MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery

MOTIVATION

Identification of interactions between bioactive small molecules and target proteins is crucial for novel drug discovery, drug repurposing and uncovering off-target effects. Due to the tremendous size of the chemical space, experimental bioactivity screening efforts require the aid of computational approaches. Although deep learning models have been successful in predicting bioactive compounds, effective and comprehensive featurization of proteins, to be given as input to deep neural networks, remains a challenge.

RESULTS

Here, we present a novel protein featurization approach to be used in deep learning-based compound-target protein binding affinity prediction. In the proposed method, multiple types of protein features such as sequence, structural, evolutionary and physicochemical properties are incorporated within multiple 2D vectors, which is then fed to state-of-the-art pairwise input hybrid deep neural networks to predict the real-valued compound-target protein interactions. The method adopts the proteochemometric approach, where both the compound and target protein features are used at the input level to model their interaction. The whole system is called MDeePred and it is a new method to be used for the purposes of computational drug discovery and repositioning. We evaluated MDeePred on well-known benchmark datasets and compared its performance with the state-of-the-art methods. We also performed in vitro comparative analysis of MDeePred predictions with selected kinase inhibitors' action on cancer cells. MDeePred is a scalable method with sufficiently high predictive performance. The featurization approach proposed here can also be utilized for other protein-related predictive tasks.

AVAILABILITY AND IMPLEMENTATION

The source code, datasets, additional information and user instructions of MDeePred are available at https://github.com/cansyl/MDeePred.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

d. Sous. Lopes SM. P–803 Novel culture conditions for the improvement of the in vitro expansion of human male fetal germ cells

Study question

Do different ECMs/substrates and growth media culture conditions improve in vitro male human primordial germ cell (hPGC) expansion?

Summary answer

We achieved in vitro expansion improvement of male hPGCs with specific growth factors such as LIF, EGF, FGF2 and GDNF on gelatin- and vitronectin-coating cultures.

What is known already

PGCs are the precursors of male and female gametes, which are specified during early mammalian post-implantation embryonic development. PGCs undergo sequential cell divisions to differentiate into pro-spermatogonia (pSPG). In vitro propagation of pSPG could be important to understand the transition to spermatogonial stem cells (SSCs), important for fertility preservation in patients with infertility. Here, we aimed at performing a comparative analysis on in vitro feeder-free culture systems, based on different extracellular matrix (ECM) and growth media culture conditions, to support the expansion of the male germline stem cell populations using second trimester human male gonads as primary material.

Study design, size, duration

We collected human 2nd trimester male fetal gonads from elective abortions. Male gonads were dissected in saline solution (0.9% NaCl) and were either fixed overnight in 4% paraformaldehyde (PFA) for immunohistochemistry or disaggregated by enzymatic digestion for in vitro culture.

Participants/materials, setting, methods

After differential plating, fetal cells were cultured for 6 days. Disaggregated gonads were cultured with two different growing media (Medium 1 supplemented with LIF, EGF, FGF–2 and GDNF and Medium 2 supplemented with RA, BMP 4 and Activin A) on gelatin, laminin, vitronectin or matrigel coated plates. Cultured cells were immunostained, quantified for the expression of DDX4 and POU5F1 after 3 days (D3) and 6 days (D6) of culture.

Main results and the role of chance

We pursued to evaluate whether germ cells dissociated from a pool of male fetal gonads could propagate in vitro when cultured for D6 in different conditions.

We observed that expansion of POU5F1-positive early PGCs and DDX4-positive late PGCs was only observed when cells were plated on gelatin or vitronectin and cultured with Medium 1, containing the growth factors LIF, EGF, FGF2 and GDNF. However, a reduced percentage of PGCs was observed in all four different coatings when grown with Medium 2, containing RA, BMP4 and Activin A.

We analyzed the relative expression of the PGC markers POU5F1, DDX4 and MAGEA4 in histological sections of gonads from embryos at 18.5 weeks of gestation. Two populations of hPGCs were observed: ∼10–30% of the gonadal cells expressed solely DDX4 (late PGCs), whereas less than 10% of gonadal cells expressed POU5F1 (early PGCs). SOX9 and STARD1 expression was evaluated, confirming the presence of Sertoli cells and Leydig cells, respectively.

Limitations, reasons for caution

Due to the limited and difficulty to obtain human fetal tissue, a limited number of samples were used.

Wider implications of the findings: We expanded human male fetal germ cells in vitro for D6 on gelatin and vitronectin coated plates with Medium 1, containing growth factors LIF, EGF, FGF2 and GDNF. Our findings provide a 2D culture system to expand hPGCs that could be useful to study propagation to pSPGs and eventually SSCs.

Trial registration number

Not applicable

P–563 Assessing ovarian age: Could we use leukocyte telomere length as a surrogate marker of cumulus cells telomere content?

Study question

Is leukocyte telomere length (LTL) correlated with cumulus cells telomere length (CCTL) in an age-heterogeneous women population?

