Consore: A Powerful Federated Data Mining Tool Driving a French Research Network to Accelerate Cancer Research.

BACKGROUND: Real-world data (RWD) related to the health status and care of cancer patients reflect the ongoing medical practice, and their analysis yields essential real-world evidence. Advanced information technologies are vital for their collection, qualification, and reuse in research projects. METHODS: UNICANCER, the French federation of comprehensive cancer centres, has innovated a unique research network: Consore. This potent federated tool enables the analysis of data from millions of cancer patients across eleven French hospitals. RESULTS: Currently operational within eleven French cancer centres, Consore employs natural language processing to structure the therapeutic management data of approximately 1.3 million cancer patients. These data originate from their electronic medical records, encompassing about 65 million medical records. Thanks to the structured data, which are harmonized within a common data model, and its federated search tool, Consore can create patient cohorts based on patient or tumor characteristics, and treatment modalities. This ability to derive larger cohorts is particularly attractive when studying rare cancers. CONCLUSIONS: Consore serves as a tremendous data mining instrument that propels French cancer centres into the big data era. With its federated technical architecture and unique shared data model, Consore facilitates compliance with regulations and acceleration of cancer research projects.

Antiseizure effect of MEK inhibitor in a child with neurofibromatosis type 1-Developmental and epileptic encephalopathy and optic pathway glioma.

BACKGROUND: Neurofibromatosis type 1 (NF1) is an autosomal dominant genetic disorder due to a mutation in NF1 gene, resulting in phenotypically heterogeneous systemic manifestations. Patients with NF1 are prone to develop neoplasms of the central nervous system (CNS) and are particularly at risk for optic pathway gliomas (OPG). Epilepsy is another recognized neurologic complication in patients with NF1, with a prevalence estimated between 4% and 14%. Several case reports and early phase clinical trials have demonstrated that the mitogen-activated protein kinase inhibitors (MEKi) are effective in NF1-low-grade gliomas (LGGs), but their influence on seizure activity in humans has not been established. CASE STUDY: Here, we report a patient with NF1 and developmental and epileptic encephalopathy (DEE) harboring pharmacoresistant tonic seizures, and progressive optic pathway glioma (OPG). By using a MEKi therapy for her OPG, we observed an end to epileptic seizures as well as a significant improvement of interictal EEG abnormalities, despite a lack of tumor reduction. CONCLUSION: MEK inhibitor therapy should be considered for patients with NF1 and refractory epilepsy.

ATP7B variant spectrum in a French pediatric Wilson disease cohort.

BACKGROUND/AIM: The spectrum of ATP7B variants varies significantly according to geographic distribution, and there is insufficient data on the variants observed in the French population. METHODS: Clinical data of 113 children included in the French WD national registry were gathered from March 01, 1995 to July 01, 2020. Data included epidemiological, clinical, laboratory, genetics. RESULTS: Diagnosis was made at a mean age of 11.0 ± 4.1 years (range 1-18 years). At diagnosis, 91 patients (79.8 %) had hepatic manifestations, 18 (15.8 %) presented neurological manifestations, and 4 patients (3.5 %) were asymptomatic. Only 29 patients (25 %) were homozygous for a variant. We have found a total of 102 different variants including 14 novel variants. Recurrent variant p.His1069Gln was the most prevalent, n = 31 alleles (14,2%), with only seven homozygous; in contrast 55% of variants are identified in only one family. 45% were truncating variants. In respect of mutated exon, the three most prevalent were exon 14 (16.5%), exon 8 (13.8%), and exon 3 (11.5%). When considering patients with two Nonsense / Frameshift variants as a group and those with two Missense variants, we found significantly lower ceruloplasmin for the former: 2.8 ± 0.7 mg/dl vs 8.4 ± 5mg/dl (p<0.05). CONCLUSION: p.His1069Gln is the most frequent variant (14,2%) and exons 14, 8, and 2 of the ATP7B gene account for 41.7% of total variants. However, there is significant heterogeneity in the French population concerning the other ATP7B variants. Nonsense / Frameshift variants were associated with lower ceruloplasmin levels.

