Corrigendum to "Comparison of baseline patient characteristics in Italian oncology drug monitoring registries and clinical trials: a real-world cross-sectional study" [The Lancet Regional Health - Europe 41 (2024) 100912].

[This corrects the article DOI: 10.1016/j.lanepe.2024.100912.].

Comparison of baseline patient characteristics in Italian oncology drug monitoring registries and clinical trials: a real-world cross-sectional study.

Background: Generalizability of registrative clinical trials to real-world clinical practice is influenced by comparability of patients in the two settings. We compared characteristics of cancer patients in registrative trials with real-world clinical practice in Italy. Methods: Data on age, sex and performance status (PS) were derived from web-based monitoring registries developed by Italian Medicines Agency (AIFA) and corresponding registrative trials reported in the European Public Assessment Reports (EPAR) of European Medicines Agency (EMA). Weighted means were calculated in registries and trials and differences were described. Multivariate analysis was performed using Principal Component Analysis and Cluster Analysis. Findings: From January, 2013 to April, 2023, 419,461 unique pairs of patients and therapeutic indications were recorded in 129 AIFA registries. Within 140 related trials, 87,452 patients had been enrolled. Median age and rate of elderly (≥65 years old) patients were higher in monitoring registries than in clinical trials [mean difference of median age 5.3 years, p < 0.001; mean difference of elderly rate 17.17% (95% CI 1.06, 1.48)]. Overall, rate of female patients was not different between registries and trials [mean difference -0.55% (95% CI -1.06, -0.05)]. Mean rate of patients with deteriorated PS was low both in trials (3.1%) and in registries (4.3%) with a mean difference of 1.27% (95% CI 1.06, 1.48). Two clusters were identified with multivariate analysis: one including more registries (higher median age and elderly rate, lower female rate, higher rate of deteriorated patients), the other more trials (lower median age and elderly rate, higher female rate, lower rate of deteriorated patients). Interpretation: This study supports that cancer patients enrolled in trials do only partially represent those who have been treated in Italy in clinical practice. Inclusiveness of registrative trials should be increased to ensure generalizability of results to real-world population. Funding: Partially supported by Italian Ministry of Health.

Real-World Effectiveness of PCSK9 Inhibitors in Reducing LDL-C in Patients With Familial Hypercholesterolemia in Italy: A Retrospective Cohort Study Based on the AIFA Monitoring Registries.

Background Information on the real-world use of proprotein convertase subtilisin kexin 9 inhibitors (PCKS9is) in familial hypercholesterolemia are limited. We evaluated the pattern of prescription and the long-term efficacy of alirocumab and evolocumab in Italian patients with familial hypercholesterolemia in clinical practice. Methods and Results The data set for analysis was extracted from the PCKS9i Italian Medicines Agency (AIFA) registry and included 2484 patients with heterozygous familial hypercholesterolemia (HeFH) and 62 patients with homozygous familial hypercholesterolemia (HoFH) who were prescribed PCKS9is from February 2017 to December 2021. As the follow-up schedules were not prespecified and could vary, persistence and adherence as well as low-density lipoprotein cholesterol (LDL-C) changes during 2 years of treatment were analyzed in a final cohort of 1299 patients with familial hypercholesterolemia. At baseline, 53.8% of patients with HeFH and 69.4% of patients with HoFH were receiving maximally tolerated lipid-lowering therapies, while 45.9% of patients with HeFH and 30.7% of patients with HoFH reported statin intolerance; mean LDL-C was 197.7±52.3 mg/dL in HeFH and 252.0±106.2 mg/dL in HoFH. The 6-month persistence and adherence to therapy were >85%, and LDL-C reduction reached 58.6% (to 79.7 mg/dL) in HeFH and 57.6% (to 95.1 mg/dL) in HoFH after 24 months of treatment. The European Atherosclerosis Society/European Society of Cardiology LDL-C goals were achieved in 43.3% of patients with HeFH and 37.5% of patients with HoFH. Conclusions PCKS9i prescribed to patients with familial hypercholesterolemia in clinical practice showed LDL-C-lowering efficacy similar to that observed in controlled trials. However, 2 of 5 HeFH cases and 2 of 6 HoFH cases achieved the recommended LDL-C goals. The full achievement of European Atherosclerosis Society/European Society of Cardiology LDL-C goals should require a lower threshold for PCKS9i initiation and a combination of multiple therapies.