Summary answer

LTL showed a positive correlation with CCTL in the studied population. Hence, its potential value as indicator of ovarian age would deserve further evaluation.

What is known already

Progressive telomere shortening has been related to ovarian aging and genomic instability during early development. A positive correlation between short telomere length of the first polar body and aneuploidy rate has been reported. CCTL has shown to be a biomarker of oocyte and embryo quality, but its assessment is impractical. LTL has been proposed as a surrogate of TL of follicular cells, but telomere lengthening through folliculogenesis could be controlled by different mechanisms. Thus, we aimed to determine if LTL in an age-heterogeneous population is correlated with CCTL and therefore considered an accurate surrogate for telomere length in the ovary.

Study design, size, duration

In this prospective non-interventional cohort study, 35 egg donors and 17 women undergoing Preimplantation Genetic Testing for Aneuploidy (PGT-A) treatment were included during sixteen months. Following controlled ovarian stimulation determined by treating physicians, oocyte retrieval was performed 36 hours after final maturation induction. Cumulus cells (CC) for telomere length (TL) measurement were obtained after the pick-up and oocyte stripping. A blood sample was collected through peripheral venous access for LTL measurement.

Participants/materials, setting, methods

Genomic DNA of CC and leukocytes from the 52 subjects was isolated. Average delta cycle threshold (ΔCt) was determined using a SYBR green quantitative real-time PCR protocol for relative TL. For normalization of measurements, a Taqman assay for the multicopy gene Alu was performed. ΔCtL and ΔCtCC were compared by a paired t-test analysis and the fold change was calculated. Additionally, the association between them and patient age was analyzed by a Pearson correlation test.

Main results and the role of chance

Mean participant’s age was 29.94 ± 7.55 years and mean values for ΔCtL and ΔCtCC were 7.99 ± 0.53 and 7.46 ± 0.75, respectively. A positive significant correlation was found between age and ΔCt (ΔCtL: R2=0.71, p-value=5.18e–09; ΔCtCC: R2=0.47, p-value=0.00049). Since ΔCt values are inversely proportional to the amount of nucleic acids amplified and, therefore, to the telomere length, this correlation means that TL in both cell types decreases as women age. Additionally, ΔCtL was significantly higher than ΔCtCC (ΔCt fold change: 0.93, p-value=9e–07), meaning that CC showed significantly longer telomeres than leukocytes, thus supporting our previous published results in young egg donors. When analyzing the ΔCtL and ΔCtCC in these age-heterogeneous sample, a positive moderate and significant correlation was observed (R2=0.42, p-value=0.002). Thus, LTL could be suggested as a potential indicator of CCTL and therefore as a candidate for a biological marker of ovarian aging.

Limitations, reasons for caution

The sample size of this study was moderate and perhaps increasing the number of subjects might give additional strength to our findings. In addition, although relative telomere length allowed for adequate comparison between subjects, this method did not allow for absolute TL measurement.

Wider implications of the findings: While reproductive implications of LTL measurement need to be further studied, our results support the potential usefulness of LTL measurement as an indicator of CCTL and ovarian aging when analyzing an age-heterogeneous population. Further, our findings suggest that CC could possess different mechanisms to cope against telomere length shortening.

Trial registration number

Not applicable

[Selective IgA deficiency]

Selective IgA deficiency (SIgAD) is defined by the European Society for Immunodeficiencies (ESID) as a serum IgA of less than 0.07g/L in patients greater than 4 years old with normal levels of IgG and IgM, normal vaccine responses, and with the exclusion of secondary causes of hypogammaglobulinemia. When serum IgA level is higher than 0.07g/L but two standard deviations below normal for age, the condition may be referred to as partial IgA deficiency, which is quite common. SIgAD is the most common primary immunodeficiency in Europe (1/600 in France) and most patients with SIgAD are asymptomatic (75-90%). The clinical complications associated with SIgAD include recurrent respiratory infections (in particular involving Haemophilus influenza and Streptococcus pneumoniae) and gastrointestinal (mainly due to Giardialamblia), autoimmune and allergic manifestations (anaphylaxis if blood products with IgA are administrated), inflammatory gastrointestinal disease. There is no specific treatment for SIgAD and each patient must be managed individually. While asymptomatic subjects do not need any treatment, it is still necessary for them to be up-to-date with vaccinations. If the patient experiences recurrent infections, prophylactic antibiotics may be beneficial. Immunoglobulin replacement therapy should be considered in patients with SIgAD and concomitant IgG subclass deficiency. Treatment for autoimmune and allergic manifestations is based on current standards of care for specific disease entities. To improve quality of life and reduce morbidity, an interdisciplinary team approach is essential.