Natural Language Processing for Patient Selection in Phase I or II Oncology Clinical Trials.

PURPOSE: Early discontinuation affects more than one third of patients enrolled in early-phase oncology clinical trials. Early discontinuation is deleterious both for the patient and for the study, by inflating its duration and associated costs. We aimed at predicting the successful screening and dose-limiting toxicity period completion (SSD) from automatic analysis of consultation reports. MATERIALS AND METHODS: We retrieved the consultation reports of patients included in phase I and/or phase II oncology trials for any tumor type at Gustave Roussy, France. We designed a preprocessing pipeline that transformed free text into numerical vectors and gathered them into semantic clusters. These document-based semantic vectors were then fed into a machine learning model that we trained to output a binary prediction of SSD status. RESULTS: Between September 2012 and July 2020, 56,924 consultation reports were used to build the dictionary and 1,858 phase I or II inclusion reports were used to train (72%), validate (14%), and test (14%) a random forest model. Preprocessing could efficiently cluster words with semantic proximity. On the unseen test cohort of 264 consultation reports, the performances of the model reached: F1 score 0.80, recall 0.81, and area under the curve 0.88. Using this model, we could have reduced the screen fail rate (including dose-limiting toxicity period) from 39.8% to 12.8% (relative risk, 0.322; 95% CI, 0.209 to 0.498; P < .0001) within the test cohort. Most important semantic clusters for predictions comprised words related to hematologic malignancies, anatomopathologic features, and laboratory and imaging interpretation. CONCLUSION: Machine learning with semantic conservation is a promising tool to assist physicians in selecting patients prone to achieve SSD in early-phase oncology clinical trials.

OSIRIS: A Minimum Data Set for Data Sharing and Interoperability in Oncology.

PURPOSE: Many institutions throughout the world have launched precision medicine initiatives in oncology, and a large amount of clinical and genomic data is being produced. Although there have been attempts at data sharing with the community, initiatives are still limited. In this context, a French task force composed of Integrated Cancer Research Sites (SIRICs), comprehensive cancer centers from the Unicancer network (one of Europe's largest cancer research organization), and university hospitals launched an initiative to improve and accelerate retrospective and prospective clinical and genomic data sharing in oncology. MATERIALS AND METHODS: For 5 years, the OSIRIS group has worked on structuring data and identifying technical solutions for collecting and sharing them. The group used a multidisciplinary approach that included weekly scientific and technical meetings over several months to foster a national consensus on a minimal data set. RESULTS: The resulting OSIRIS set and event-based data model, which is able to capture the disease course, was built with 67 clinical and 65 omics items. The group made it compatible with the HL7 Fast Healthcare Interoperability Resources (FHIR) format to maximize interoperability. The OSIRIS set was reviewed, approved by a National Plan Strategic Committee, and freely released to the community. A proof-of-concept study was carried out to put the OSIRIS set and Common Data Model into practice using a cohort of 300 patients. CONCLUSION: Using a national and bottom-up approach, the OSIRIS group has defined a model including a minimal set of clinical and genomic data that can be used to accelerate data sharing produced in oncology. The model relies on clear and formally defined terminologies and, as such, may also benefit the larger international community.

The blood copper isotopic composition is a prognostic indicator of the hepatic injury in Wilson disease.