From Prioritization to Universal Treatment: Successes and Challenges of Hepatitis C Virus Elimination in Italy.

Italy has had the highest prevalence of hepatitis C virus (HCV) infection and mortality from HCV-related liver cancer in Europe. Although direct-acting antivirals (DAA) were initially restricted to persons with advanced fibrosis, their use has since been extended to all infected individuals; more than 244 000 persons have been treated to date. HCV liver-related mortality is expected to decline by 75% by 2030, achieving the World Health Organization target for mortality. However, Italy risks failing to meet the overall goal of eliminating HCV infection by 2030. In this light, €71.5 million have been allocated for screening initially specific target populations (persons who inject drugs, prison inmates, and the 1969-1989 birth cohort). Herein, we outline the challenges and recommendations for how to move Italy toward HCV elimination, including expanding screening programs in other populations, increasing awareness through strategic communication, sustaining DAA access, and tailoring care models to meet the needs of key populations.

Real-life comparison of mortality in patients with SARS-CoV-2 infection at risk for clinical progression treated with molnupiravir or nirmatrelvir plus ritonavir during the Omicron era in Italy: a nationwide, cohort study.

Background: Comparative data on mortality in COVID-19 patients treated with molnupiravir or with nirmatrelvir plus ritonavir are inconclusive. We therefore compared all-cause mortality in community-dwelling COVID-19 patients treated with these drugs during the Omicron era. Methods: Data collected in the nationwide, population-based, cohort of patients registered in the database of the Italian Medicines Agency (AIFA) were used. To increase completeness of the recorded deaths and date correctness, a cross-check with the National Death Registry provided by the Ministry of the Interior was performed. We included in this study all patients infected by SARS-CoV-2 treated within 5 days after the test date and symptom onset between February 8 and April 30, 2022. All-cause mortalities by day 28 were compared between the two treatment groups after balancing for baseline characteristics using weights obtained from a gradient boosting machine algorithm. Findings: In the considered timeframe, 17,977 patients treated with molnupiravir and 11,576 patients with nirmatrelvir plus ritonavir were included in the analysis. Most patients (25,617/29,553 = 86.7%) received a full vaccine course including the booster dose. A higher crude incidence rate of all-cause mortality was found among molnupiravir users (51.83 per 100,000 person-days), compared to nirmatrelvir plus ritonavir users (22.29 per 100,000 person-days). However, molnupiravir-treated patients were older than those treated with nirmatrelvir plus ritonavir and differences between the two populations were found as far as types of co-morbidities were concerned. For this reason, we compared the weight-adjusted cumulative incidences using the Aalen estimator and found that the adjusted cumulative incidence rates were 1.23% (95% CI 1.07%-1.38%) for molnupiravir-treated and 0.78% (95% CI 0.58%-0.98%) for nirmatrelvir plus ritonavir-treated patients (adjusted log rank p = 0.0002). Moreover, the weight-adjusted mixed-effect Cox model including Italian regions and NHS centers as random effects and treatment as the only covariate confirmed a significant reduced risk of death in patients treated with nirmatrelvir plus ritonavir. Lastly, a significant reduction in the risk of death associated with nirmatrelvir plus ritonavir was confirmed in patient subgroups, such as in females, fully vaccinated patients, those treated within day 2 since symptom onset and patients without (haemato)-oncological diseases. Interpretation: Early initiation of nirmatrelvir plus ritonavir was associated for the first time with a significantly reduced risk of all-cause mortality by day 28 compared to molnupiravir, both in the overall population and in patient subgroups, including those fully vaccinated with the booster dose. Funding: This study did not receive funding.