POS0877 THE EFFECT OF PLATELET INHIBITORS ON DIGITAL ULCERS IN SYSTEMIC SCLEROSIS - A DERIVATION AND VALIDATION EUSTAR STUDY

Background:

Digital ulcers (DUs) affect half of the patients with systemic sclerosis (SSc) and can be complicated by gangrene and amputation. The direct involvement of platelets in the development of DUs has been suggested by in vitro studies, which encouraged physicians to consider platelet inhibitors as a therapeutic option in the management of DUs. However, until now, there is no clinical study to assess the efficacy of platelet inhibitors for DUs in SSc patients.

Objectives:

To demonstrate a possible relationship between treatment with platelet inhibitors and the occurrence of DUs at the next follow-up visit in patients with SSc.

Methods:

This study used prospectively collected data from the European Scleroderma Trials and Research group (EUSTAR) registry. Patients fulfilling the 2013 ACR/EULAR SSc classification criteria with complete longitudinal data on the presence of DUs and platelet inhibitors were included in the analysis. Multiple imputation using a random forest algorithm was implemented to handle missing values.

The dataset was split into a derivation and validation cohort. To investigate the response for the binary dependent variable of DUs, a generalized linear mixed model (GLMM) was developed in the derivation cohort and validated using ROC analysis and Brier scores to address discrimination and calibration, respectively.

Results:

Of 3,463 patients (2,961 in the derivation cohort, 722 in the validation cohort), 453 had current DUs at the baseline and 245 were exposed to platelet inhibitors (table 1).

Our GLMM revealed that the exposure to platelet inhibitors is associated with a reduced risk of DUs at the next follow up visit (OR = 0.33, 95% CI = [0.13 to 0.82]). Further factors associated with absence or presence of DUs at the next follow-up visit are shown in figure 1. This confirmed the previously identified risk factors for the presence of DUs, supporting the overall robustness and the validity of our model.

The performance was evaluated by ROC curve analysis and showed an AUC = 97.97% (95% CI = [96.93% to 97.67%]) for the derivation cohort and AUC = 77.3% (95% CI = [74.01% to 81.39%]) for the validation cohort, respectively, showing an acceptable discrimination. The Brier score was 0.05 in the derivation cohort and 0.07 in the validation cohort, suggesting a good calibration of the model.

Conclusion:

Our model, with acceptable discrimination and good calibration, suggests a positive treatment effect of platelet inhibitors on DUs in clinical practice.

Table 1.

Baseline characteristics of patients before imputation

CharacteristicsOverallDerivation setValidation setn3,4632,691772Age (median [IQR])56.00 [47.00, 66.00]56.00 [47.00, 65.00] 57.00 [48.00, 67.00]Disease duration (median [IQR]) 9.00 [4.00, 16.00] 9.00 [4.00, 16.00] 8.00 [4.00, 15.00]Disease subset = Limited cutaneous SSc (%) 1562 (65.2) 1164 (64.6) 398 (66.9)DUs (%): Current 453 (13.1) 378 (14.0) 75 (9.7)DUs (%): Never 1783 (51.5) 1326 (49.3) 457 (59.2)DUs (%): Previously 1227 (35.4) 987 (36.7) 240 (31.1)mRSS (median [IQR]) 5.00 [2.00, 11.00] 6.00 [2.00, 12.00] 4.00 [1.00, 11.00]Joint Contractures = Yes (%) 881 (26.8) 770 (29.4) 111 (16.5)LVEF (median [IQR])62.00 [60.00, 65.00]60.00 [60.00, 65.00] 65.00 [60.00, 67.00]Dyspnea NYHA III and IV (%)300 (9.5)214 (8.6)86 (12.7)Pulmonary hypertension = Yes (%) 244 (10.7) 200 (11.3) 44 (8.4)Lung fibrosis on HRCT = Yes (%) 685 (46.6) 600 (47.7) 85 (39.7)FVC % predicted (median [IQR])97.00 [82.00, 111.00]95.00 [81.00, 110.00]101.00 [85.00, 115.00]Serum creatinine mg/dl (median [IQR]) 0.70 [0.60, 0.90] 0.70 [0.60, 0.90] 0.70 [0.70, 0.90]Anti-Scl-70 positive = Yes (%) 1147 (33.1) 958 (35.6) 189 (24.5)CRP elevation = Yes (%) 639 (21.1) 490 (20.8) 149 (22.1)Platelet inhibitors therapy = Yes (%) 245 (7.1) 206 (7.7) 39 (5.1)Oral anti-coagulants therapy = Yes (%) 53 (1.5) 50 (1.9) 3 (0.4)

Disclosure of Interests:

None declared

AB0058 ASSOCIATION BETWEEN HLA-DRB1*04:01, RHEUMATOID NODULES AND PARTICULAR EPITOPES OF CITRULLINATED FIBRIN IN PATIENTS WITH RHEUMATOID ARTHRITIS

Background:

Rheumatoid arthritis (RA) is associated with HLA-DRB1 genes encoding the shared epitope (SE), a 5 amino acid motive. RA is usually preceded by the emergence of anti-citrullinated protein antibodies (ACPAs) detected by anti-CCP2 tests. Citrullin is a neutral amino acid resulting from post translational modification of arginin by Peptidyl Arginyl Deiminases (PADs). ACPAs recognize epitopes from citrullinated human fibrinogen (Fib-cit) and can be specifically detected by the AhFibA assay. Five peptides derived from Fib-cit together represent almost all of the epitopes recognized by patients with ACPA-positive RA: β60–74cit, α36–50cit, α621–635cit, α501–515cit and α171–185cit. As RA is a pleiomorphic disease, whose evolution is difficult to predict, the use of antibody fine specificity as a marker of clinical phenotypes has become a major challenge.