Wilson disease (WD) is an autosomal recessive disorder of copper (Cu) metabolism. The gene responsible for WD, ATP7B, is involved in the cellular transport of Cu, and mutations in the ATP7B gene induce accumulation of Cu in the liver and ultimately in the brain. In a pilot study, the natural variations of copper stable isotope ratios (65Cu/63Cu) in the serum of WD patients have been shown to differ from that of healthy controls. In the present study, we challenged these first results by measuring the 65Cu/63Cu ratios in the blood of treated (n = 25), naïve patients (n = 11) and age matched healthy controls (n = 75). The results show that naïve patients and healthy controls exhibit undistinguishable 65Cu/63Cu ratios, implying that the Cu isotopic ratio cannot serve as a reliable diagnostic biomarker. The type of treatment (d-penicillamine vs. triethylenetetramine) does not affect the 65Cu/63Cu ratios in WD patients, which remain constant regardless of the type and duration of the treatment. In addition, the 65Cu/63Cu ratios do not vary in naïve patients after the onset of the treatment. However, the 65Cu/63Cu ratios decrease with the degree of liver fibrosis and the gradient of the phenotypic presentation, i.e. presymptomatic, hepatic and neurologic. To get insights into the mechanisms at work, we study the effects of the progress of the WD on the organism by measuring the Cu concentrations and the 65Cu/63Cu ratios in the liver, feces and plasma of 12 and 45 week old Atp7b-/- mice. The evolution of the 65Cu/63Cu ratios is marked by a decrease in all tissues. The results show that 63Cu accumulates in the liver preferentially to 65Cu due to the preferential cellular entry of 63Cu and the impairment of the 63Cu exit by ceruloplasmin. The hepatic accumulation of monovalent 63Cu+ is likely to fuel the production of free radicals, which is potentially an explanation of the pathogenicity of WD. Altogether, the results suggest that the blood 65Cu/63Cu ratio recapitulates WD progression and is a potential prognostic biomarker of WD.

Craniofacial bone alterations in patients with neurofibromatosis type 1.

Osseous manifestations of neurofibromatosis 1 (NF-1) occur in a minority of the affected subjects but may be because of significant clinical impairment. Typically, they involve the long bones, commonly the tibia and the fibula, the vertebrae, and the sphenoid wing. The pathogenesis of NF-1 focal osseous lesions and its possible relationships with other osseous NF-1 anomalies leading to short stature are still unknown, though it is likely that they depend on a common mechanism acting in a specific subgroup of NF-1 patients. Indeed, NF-1 gene product, neurofibromin, is expressed in all the cells that participate to bone growth: osteoblasts, osteoclasts, chondrocytes, fibroblasts, and vascular endothelial cells. Absent or low content of neurofibromin may be responsible for the osseous manifestations associated to NF-1. Among the focal NF-1 osseous anomalies, the agenesis of the sphenoid wing is of a particular interest to the neurosurgeon because of its progressive course that can be counteracted only by a surgical intervention. The sphenoid wing agenesis is regarded as a dysplasia, which is a primary bone pathology. However, its clinical progression is related to a variety of causes, commonly the development of an intraorbital plexiform neurofibroma or the extracranial protrusion of temporal lobe parenchyma and its coverings. Thus, the cranial bone defect resulting by the primary bone dysplasia is progressively accentuated by the orbit remodeling caused by the necessity of accommodating the mass effect exerted by the growing tumor or the progression of the herniated intracranial content. The aim of this paper is to review the neurosurgical and craniofacial surgical modalities to prevent the further progression of the disease by "reconstructing" the normal relationship of the orbit and the skull.

Attention and Executive Disorders in Neurofibromatosis 1: Comparison Between NF1 With ADHD Symptomatology (NF1 + ADHD) and ADHD Per Se.

Objective: To compare children with Neurofibromatosis type 1 and associated ADHD symptomatology (NF1 + ADHD) with children having received a diagnosis of ADHD without NF1. The idea was that performance differences in tasks of attention between these two groups would be attributable not to the ADHD symptomatology, but to NF1 alone. Method: One group of children with NF1 + ADHD (N = 32), one group of children with ADHD (N = 31), and one group of healthy controls (N = 40) participated in a set of computerized tasks assessing intensive, selective, and executive aspects of attention. Results: Differences were found between the two groups of patients in respect of several aspects of attention. Children with NF1 + ADHD did not always perform worse than children with ADHD. Several double dissociations can be established between the two groups of patients. Conclusion: ADHD symptomatology in NF1 does not contribute to all attention deficits, and ADHD cannot account for all attention impairments in NF1.

