Results and table 3: where are the results of the matching cohort described? It seems from table 3 that 105 patients are included, i.e. 49+56. If a 1:1 matching was performed, the number of patients should be different.

R: As reported in Table 1, matching cohort 1 and 2 (CG1 and CG2) were composed, respectively, by 49 and 48 patients. Unfortunately, to respect eligibility and inclusion criteria for controls, we were not able to reach exact 1:1 matching.

10. The association between vaccine status and outcome is not statistically significant at univariate and multivariate analysis, so I would delete the phrase “Being vaccinated was in fact associated with a trend towards higher odds of disease progression, but this may be biased by the fact that vaccinated people were older and generally presented more risk factors for disease progression than non-vaccinated people (appendix, pg 4).”, while I would keep the following one (Line 272-275).

R: We are grateful to the Reviewer for the observation. The phrase was removed from the text.

11. How did you exclude patients considered for admission to ICU?

R: We excluded patients considered for admission in ICU as they did not fulfil inclusion and exclusion criteria: in our center, all patients considered for COVID-ICU presented with severe respiratory failure with PaO2/FiO2 < 150mmHg requiring either high-flow oxygen therapy or NIV/MV.

12. Figure 1: The difference between the two groups appears more significant in the first 24-48h. It seems that about 30% of patients in the control group progressed to ARDS in the first 24h, compared to 10% of patients in the ANK group, so it would be important to know the time of administration of ANK (see also the previous comment).

R: We warmly thank the reviewer for this observation. It is correct, and it matches with the time of ANK administration (median: 1 day after admission). A dedicated sentence has been added in the Discussion section (Lines 306-310).

Minor comments:

13. Line 92: 31rd should be changed to 31st

14. Line 194: “co-infections” should probably be changed to “superinfections”

15. Line 203: “defines” should be “defined”;

R: The above sentences have been corrected.

16. Secondary outcomes are “crude in-hospital mortality rate, length of hospitalization, development of severe respiratory failure with PaO2/FiO2 below 100 and 150 mmHg, and incidence of anakinra-related adverse events”; however, in the results section, supplementary oxygen and ICU admissions are also described. This should be added in the methods section.

R: All secondary outcomes have been added in the Methods section (Lines 149-162).

17. Lines 230-233: I would specify that patients analyzed did not receive anakinra (i.e: “performances of baseline suPAR and SCOPE score in predicting progression towards severe disease or death at day 14 from admission in patients non receiving ANK…”)

18. Line 320-321: baseline characteristics were not very similar between patients with suPAR >6 and <6, so I would just say that patients with suPAR >6 had similar characteristics.

R: Thank you. We modified the sentences as suggested (Line 272 and 386).

Response to Reviewer #2

1. As the study was retrospective, please make clear how written informed consent was received from participants. This is not clearly described and easy to follow.

R: We thank the Reviewer for the observation. Along with (when necessary) asking for consent to off-label medications, in our center all COVID patients were asked for informed consent to use anonymized data for research purposes. This was a routine procedure in our hospital. This has been clarified in the methods section (Lines 126-127).

2. Please describe in more detail the matching statistical procedure.

R: Thank you for the observation. Matching was done by the authors of this study by directly looking for a suitable patient on the internal informatic system. For every patient treated with anakinra, all collectors followed the same matching procedure:

1. Searched for patients admitted for COVID-19 in the same time period (± 1 week).

2. Among patients admitted in the same time period, data collectors identified the ones with similar age (± 5 years), gender and vaccinal status. Those patients were then considered eligible for the study.

3. Screened for inclusion criteria.

4. Screened for exclusion criteria.

More details about the matching procedure have been added in the text (Lines 112-120).

3. In the manuscript the authors describe that tocilizumab was an exclusion criterion but in Table 1 some participants have received tocilizumab. Please explain.

R: We thank the reviewer for the observation. Anti-IL6 treatment has been considered as an exclusion criterion for study enrollment as in our institutional protocol it was listed among the contraindications to anakinra administration. However, 18% (9/49) patients included in CG1 and 4.3% (2/47) patients included in CG2 received later during hospitalization, as part of the standard of treatment for COVID-19, accounting for 7.2% of the total population. In contrast, as shown in Table 1, patients who received anakinra did not receive anti-IL6 during the whole course of the hospitalization. The issue has been clarified in the text (Lines 121-124).

4. Table 1 and 2: it would be easier for the reader to provide here also p values of comparison with CG2 instead of supplement.