Objectives:

Our objective was to study whether clinical characteristics and HLA-DRB1 genetic background were associated with a specific reactivity against these epitopes.

Methods:

184 ACPA positive RA patients fulfilling the 2010 ACR/EULAR criteria were studied. Patients characteristics, including HLA-DRB1 genotype, were collected from their medical files. Anti-CCP2, AhFibA, Rheumatoid Factors (RF), and antibodies against the five major Fib-cit peptides were analyzed using ELISA assays.

Results:

Anti-CCP2 and AhFibA titres were strongly correlated (rs: 0.7037; p = 5.69x10-29, Pearson’s). Anti-α505-515cit antibodies were associated with HLA-DRB1*04:01 (OR = 5.52 [2.00 – 13.64]; p = 0.0003). High level anti-α505-515cit antibodies were significantly associated with rheumatoid nodules (OR = 2.71 [1.00 – 7.16], p= 0.044). Anti α501–515cit antibodies were associated with RF (OR=2.31 [1.10 – 4.78], p= 0.026).

Conclusion:

Immune complexes containing anti-α501–515cit antibodies and rheumatoid factors might be involved in the development of rheumatoid nodules on the HLA-DRB1*04:01 background. These findings highlight the role played by the HLA-DRB1*04:01 molecule and its rapid intracellular route into the lysosomes, enabling original antigen processing. Finally, purifying these epitope specific antibodies might be a new therapeutic opportunity for rheumatoid nodules.

Disclosure of Interests:

None declared

[Heredity and cancer]

A personal or family history of cancer has now become the primary cause of genetic consultations. In recent years, various genes have been identified that are associated with a more or less marked genetic predisposition to the development of cancers. The syndrome associated with the hereditary risk of breast and ovarian cancer and the Lynch syndrome are the most frequent ones, but there are many other, much less common, situations associated with familial cancer risk. In most cases, there are clear recommendations regarding the indications for genetic testing and the follow-up of patients identified as having a predisposition to cancer. At the CHU of Liège, we currently perform more than 1.400 oncogenetic consultations per year and we maintain a positivity rate of genetic tests performed in this indication higher than 10%. In this way, we allow a multidisciplinary care of patients with a high oncological risk and participate in a prevention and surveillance activity. We also pay increasing attention to the hereditary risk associated with pediatric cancers and to patients with multiple cancers, especially when these develop at an early age. Finally, the oncogenetic consultation must consider the psychological, ethical and legal aspects of a diagnosis that involves the patient and his or her future, but also the whole family.

[EBV and immunodeficiency]

Epstein-Barr virus (EBV), discovered in 1964, is a double-stranded DNA virus belonging to the Herpesviridae family. EBV has a lymphoid tropism with transforming capacities using different oncogenic viral proteins. This virus has two replication cycles: a lytic cycle mainly occuring during primary infection and a latent cycle allowing viral persistence into host memory B cells. More than 90% of adults are seropositive for EBV worldwide, with a past history of asymptomatic or mild primary infection. EBV infection can sometimes cause life-threatening complications such as hemophagocytic lymphohistiocytosis, and lead to the development of lymphoproliferative disorders or cancers. Risk factors associated with these phenotypes have been recently described through the study of monogenic primary immune deficiencies with EBV susceptibility. We here review the virological and immunological aspects of EBV infection and EBV-related complications with an overview of current available treatments.

Seasonal variations in the optical characteristics of dissolved organic matter in glacial pond water

Large amounts of dissolved organic matter (DOM) are stored in mountain glaciers. However, few researches have analysed the optical characteristics of DOM in surface waters fed by mountain glaciers and their seasonal variations. In a pond fed by a glacier we observed simultaneous decreases in the dissolved organic carbon, and increases in both absorbance at 254 nm and specific absorption coefficient (SUVA₂₅₄) during the ice-free season 2015. This behaviour differs from the typical behaviour of lake/pond water in summer, and from the trends observed in a nearby pond not fed by a glacier. The trends of DOM properties, main ions and water stable isotopes at the glacier-fed pond could be attributed to transient modifications of the subglacial hydrological system. Flushing of previously isolated pools of subglacially stored water, containing terrestrial DOM derived from glacially-overridden soil and vegetation, would be driven by intense rainfall events during the melting season. These findings suggest that heavy rainfall events during the melting season have the capability to transiently modify the characteristics of DOM in a glacial pond. These events may be further exacerbated in the future, as summer rainfall events in the Alps are predicted to increase due to global warming.