Postnatal clinical phenotype of five patients with Pallister-Killian Syndrome (tetrasomy 12p): Interest of array CGH for diagnosis and review of the literature.

BACKGROUND: Pallister-Killian syndrome (PKS) is a rare sporadic disorder caused by tetrasomy of the short arm of chromosome 12. The main clinical manifestations are global developmental delay, intellectual disability, epilepsy, dysmorphic features, hypopigmented and/or hyperpigmented lesions, and multiple congenital anomalies. PKS is associated with tissue mosaicism, which is difficult to diagnose through peripheral blood sample by conventional cytogenetic methods and fluorescence in situ hybridization. METHODS: Here, we report five patients with PKS. We delineate their clinical phenotypes and we compare them with previously published cases. We used array Comparative Genomic Hybridization (aCGH) with DNA extracted from peripheral blood samples. The five patients have also been tested by conventional cytogenetics techniques. RESULTS: Four out of five patients showed tetrasomy 12p by aCGH. Three of the four patients have typical i(12p) and one of the four demonstrated atypical tetrasomy 12p. The percentage of mosaicism was as low as 20%. Our cohort exhibited the typical PKS phenotypes. CONCLUSION: Our results demonstrate the efficacy of aCGH for the diagnosis of PKS from DNA extracted from lymphocytes. Thus, for patients suspected of PKS, we recommend performing aCGH on lymphocytes at an early age before  proceeding to skin biopsy. aCGH on peripheral blood samples is sensitive in detecting low level of mosaicism and it is less invasive method than skin biopsy. We reviewed also the literature concerning the previously published PKS patients diagnosed by aCGH.

Mediastinitis superinfected by Achromobacter xylosoxidans. A case report.

We describe an extremely rare case of mediastinitis superinfected by emerging Achromobacter xylosoxidans. After mitral and aortic valves replacement, the patient first developed a Staphylococcus aureus mediastinitis, and five days after starting adapted antibiotic therapy, superficial pus analysis revealed the presence of Achromobacter xylosoxidans. This superinfection was considered superficial and focus was made on Staphylococcus aureus mediastinitis. Three weeks later, no more Staphylococcus aureus was found in pus samples and the sepsis seemed under control. Unfortunately, blood cultures were again positive for Achromobacter xylosoxidans three weeks later and the patient died from septic shock.

Deficit in phonological processes: a characteristic of the neuropsychological profile of children with NF1.

Learning disabilities are one of the most frequent complications of neurofibromatosis type 1 (NF1) in children. Studies of the effects of the neurocognitive deficit on academic performance are relatively rare, owing to the small size of the populations concerned. However, research is needed to develop effective rehabilitation programs. In the present study, we explored the impact of a possible phonological deficit on the reading abilities of children with NF1. A multicenter, cross-sectional study was conducted in France on two groups of 75 children with or without NF1 aged 8-12 years, matched for age, sex, handedness, and reading level. All participants underwent a neuropsychological evaluation to assess their general cognitive level, reading skills, phonological processes, visuoperceptual abilities, and attentional capacity. Phonological skills were assessed by means of two phonological awareness tasks and one short-term memory task. In the group of children with NF1, 41% had reading difficulties. Phonological processes were impaired in this group, compared with the children without NF1. Similar differences were found for a phoneme deletion task after adjustment for reading difficulties, IQ level, and visuoperceptual abilities. Phonological awareness, but not phonological short-term memory, was impaired in children with NF1, and not just those whose reading was impaired. Results suggest that children with NF1 have a phonological awareness deficit, whatever their reading level. Identification of reduced phonological skills may warrant the implementation of a specific rehabilitation program before early reading difficulties emerge.