Outcomes in patients with chronic lymphocytic leukemia and TP53 aberration who received first-line ibrutinib: a nationwide registry study from the Italian Medicines Agency.

In this analysis we describe the effectiveness of first-line ibrutinib in 747 patients with chronic lymphocytic leukemia (CLL) and TP53 aberrations in a nationwide study with a 100% capture of patients who received the study drug. Median age was 71 years (range 32-95). An estimated treatment persistence rate of 63.4% (95% CI 60.0%-67.0%) and survival rate of 82.6% (95% CI 79.9-85.4%) were recorded at 24 months. Disease progression or death were the reasons for discontinuation in 182/397 patients (45.8%). A higher risk of treatment discontinuation was found to be associated with age, ECOG-PS and pre-existing heart disease, whereas ECOG ≥ 1, age ≥ 70 years and male sex were associated with an increased risk of death. Median post-progression overall survival (OS) was 12.2 months (95% CI 9.2-22.0). Post-discontinuation median OS in patients who discontinued ibrutinib for other reasons was not reached (95% CI 42.3 months - NA). Ibrutinib was an effective first-line treatment for CLL and TP53 aberrations in patients treated at large academic centers and community practice hospitals. Clinical characteristics at baseline may influence the effectiveness of ibrutinib, whereas the experience of prescribing centers and multi-hit or single-hit TP53 aberrations had no impact on outcome in this high-risk population.

Management of chronic myeloid leukaemia patients treated with ponatinib in a real-life setting: A retrospective analysis from the monitoring registries of the Italian Medicines Agency (AIFA).

Real-world data on daily practice management, treatment modifications and outcome of a large cohort of chronic myeloid leukaemia (CML) patients treated with ponatinib was performed through monitoring Registries of the Italian Medicines Agency (AIFA). Overall, 666 CML subjects were included in the ponatinib registry from February 2015 to December 2020 and were eligible for analysis: 515 in chronic phase (CP), 50 in accelerated phase (AP) and 101 in blast crisis (BC). Median age at baseline was 58.7 years with a predominance of male subjects (57.1%). The median time from diagnosis to start of ponatinib was 2.35 years: 259 (38.9%) subjects had received two previous lines of treatment, 260 (39.0%) three lines and 147 (22.1%) four or more lines. A molecular response [from major molecular response (MMR) to a score of ≤0.01% on the international reporting scale (IS)] was reported for 59% of patients out of 593 patients analysed. With a median follow-up of 14.4 months, 136 subjects (20.4%) required at least one dose reduction due to adverse events (AEs), whereas 309 patients (46.4%) required dose reduction in the absence of any evidence of side effects. Treatment discontinuation occurred in 261 patients (39%). This real-life analysis shows that dose reductions were made primarily as a precaution rather than due to the occurrence of adverse reactions.

Shape Complementarity Optimization of Antibody-Antigen Interfaces: The Application to SARS-CoV-2 Spike Protein.

Many factors influence biomolecule binding, and its assessment constitutes an elusive challenge in computational structural biology. In this aspect, the evaluation of shape complementarity at molecular interfaces is one of the main factors to be considered. We focus on the particular case of antibody-antigen complexes to quantify the complementarities occurring at molecular interfaces. We relied on a method we recently developed, which employs the 2D Zernike descriptors, to characterize the investigated regions with an ordered set of numbers summarizing the local shape properties. Collecting a structural dataset of antibody-antigen complexes, we applied this method and we statistically distinguished, in terms of shape complementarity, pairs of the interacting regions from the non-interacting ones. Thus, we set up a novel computational strategy based on in silico mutagenesis of antibody-binding site residues. We developed a Monte Carlo procedure to increase the shape complementarity between the antibody paratope and a given epitope on a target protein surface. We applied our protocol against several molecular targets in SARS-CoV-2 spike protein, known to be indispensable for viral cell invasion. We, therefore, optimized the shape of template antibodies for the interaction with such regions. As the last step of our procedure, we performed an independent molecular docking validation of the results of our Monte Carlo simulations.