R: We agree with the Reviewer. P-values obtained from the comparison of AG and CG2 have been moved from supplement to Table 1 and 2.

5. Incidence of bacterial co-infection was similar: it would be very interesting to provide these data.

R: The seven co-infections reported in the study were all presumptive bacterial pneumonia complicating COVID-19. Clinical suspicion raised mainly from CT-scan presentation and elevation in the polymorphonucleate count at admission. All patients were prescribed wide-spectrum empirical antimicrobial therapy. Unfortunately, none of the reported co-infections resulted positive to blood or sputum cultures.

6. Lines 288-299: here the authors discuss something very important, namely the Hawthorne effect. It is very important to have real world data and see how a strategy developed in the context of a clinical trial finds applicability and is easily implemented in everyday routine. This is of great value in real world data studies such as this one, which is the first after the two clinical trials for suPAR guided anakinra.

R: We warmly thank the Reviewer for this comment.

We are thankful for all the issues highlighted by reviewers. Hence, we believe that reviewer’s observations substantially improved the quality of our work.

Kind regards,

Francesco Vladimiro Segala

Attachment

Submitted filename: Response to Rewievers.docx

Decision Letter 1

Cecilia Acuti Martellucci

2 Jan 2023

PONE-D-22-21590R1Anakinra in hospitalized COVID-19 patients guided by baseline soluble urokinase plasminogen receptor plasma levels: a real world, retrospective cohort studyPLOS ONE

Dear Dr. Segala,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Feb 16 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Cecilia Acuti Martellucci, M.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

I thank the authors for the work done to improve the manuscript. Reviewer 2 has some further points that should be addressed before this paper can be considered for publication.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: (No Response)

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: (No Response)

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: (No Response)

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: (No Response)

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: I commend the Authors of the article for adequately addressing most of the comments raised in the first round of review. However, I believe that some issues still have to be resolved regarding the statistical analysis. Specifically:

- For the analysis of the primary outcome, the matching between the CG1 and the anakinra group should be 1:1 to respect the assumption of a matched-cohort study; in order to reach a 1:1 matching, therefore, some patients of the anakinra group who do not have an exact matching should be excluded from the analysis;

- The Authors state that ordinal regression analysis was used to explore risk factors associated with progression to severe disease or death; however, if the ordinal scale ranging from 6 to 10 was used as dependent variable, some of the categories would have 0 patients (especially in the anakinra group, where there are 2 patients in the “severe disease” group, ranging from 6 to 9); it would be more adequate to perform a binomial logistic regression analysis using as dependent variable progression to severe disease or death vs. no progression to severe disease or death);

- Given the number of patients with the outcome of interest (14 patients, according to table 1), the number of variables used in the multivariate analysis appears too high, according to the commonly used rule-of-thumb; moreover, it is not clear how the variables were chosen to be included in the multivariate analysis (as, for example, BMI and sex were not associated with the outcome in the univariate analysis); it would be more prudent to reduce the number of variables included in the multivariate analysis, possibly by selecting variable with significant p-values at univariable analysis;

- The statistical methods for the primary outcome should then be better specified in the “Statistical analysis” section.

Minor comment:

- I would add the word “manually” in line 111 (...patients included in both control groups were manually matched…)

Reviewer #2: (No Response)

**********

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Reviewer #1: No

Reviewer #2: Yes: Evdoxia Kyriazopoulou

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PLoS One. 2023 Apr 4;18(4):e0273202. doi: 10.1371/journal.pone.0273202.r005

Author response to Decision Letter 1


23 Jan 2023

Major comments:

1. For the analysis of the primary outcome, the matching between the CG1 and the anakinra group should be 1:1 to respect the assumption of a mahed-cohort study; in order to reach a 1:1 matching, therefore, some patients of the anakinra group who do not have an exact matching should be excluded from the analysis

R: Thank you for your considerable observation. In order to improve the internal validity of our study, we performed the analysis with a more rigorous methodology. Indeed, although the two cohorts initially appeared to be well-balanced with respect to important baseline characteristics, subtle imbalance may still be present if only looking at the p-value due to a small sample size effect. Thus, we evaluated the standardized mean differences (SMD) of the covariates between the two groups; in this way, we found that several covariates were actually differently distributed. For this reason, we went further by creating a propensity score (PS) of receiving anakinra to avoid unbalanced distribution of variables. After that, we use the PS to estimate the inverse probability of treatment weighting (IPTW), conducting the analysis adjusting for these weights. By such a method, we were able to use all patients, regardless of exactly matching 1:1, by assigning each patient a weight [1].