A173 INNOVATIVE CARE FOR INFLAMMATORY BOWEL DISEASE PATIENTS DURING THE COVID-19 PANDEMIC: USE OF BEDSIDE INTESTINAL ULTRASOUND TO OPTIMIZE MANAGEMENT

Background

The COVID-19 pandemic has led to significant alterations in the ability to deliver outpatient care to patients with inflammatory bowel disease (IBD) including endoscopic evaluation. This has highlighted the need for alternative, accurate, non-invasive strategies to safely assess disease activity.

Aims

The aim of this study is to describe the impact of point of care intestinal ultrasound (IUS) in a university-based tertiary care IBD urgent access clinic.

Methods

We prospectively evaluated a comprehensive care pathway which incorporated outpatient sigmoidoscopy and intestinal ultrasound with the purpose of directing further ambulatory clinical care and avoiding hospitalization or hospital-based investigations including endoscopy during the COVID pandemic for patients with established IBD with symptoms suggestive of a disease flare, or those at high risk of a new diagnosis of IBD. Non-invasive markers C Reactive Protein (CRP) and fecal calprotectin (fCal) were collected where available. Patients were pre-screened for influenza-like illness, as COVID-19 testing was not available for this population during the study period. Substantial management changes were defined as addition of any medications, biologic switch/ optimization, and or referral for surgical consultation.

Results

Between March 15^th and June 30^th 2020, a total of 72 patients were seen in the urgent access clinic. All patients were seen within 7 days of referral. The majority were female 57% (41/72) and/ or had Crohn’s disease 65.5% (47/72) (Table 1). Of these, 84.7% (61/72) underwent a substantial management change based on features of active inflammation detected by either IUS alone (53% 38/72) sigmoidoscopy alone (12.5% 9/72) or combination IUS with in-clinic sigmoidoscopy (32% 23/72) in addition to CRP and fCal. Three new diagnoses of IBD were made: one colonic Crohn’s and 2 with ulcerative colitis. One pregnant patient avoided all acute care utilization. Five patients were referred to colorectal surgery for urgent resection including two patients admitted directly for emergent operations. No patients required visits to the emergency department. Furthermore, there have been no unscheduled hospitalizations occurred in this cohort since inception March 23, 2020 til November 15^th 2020.

Conclusions

The implementation of IUS in a centralized, urgent access clinic pathway resulted in efficient and meaningful changes in IBD management while sparing the need for acute care services including ER visits, need for in-hospital endoscopy, and hospitalization. The pandemic highlights the utility of this patient-center tool and supports expansion of wider IUS adoption.

Funding Agencies

None

Characterisation of the T-cell response to Ebola virus glycoprotein amongst survivors of the 2013-16 West Africa epidemic

Zaire ebolavirus (EBOV) is a highly pathogenic filovirus which can result in Ebola virus disease (EVD); a serious medical condition that presents as flu like symptoms but then often leads to more serious or fatal outcomes. The 2013-16 West Africa epidemic saw an unparalleled number of cases. Here we show characterisation and identification of T cell epitopes in surviving patients from Guinea to the EBOV glycoprotein. We perform interferon gamma (IFNγ) ELISpot using a glycoprotein peptide library to identify T cell epitopes and determine the CD4+ or CD8+ T cell component response. Additionally, we generate data on the T cell phenotype and measure polyfunctional cytokine secretion by these antigen specific cells. We show candidate peptides able to elicit a T cell response in EBOV survivors and provide inferred human leukocyte antigen (HLA) allele restriction. This data informs on the long-term T cell response to Ebola virus disease and highlights potentially important immunodominant peptides.

Ghrelin treatment leads to dendritic spine remodeling in hippocampal neurons and increases the expression of specific BDNF-mRNA species

Ghrelin (Gr) is an orexigenic peptide that acts via its specific receptor, GHSR-1a distributed throughout the brain, being mainly enriched in pituitary, cortex and hippocampus (Hp) modulating a variety of brain functions. Behavioral, electrophysiological and biochemical evidence indicated that Gr modulates the excitability and the synaptic plasticity in Hp. The present experiments were designed in order to extend the knowledge about the Gr effect upon structural synaptic plasticity since morphological and quantitative changes in spine density after Gr administration were analyzed "in vitro" and "in vivo". The results show that Gr administered to hippocampal cultures or stereotactically injected in vivo to Thy-1 mice increases the density of dendritic spines (DS) being the mushroom type highly increased in secondary and tertiary extensions. Spines classified as thin type were increased particularly in primary extensions. Furthermore, we show that Gr enhances selectively the expression of BDNF-mRNA species.

Characterizing robotic surgical expertise: An exploratory study of neural activation during mental imagery of robotic suturing

BACKGROUND

Mental imagery (MI) aids skill acquisition, however, it is unclear to what extend MI is used by experienced surgeons. The purpose of this study was to assess differences in MI of participants with varying surgical expertise in robotic surgery.