Mortality in SARS-CoV-2 Hospitalized Patients Treated with Remdesivir: A Nationwide, Registry-Based Study in Italy.

Remdesivir is the first drug approved for treatment of COVID-19 but current evidence for recommending its use for the treatment of moderate-to-severe disease is still controversial among clinical guidelines. We performed a nationwide, registry-based study including all Italian hospitalized patients with COVID-19 treated with remdesivir to assess the impact of major confounders on crude 15-day and 29-day mortality. Mortality was calculated using the Kaplan-Meier estimator and the Cox proportional-hazards model was applied to analyze the risks by patient's baseline features. In total, 16,462 patients treated with remdesivir from 29 October 2020 to 17 December 2020 were entered in the study. Crude 15-day and 29-day mortality were 7.1% (95% CI, 6.7-7.5%) and 11.7% (95% CI, 11.2-12.2%), respectively. Being treated within two days of admission reduced the risk of death by about 40% (HR 1.4, 95% CI, 1.2-1.6). Results from the largest cohort of remdesivir-treated patients suggests that mortality in SARS-CoV-2 hospitalized patients is substantially influenced by the days between SARS-CoV-2 diagnosis and drug prescription. Current recommendations and future clinical trials for remdesivir alone or in combination should carefully consider the target population and timing for best efficacy of treatment.

An N-glycosylation hotspot in immunoglobulin κ light chains is associated with AL amyloidosis.

Immunoglobulin light chain (AL) amyloidosis is caused by a small, minimally proliferating B-cell/plasma-cell clone secreting a patient-unique, aggregation-prone, toxic light chain (LC). The pathogenicity of LCs is encrypted in their sequence, yet molecular determinants of amyloidogenesis are poorly understood. Higher rates of N-glycosylation among clonal κ LCs from patients with AL amyloidosis compared to other monoclonal gammopathies indicate that this post-translational modification is associated with a higher risk of developing AL amyloidosis. Here, we exploited LC sequence information from previously published amyloidogenic and control clonal LCs and from a series of 220 patients with AL amyloidosis or multiple myeloma followed at our Institutions to define sequence and spatial features of N-glycosylation, combining bioinformatics, biochemical, proteomics, structural and genetic analyses. We found peculiar sequence and spatial pattern of N-glycosylation in amyloidogenic κ LCs, with most of the N-glycosylation sites laying in the framework region 3, particularly within the E strand, and consisting mainly of the NFT sequon, setting them apart with respect to non-amyloidogenic clonal LCs. Our data further support a potential role of N-glycosylation in determining the pathogenic behavior of a subset of amyloidogenic LCs and may help refine current N-glycosylation-based prognostic assessments for patients with monoclonal gammopathies.

Impact of the COVID-19 pandemic on prescription of sacubitril/valsartan in Italy.

AIMS: The present study sought to examine the effect of the COVID-19 pandemic and lockdown measures on the prescription of sacubitril/valsartan in patients with heart failure (HF) in Italy. METHODS AND RESULTS: Data from Italian Medicines Agency (AIFA) monitoring registries were analysed. The sacubitril/valsartan monitoring registry is based on 6-month prescriptions. A monthly aggregation on new activations throughout the observational period was computed. From March to December 2020, the initiation of new HF patients on sacubitril/valsartan decreased by nearly 40% with prescriptions dropping to values similar to 2018 when the registry was still operated off-line. A slight increase in prescriptions was observed after the lockdown measures were lifted, but prescriptions remained constantly below the pre-lockdown period. CONCLUSION: A marked and worrisome decline during the COVID-19 pandemic in the activation of a life-saving treatment such as sacubitril/valsartan was observed. This decline was clearly linked to the lockdown measures instated to counteract the COVID-19 pandemic. Upcoming studies should analyse the occurrence of new cases of HF as well as the severity of patients admitted to hospitals and their mortality compared to pre-pandemic levels.