2. The Authors state that ordinal regression analysis was used to explore risk factors associated with progression to severe disease or death; however, if the ordinal scale ranging from 6 to 10 was used as dependent variable, some of the categories would have 0 patients (especially in the anakinra group, where there are 2 patients in the “severe disease” group, ranging from 6 to 9); it would be more adequate to perform a binomial logistic regression analysis using as dependent variable progression to severe disease or death vs. no progression to severe disease or death)

R: Thank you for the observation. For ordinal logistic regression, we used a simplified version of the simplified version of the 11-point World Health Organization Clinical Progression Scale, ranging from 1 (uninfected/ambulatory disease) to 4 (death). Severe disease (WHO-CPS score 6-9) are categorized with a score of 3 in the simplified version (lines 129-134, methods section), thus all patients are categorized. Unfortunately, due to the retrospective nature of our data, we were not able to use the full WHO-CPS scale. We agree with the reviewer that this represents a limitation, and we added a paragraph to highlight this in the dedicated section (lines 407-409). However, even using a simplified scale, with the aim to be more comparable with the SAVE-MORE results, the authors of this work consider ordinal regression analysis as a good tool to represent our results.

3. Given the number of patients with the outcome of interest (14 patients, according to table 1), the number of variables used in the multivariate analysis appears too high, according to the commonly used rule-of-thumb; moreover, it is not clear how the variables were chosen to be included in the multivariate analysis (as, for example, BMI and sex were not associated with the outcome in the univariate analysis); it would be more prudent to reduce the number of variables included in the multivariate analysis, possibly by selecting variable with significant p-values at univariable analysis.

R: Thank you very much for the precious observation. As stated in the response to the first comment, we modified the analysis using a propensity score of receiving anakinra along with the IPTW. We selected the variables to include in the PS by looking if the standardized mean differences of the covariates between the two groups were > 0.1 since this cutoff is generally considered a meaningful difference. Concerning the variables to include in the propensity-adjusted multiple logistic regression, we follow the rule of thumb as suggested to improve the validity of the results. Indeed, we included only 3 variables: anakinra use, age in years, and PaO2/FiO2 ratio. Those variables were selected by investigators’ consensus and clinical importance. We used these variables due to their profound impact on the outcome in order to evaluate the role of anakinra independently of them. Moreover, even if some covariates were not perfectly balanced in the PS (WBC, CRP, and PaO2/FiO2 ratio), we included only the PaO2/FiO2 ratio to further adjust for it; with respect to the other two variables, we avoided including them due to their SD < 0.25 not deeply influencing the overall balance, and to limit the number of predictors. We preferred not to use variables below a certain cutoff of p due to some caveats associated with this method, similar to stepwise selection strategies [2]. Doing so, we argued that our model is more explanatory respecting its original purpose and avoiding possible misleading results due to possible false-positive p.

4. The statistical methods for the primary outcome should then be better specified in the “Statistical analysis” section.

R: Thank you for your observation. We also agree with your considerations and rewrite the entire section as follows:

“The analysis aimed to investigate clinical and laboratory characteristics by comparing patients included in the anakinra group with patients belonging to the two control groups, as follows: patients treated with anakinra vs. patients with suPAR levels ≥ 6 ng/mL who were not treated with anakinra (CG1), and patients treated with anakinra vs. patients with suPAR levels < 6 ng/mL (CG2). Continuous variables were described using median and interquartile ranges, and categorical variables using frequencies and percentages. Wilcoxon rank-sum test was used to compare continuous variables and Pearson’s χ2 test for categorical variables. A p-value of <0.05 was used to consider differences statistically significant. Since the p-value was potentially affected by small sample sizes, standardized differences (SD) were calculated by dividing the difference between the groups by the pooled standard deviation of the two groups. An SD > 0.1 was interpreted as a meaningful difference. A propensity score (PS) of receiving anakinra was estimated through the use of a generalized boosted model. Covariates to include in the PS were identified by selecting variables with an SD > 0.1 in the comparison between patients with suPAR ≥ 6 ng/mL who were treated with anakinra, and patients not treated with anakinra (CG1). Variables with SD > 0.1 included in the PS were: age, smoker status, coronary artery disease, cerebrovascular disease, chronic kidney disease, PaO2/FiO2 ratio, C-reactive protein levels, white blood cells count, ferritin levels, D-dimer levels, use of dexamethasone, use of remdesivir, and the co-presence of a bacterial infection. A patient who was treated with anakinra was weighted by the inverse of the probability that he or she would be treated with anakinra, and a patient who did not receive anakinra was weighted by the inverse of the probability that he or she would not receive anakinra, equivalent to 1 minus his or her propensity score. The balance of the propensity model was later evaluated by verifying the obtained balance of PS covariates and by comparing the baseline characteristics of the two exposure groups after applying the IPTW. After that, crude and propensity-weighted single and multiple logistic regression models were performed to evaluate risk factors independently associated with the modified-WHO progression scale. Variables in the multiple logistic regression were restricted to only three due to respect the numerosity of outcomes and they were included if they had an influence on the primary outcome based on clinical importance by investigators’ consensus. Variables included in the model were: anakinra use, age, and PaO2/FiO2 ratio. Odds ratios and 95% confidence intervals (CI) were calculated. Multicollinearity was assessed by computing the variance inflation factor. Model predictive performances were assessed by calculating the ROC curve and the R2. In the population of patients not treated with anakinra (CG1 and CG2), baseline suPAR and SCOPE score performances in predicting progression to severe disease and death were analyzed. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated by a 2 x 2 table. Diagnostic odds ratio and positive and negative likelihood ratios (LR+, LR−) were also estimated. Pearson’s χ2 tests were run to assess heterogeneity of sensitivities and specificities between the two predictors, the null hypothesis being in both cases that all are equal.”.

Minor comments:

5. I would add the word “manually” in line 111 (...patients included in both control groups were manually matched…)

R: We added the word “manually” as suggested.

Attachment

Submitted filename: Response to Reviewers v2.docx

Decision Letter 2

Cecilia Acuti Martellucci

23 Feb 2023

PONE-D-22-21590R2Anakinra in hospitalized COVID-19 patients guided by baseline soluble urokinase plasminogen receptor plasma levels: a real world, retrospective cohort studyPLOS ONE

Dear Dr. Segala,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Apr 09 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Cecilia Acuti Martellucci, M.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments (if provided):

The manuscript is acceptable for publication, however please first amend the abstract according to the suggestion by Reviewer 1.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: (No Response)

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: (No Response)

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: (No Response)

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: (No Response)

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The Authors adequately addressed all the raised concerns.

The abstract should be modified according to the final version of the manuscript.

Reviewer #2: (No Response)

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

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Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: Yes: Evdoxia Kyriazopoulou

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2023 Apr 4;18(4):e0273202. doi: 10.1371/journal.pone.0273202.r007

Author response to Decision Letter 2


28 Feb 2023

Response to Reviewer #1

The Authors adequately addressed all the raised concerns. The abstract should be modified according to the final version of the manuscript.

R: Thank you. Abstract was modified.

Decision Letter 3

Cecilia Acuti Martellucci

7 Mar 2023

Anakinra in hospitalized COVID-19 patients guided by baseline soluble urokinase plasminogen receptor plasma levels: a real world, retrospective cohort study

PONE-D-22-21590R3

Dear Dr. Segala,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Cecilia Acuti Martellucci, M.D.

Academic Editor

PLOS ONE

Acceptance letter

Cecilia Acuti Martellucci

23 Mar 2023

PONE-D-22-21590R3

Anakinra in hospitalized COVID-19 patients guided by baseline soluble urokinase plasminogen receptor plasma levels: a real world, retrospective cohort study

Dear Dr. Segala:

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Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Cecilia Acuti Martellucci

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Fig. Covariates balance after applying the generalized boosted model to estimate the propensity score of receiving anakinra.

    (DOCX)

    S1 Table. Patients with suPAR < 6 ng/mL vs patients treated with anakinra.

    (DOCX)

    S2 Table. Fully vaccinated vs non vaccinated individuals, descriptive statistics.

    (DOCX)

    S3 Table. Standardized mean differences (SMD) comparing patients with suPAR≥ 6 ng/mL treated with anakinra (1) and not treated with anakinra (0).

    (DOCX)

    S1 Dataset

    (XLSX)

    Attachment

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    Attachment

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    Attachment

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    Data Availability Statement

    Minimal data set has been added as Supporting Information file. Some data cannot be shared publicly because of Ethical Committee requirements. Data are available from the Policlinico Gemelli Institutional Data Access (contact via Silvia Lamonica, silvia.lamonica@policlinicogemelli.it) for researchers who meet the criteria for access to confidential data.


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