METHODS

Students, residents, and surgeons completed the Mental Imagery Questionnaire to assess MI for robotic suturing. Participants then completed robotic simulator tasks, and imagined performing robotic suturing while being assessed with electroencephalogram (EEG).

RESULTS

Attending surgeons reported higher MI for robotic suturing, and EEG revealed higher neural activation during imagery of robotic suturing than other groups.

CONCLUSIONS

Experienced surgeons displayed higher MI ability for robotic suturing, and displayed higher cortical activity in the frontal and parietal areas of the brain, which is associated with more advanced motor imagery. MI appears to be a component of robotic surgery expertise.

Palbociclib in combination with endocrine therapy versus capecitabine in hormonal receptor-positive, human epidermal growth factor 2-negative, aromatase inhibitor-resistant metastatic breast cancer: a phase III randomised controlled trial-PEARL

BACKGROUND

Palbociclib plus endocrine therapy (ET) is the standard treatment of hormone receptor-positive and human epidermal growth factor receptor 2-negative, metastatic breast cancer (MBC). However, its efficacy has not been compared with that of chemotherapy in a phase III trial.

PATIENTS AND METHODS

PEARL is a multicentre, phase III randomised study in which patients with aromatase inhibitor (AI)-resistant MBC were included in two consecutive cohorts. In cohort 1, patients were randomised 1 : 1 to palbociclib plus exemestane or capecitabine. On discovering new evidence about estrogen receptor-1 (ESR1) mutations inducing resistance to AIs, the trial was amended to include cohort 2, in which patients were randomised 1 : 1 between palbociclib plus fulvestrant and capecitabine. The stratification criteria were disease site, prior sensitivity to ET, prior chemotherapy for MBC, and country of origin. Co-primary endpoints were progression-free survival (PFS) in cohort 2 and in wild-type ESR1 patients (cohort 1 + cohort 2). ESR1 hotspot mutations were analysed in baseline circulating tumour DNA.

RESULTS

From March 2014 to July 2018, 296 and 305 patients were included in cohort 1 and cohort 2, respectively. Palbociclib plus ET was not superior to capecitabine in both cohort 2 [median PFS: 7.5 versus 10.0 months; adjusted hazard ratio (aHR): 1.13; 95% confidence interval (CI): 0.85-1.50] and wild-type ESR1 patients (median PFS: 8.0 versus 10.6 months; aHR: 1.11; 95% CI: 0.87-1.41). The most frequent grade 3-4 toxicities with palbociclib plus exemestane, palbociclib plus fulvestrant and capecitabine, respectively, were neutropenia (57.4%, 55.7% and 5.5%), hand/foot syndrome (0%, 0% and 23.5%), and diarrhoea (1.3%, 1.3% and 7.6%). Palbociclib plus ET offered better quality of life (aHR for time to deterioration of global health status: 0.67; 95% CI: 0.53-0.85).

CONCLUSIONS

There was no statistical superiority of palbociclib plus ET over capecitabine with respect to PFS in MBC patients resistant to AIs. Palbociclib plus ET showed a better safety profile and improved quality of life.

Talazoparib versus chemotherapy in patients with germline BRCA1/2-mutated HER2-negative advanced breast cancer: final overall survival results from the EMBRACA trial

BACKGROUND

In EMBRACA, talazoparib prolonged progression-free survival versus chemotherapy (hazard ratio [HR] 0.542 [95% confidence interval (CI) 0.413-0.711]; P < 0.0001) and improved patient-reported outcomes (PRO) in germline BRCA1/2 (gBRCA1/2)-mutated advanced breast cancer (ABC). We report final overall survival (OS).

PATIENTS AND METHODS

This randomized phase III trial enrolled patients with gBRCA1/2-mutated HER2-negative ABC. Patients received talazoparib or physician's choice of chemotherapy. OS was analyzed using stratified HR and log-rank test and prespecified rank-preserving structural failure time model to account for subsequent treatments.

RESULTS

A total of 431 patients were entered in a randomized study (287 talazoparib/144 chemotherapy) with 412 patients treated (286 talazoparib/126 chemotherapy). By 30 September 2019, 216 deaths (75.3%) occurred for talazoparib and 108 (75.0%) chemotherapy; median follow-up was 44.9 and 36.8 months, respectively. HR for OS with talazoparib versus chemotherapy was 0.848 (95% CI 0.670-1.073; P = 0.17); median (95% CI) 19.3 months (16.6-22.5 months) versus 19.5 months (17.4-22.4 months). Kaplan-Meier survival percentages (95% CI) for talazoparib versus chemotherapy: month 12, 71% (66% to 76%)/74% (66% to 81%); month 24, 42% (36% to 47%)/38% (30% to 47%); month 36, 27% (22% to 33%)/21% (14% to 29%). Most patients received subsequent treatments: for talazoparib and chemotherapy, 46.3%/41.7% received platinum and 4.5%/32.6% received a poly(ADP-ribose) polymerase (PARP) inhibitor, respectively. Adjusting for subsequent PARP and/or platinum use, HR for OS was 0.756 (95% bootstrap CI 0.503-1.029). Grade 3-4 adverse events occurred in 69.6% (talazoparib) and 64.3% (chemotherapy) patients, consistent with previous reports. Extended follow-up showed significant overall improvement and delay in time to definitive clinically meaningful deterioration in global health status/quality of life and breast symptoms favoring talazoparib versus chemotherapy (P < 0.01 for all), consistent with initial analyses.