A nationwide prospective registry of bortezomib-based therapy in light chain (AL) amyloidosis.

Until recently, no drug was labeled for AL amyloidosis. In 2011, the Italian Medicines Agency started a program to grant access to upfront bortezomib to patients with AL amyloidosis. All subjects were enrolled in a prospective online registry. Response was evaluated after two cycles to assess the possibility of continuing treatment. A total of 764 patients were included until 2019, and 615 were evaluable. Sixteen percent of patents had advanced (stage-IIIb) heart involvement, and 27% had severe or end-stage renal failure. Bortezomib delivery was possible in stage-IIIb patients at a reduced dose. Bortezomib discontinuation was associated with increasing age, advanced heart involvement and bi-weekly administration. Fifty-nine percent of subjects attained a hematologic response and 14% a cardiac response. Bortezomib-based therapy tends to be discontinued early in elderly patients and in advanced disease. Nevertheless, early response to therapy is possible in this challenging population.

Mortality rate in patients with chronic myeloid leukemia in chronic phase treated with frontline second generation tyrosine kinase inhibitors: a retrospective analysis by the monitoring registries of the Italian Medicines Agency (AIFA).

The introduction of tyrosine kinase inhibitors (TKIs) has improved the overall survival of chronic myeloid leukemia patients in chronic phase (CP-CML) and reduced the rate of disease-related mortality. Conflicting results have been however reported between data emerged from sponsored clinical trials and from population-based registries. Moreover, no data are so far available for patients treated with frontline second-generation TKIs, excluding those from sponsored studies. We analyzed the mortality rate of 2315 CP-CML patients treated with frontline second-generation TKIs through the Italian Medicines Agency (AIFA) registries and compared it with the ISTAT mortality rate of the general population. The estimated differences show that the increased rate of mortality in CP-CML patients is less than 1% for the class 0-29 years, stable around 2% for the intervals 30-44 years and 45-59 years, and 1.4% for the interval 60-74 years; interestingly this rate is reduced for patients aged 75 years and more as compared to the general population (- 0.65%). The difference between potential and estimated deaths is higher among women in the age classes between 30 and 74 years.

proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking.

MOTIVATION: Monoclonal antibodies are essential tools in the contemporary therapeutic armory. Understanding how these recognize their antigen is a fundamental step in their rational design and engineering. The rising amount of publicly available data is catalyzing the development of computational approaches able to offer valuable, faster and cheaper alternatives to classical experimental methodologies used for the study of antibody-antigen complexes. RESULTS: Here, we present proABC-2, an update of the original random-forest antibody paratope predictor, based on a convolutional neural network algorithm. We also demonstrate how the predictions can be fruitfully used to drive the docking in HADDOCK. AVAILABILITY AND IMPLEMENTATION: The proABC-2 server is freely available at: https://wenmr.science.uu.nl/proabc2/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

How many chronic myeloid leukemia patients who started a frontline second-generation tyrosine kinase inhibitor have to switch to a second-line treatment? A retrospective analysis from the monitoring registries of the italian medicines agency (AIFA).