CONCLUSIONS

In gBRCA1/2-mutated HER2-negative ABC, talazoparib did not significantly improve OS over chemotherapy; subsequent treatments may have impacted analysis. Safety was consistent with previous observations. PRO continued to favor talazoparib.

Organic phosphorus affects the retention of arsenite and arsenate by goethite

The hazardous effects of arsenic are closely linked to its speciation and interaction with different soil minerals, which influence both As mobility and bioavailability. Adsorption onto iron (oxyhydr)oxides is one of the main processes controlling the partitioning of arsenite [As(III)] and arsenate [As(V)] between aqueous and solid phases. Arsenic retention can be affected by changes in soil pH and the presence of competing anions, like phosphate. Although competition with inorganic phosphorus (P) for sorption sites on mineral surfaces has been widely studied, little is known about the interactions with organic P (P_o ) compounds, in particular inositol phosphates, even though they may represent a large fraction of total soil P. We quantified the effects of myo-inositol hexaphosphate (InsP6) on the adsorption and retention of As(III) and As(V) on goethite as influenced by pH, the order of anion addition, and residence time. The efficiency of InsP6 in displacing adsorbed As(III) decreased with increasing pH values and interaction time, which may be attributed to the increase in bonding strength of the As(III) complexes on the surface of goethite. Adsorption and retention of As(V) by goethite generally decreased with increasing pH, particularly in the presence of InsP6 due to the similar pK_a values and the competition for the same binding sites. The addition of InsP6 before, together with, or after adsorption of As(III) and As(V) strongly reduced the amounts of sorbed As, suggesting that the addition of P_o -rich matrices to As-contaminated soils may strongly enhance As mobility.

Newer glucose-lowering drugs at discharge from cardiology hospitalization department: safetyness, effectiveness and mortality reduction

Background

In recent years, the paradigm of glycemic treatment has changed due to the cardiovascular impact of newer glucose-lowering drugs (GLD) (sodium-glucosa cotransporter 2 inhibitor (SGLT2i) and GLP-1 receptor agonist (GLP1a)). The cardiological patient with type 2 diabetes (2DM) is a very high cardiovascular risk patient in which the benefit of these therapies is greater. However, to date, different studies have demonstrated the efficacy and safety of newer GLD only in the outpatient setting. So its impact when they are initiated to discharge after a cardiovascular event is unknown.

Objective

To evaluate the efficacy and safety of the onset of these newer GLD in 2DM patients at discharge from cardiology hospitalization. And to compare mortality and readmissions among patients treated with or without newer GLD.

Methods

Prospective, it includes patients admitted to cardiology at a 3er level hospital between April/2018 and February/2019 with a history of 2DM or diagnosed with 2DM during hospitalization. They were followed at 6, 12 and 18 months. The evolution of anthropometric parameters, glycemic profile, renal function and blood pressure were analyzed; renal events, readmissions, mortality and combined clinical outcome (mortality or readmission) were collected during follow-up. Quantitative variables are expressed in mean/SD and categorical variables in number of patients (%). For the comparison between the parameters at discharge and thefollow-up, a T student was used for paired data. Survival analysis by K-M was performed crude and adjusted data by propensity score matching (PSM).

Results

Population: Diagnoses at discharge: Acute coronary syndrome 66 (64%), Heart failure 22 (21%), Arrhythmias 16 (15%). 104 diabetic patients, 39 of them (38%) were treated on discharge with newer GLD. 35 Patients with SGLT2i without GLP1a, 3 patients with SGLT2i and GLP1a and 1 patient with GLP1a without SGLT2i. The mean follow-up was 16±2 months. Regarding the subgroup of patients with newer GLD: mean age was 65±21 y, male 26 (67%). A significant decrease was observed in glycated hemoglobin (7.6 to 6.9%, p=0.04) and weight (81 to 78 kg, p&lt;0.01) without significant changes in blood pressure or glomerular filtration rate (GFR). Only 1 patient presented deterioration of their GFR that forced the transient suspension of newer GLD.

10 deaths were registered in the classical GLD group (15%) and none in the newer GLD group (HR 0.81 [0.71–0.92] p=0.002, Figure 1A, HR adjusted by PSM 0.9 [0.82–0.99], p=0.04), Figure 1B. The combined clinical outcome appeared in 38 patients (58%) in the the classical GLD group and in 9 (23%) in the newer GLD group (HR 0.70 [0.58–0.85] p&lt;0.001, Figure 1C, PSM adjusted HR 0.75 [0.61–0.92], p=0.001), Figure 1D.