The frequency of patients who switch to a second-line therapy from a frontline second-generation (2gen) tyrosine kinase inhibitor (TKI) such as dasatinib and nilotinib, is still substantially unknown. We retrospectively investigated a large series of chronic phase chronic myeloid leukemia (CP-CML) patients initially treated with 2gen TKIs monitored through the Italian Medicines Agency (AIFA Agenzia Italiana del farmaco) registries. Overall, 2420 patients were analyzed over a period of 6 years. One hundred and fifty-seven patients (16.3%) treated with dasatinib and 164 treated with nilotinib (11.3%) have switched to another drug, with an overall frequency of 13.2%. In the dasatinib cohort, 39.4% of patients changed treatment for failure and 36.3% for intolerance as compared to 45.7% and 27.4% respectively in the nilotinib cohort. Overall, the median time to switch due to resistance was 293 days, whereas it was 317 days in case of intolerance. Resistance was observed mainly in younger male patients with high-risk features, while intolerance was not related to any baseline parameter. After resistance/intolerance to nilotinib, the majority of patients switched to dasatinib (53.8%) whereas in case of frontline dasatinib to ponatinib (43.2%). To the best of our knowledge these data provide the first report on the frequency of discontinuation of frontline 2gen TKIs and on the main causes and pattern of choice to a second-line therapy in the real-life setting.

Investigation of the binding between olfactory receptors and odorant molecules in C. elegans organism.

The molecular mechanisms regulating the complex sensory system that underlies olfaction are still not completely understood. The compounds formed from the interaction of Olfactory Receptors (ORs) with volatile molecules play a crucial role in producing the sense of olfaction. Therefore, it is necessary to investigate the binding mechanisms between these receptors and small ligands. In this work, we focus our attention on C.elegans, this is a particularly suitable model organism because it is characterized by a nervous system composed of only 302 neurons. To study olfaction in C.elegans, we select 21 ORs from its olfactory neurons, and present a pipeline, consisting of several computational methods, with the aim of proposing a set of possible candidates for binding the selected C.elegans ORs. This pipeline introduces an approach based on the selection of templates, and threading, that takes advantage of the structural redundancy among membrane receptors. This procedure is widely replicable because it is based on algorithms that are publicly available and are freely hosted on institutional servers.

Correlation analysis based on the hydropathy properties of non-steroidal anti-inflammatory drugs in solid-phase extraction (SPE) and reversed-phase high performance liquid chromatography (HPLC) with photodiode array detection and their applications to biological samples.

In the present work we analyzed the hydrophobicity and hydrophilicity properties of several non-steroidal anti-inflammatory drugs (NSAIDs) by investigating the structural changes of the dynamic hydrogen bond network in order to predict the extraction recovery of NSAIDs from biological fluids set by solid phase extraction (SPE). This work allows investigating the relationship between theoretical descriptors and experimental data using a parameter free method with a strong correlation (Pearson correlation 0.95, p-value 0.0003). The identification and quantification of analytes in human plasma were carried out by high performance liquid chromatography coupled with photodiode array detection (HPLC-PDA) using a Kinetex Evo C18 (150 x 4.6 mm I.D) protected by a guard column and a mixture of acetonitrile and 10 mM phosphate buffer (pH 2.5) (50:50, v/v) as mobile phase at isocratic conditions. Accuracy (BIAS%) ranged within -2.33% and + 8.05% while precision (RSD%) was less than 5.73%.The mean extraction recovery of the carprofen (IS) was 84.1% and the recovery of NSAIDs from human plasma ranged between 81.9% to 86.6%. LODs and LOQs for all the investigated NSAIDs were 0.003 and 0.01 µg/mL, respectively. The method was validated according to the ICH guide line in the range 0.010-20.0 µg/mL.

Insights on protein thermal stability: a graph representation of molecular interactions.

MOTIVATION: Understanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing the temperature at which proteins are stable has important theoretical implications, which are intimately linked with properties of the native fold, and a wide range of potential applications from drug design to the optimization of enzyme activity. RESULTS: Here, we present a novel graph-theoretical framework to assess thermal stability based on the structure without any a priori information. In this approach we describe proteins as energy-weighted graphs and compare them using ensembles of interaction networks. Investigating the position of specific interactions within the 3D native structure, we developed a parameter-free network descriptor that permits to distinguish thermostable and mesostable proteins with an accuracy of 76% and area under the receiver operating characteristic curve of 78%. AVAILABILITY AND IMPLEMENTATION: Code is available upon request to edoardo.milanetti@uniroma1.it. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.