Conclusion

The use of newer GLD at discharge from cardiology hospitalization reduce mortality and readmissions. Newer GLD were safe and showed significant reduction in weigth and glycated hemoglobin.

Figure 1. Kaplan-Meier survival analysis crude and adjusted

Funding Acknowledgement

Type of funding source: None

Analyse des demandes d’appui en matière de prévention et contrôle de l’infection d’un CPias pendant la crise COVID-19

Introduction

Pendant la crise sanitaire liée au SARS-CoV-2, le Centre d’appui pour la Prévention des infections associées aux soins (CPias) a fortement été sollicité par les différents secteurs de l’offre de soins. Un outil informatique commun a été créé en 2019 pour tracer les demandes d’appui du CPias. L’objectif est d’analyser les thèmes abordés, les demandeurs et les réponses émises.

Matériels et méthodes

La saisie de ces données se fait à partir d’un formulaire en ligne. L’analyse des données est réalisée avec le logiciel statistique SAS®. Après un contrôle de la qualité des données, une analyse descriptive des conseils donnés a été réalisée. Ainsi, les variables recensées sont : la date, la fonction des appelants, le statut et le type de leurs établissements (sanitaire, ESMS, secteur libéral…) et les thèmes des demandes. Une fois la base de données exportée et les demandes étiquetées « COVID-19 » filtrées, une seconde analyse qualitative des sous-thèmes a été faite.

Résultats

Entre le 1^er février et le 31 mai 2020, le CPias a répondu à 886 sollicitations sur le thème du COVID-19 contre 640 sur toute l’année 2019 (tous thèmes confondus), avec un pic visible autour de la semaine 12. Ainsi, 64 % (466) des demandes émanent d’établissements médicosociaux, 26 % (189) d’établissements sanitaires, 7 % (48) de tutelles et 3 % (22) de la médecine ambulatoire. Quarante-trois pour cent (363) de ces demandes sont faites par des professionnels de santé (à parts égales entre professionnels médicaux et paramédicaux), 26 % (217) par des personnels non soignants (dont 80 % (174) de directeurs de structures médicosociales), 21 % (175) par des hygiénistes (praticiens et infirmiers) et 10 % (90) d’autres professionnels. Les thèmes les plus souvent abordés concernent pour 30 % (264) les équipements de protection individuelle (conseils pour leur bonne utilisation, gestion de la pénurie), pour 23 % (206) l’environnement (entretien des locaux, gestion du risque environnemental) et pour 21 % (185) la conduite à tenir face à des patients/résidents suspects, positifs ou revenant d’hospitalisation. Viennent ensuite des questions sur la conduite à tenir pour les professionnels soit 14 % (123) (suspects/contact, ceux travaillant en ville ou à domicile) et 14 % (120) sur la maladie elle-même (contagiosité, symptômes, prélèvement, unité dédiée aux patients COVID ou suspects). Parfois ces questions ont été relayées aux infectiologues selon le niveau d’expertise requis. Enfin, 11 % (98) des demandes sont d’ordre organisationnel autour des flux internes et de l’organisation des consultations.

Conclusion

Le CPias a été très investi dans ses missions régionales de prévention et contrôle de l’infection pendant cette crise sanitaire. Nous en tirons que de nombreux acteurs en santé avaient besoin d’une adaptation ou d’une interprétation pratique des doctrines nationales et/ou d’être confortés dans les conduites à tenir. L’analyse montre également la diversité des appelants sortants du cadre habituel de nos interlocuteurs témoignant de l’importance de l’épidémie.

Circulating nucleic acids in the plasma and serum as potential biomarkers in neurological disorders

Neurological diseases are responsible for approximately 6.8 million deaths every year. They affect up to 1 billion people worldwide and cause significant disability and reduced quality of life. In most neurological disorders, the diagnosis can be challenging; it frequently requires long-term investigation. Thus, the discovery of better diagnostic methods to help in the accurate and fast diagnosis of neurological disorders is crucial. Circulating nucleic acids (CNAs) are defined as any type of DNA or RNA that is present in body biofluids. They can be found within extracellular vesicles or as cell-free DNA and RNA. Currently, CNAs are being explored as potential biomarkers for diseases because they can be obtained using non-invasive methods and may reflect unique characteristics of the biological processes involved in several diseases. CNAs can be especially useful as biomarkers for conditions that involve organs or structures that are difficult to assess, such as the central nervous system. This review presents a critical assessment of the most current literature about the use of plasma and serum CNAs as biomarkers for several aspects of neurological disorders: defining a diagnosis, establishing a prognosis, and monitoring the disease progression and response to therapy. We explored the biological origin, types, and general mechanisms involved in the generation of CNAs in physiological and pathological processes, with specific attention to neurological disorders. In addition, we present some of the future applications of CNAs as non-invasive biomarkers for these diseases.