Systematic MRI in NF1 children under six years of age for the diagnosis of optic pathway gliomas. Study and outcome of a French cohort.

BACKGROUND/PURPOSE: Optic pathway glioma (OPG) is the most common central nervous system tumor in children with neurofibromatosis type 1 (NF1), affecting 15-20% of patients. We reviewed the medical records of children systematically screened by ophthalmologic and MRI examinations to determine the influence of screening on the therapeutic management of children with OPG. METHODS: Data were collected on 306 newly diagnosed cases screened with systematic MRI from January 2001 to July 2007. In the OPG group, we distinguished the asymptomatic or symptomatic groups according to their initial status. RESULTS: Forty-five patients had confirmed OPG (14.7%). Thirty-six patients (80%) were asymptomatic and nine (20%) were symptomatic at the time of diagnosis with visual symptoms in six cases. The average age at OPG diagnosis was 3.4 years with six patients (13%) over six years old. Average follow-up was 7.7 years. Progression was observed in 16 cases (35%). Most patient conditions were managed conservatively (87%). Six children (13%) were treated with chemotherapy due to worsening visual function. All of these children had severe or mild visual impairment at the end of follow-up. CONCLUSION: Our study does not support a clear benefit of systematic MRI screening in NF1 children under six years old. Systematic neuroimaging in our study did not influence therapeutic management. Although OPG diagnosis was made early, treatment with chemotherapy did not improve the final visual outcome. If MRI remains the best tool for the diagnosis of cerebral and spinal pathologies in the NF1 population, our current study questions the usefulness of systematic MRI screening for OPG diagnosis. Conversely, this study suggests that the indication of neuroimaging should be dictated by the results of annual clinical and ophthalmological assessments.

The effect of methylphenidate on neurofibromatosis type 1: a randomised, double-blind, placebo-controlled, crossover trial.

BACKGROUND: Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder with an estimated prevalence of about 1/3000, independent of ethnicity, race, or gender. Attention Deficit Hyperactivity like Disorder (ADHD)-like characteristics are often reported in patients with NF1. We hypothesised that learning disabilities in NF1 children were related to ADHD symptoms. Treatment with methylphenidate (MPD) has improved learning disabilities in ADHD by acting on neurotransmitters. Our objective was to evaluate its efficacy on ADHD-like symptoms in neurofibromatosis type 1 children (7-12 years). METHODS: This was a randomised, double blind, placebo controlled, and crossover trial comparing 0.5 to 0.8 mg/kg/d of MPD as it is indicated for ADHD to placebo in NF1 children with ADHD-like symptoms. Children aged 7 to 12 years were eligible when their IQ was between 80 and 120. The total follow-up was 9 weeks including 4 weeks for each period and 1 week wash out. Fifty subjects (25 for each period) were required for testing the primary study hypothesis. The main outcome was an improvement in scores on the simplified Conners' Parent Rating Scale. RESULTS: Thirty-nine patients were included between April 2004 and December 2010. Twenty participants received MPD and 19 placebo during the first period. They all completed the trial. MPD decreased the simplified Conners by 3.9 points (±1.1, p = 0. 0003). CONCLUSIONS: This is the first randomised controlled trial showing the short-term benefit of MPD on simplified Conners scores in NF1 children. TRIAL REGISTRATION: ClinicalTrials.gov NCT00169611.

Reactivity to visual signals in neurofibromatosis type 1: is everything ok?

OBJECTIVE: Deficits in multiple aspects of attention are a hallmark of the cognitive impairments found with neurofibromatosis type I (NF1). Given, however, that some attention components are hierarchically organized, it is possible that sustained attention, flexibility, and resistance to interference deficits observed in NF1 may be because of weakened lower order attention components. This study investigated the state of these low-level components in NF1. METHOD: Twenty participants with NF1 (ages 7-13) and 20 matched controls participated in a visual task. They were required to locate a target as quickly and as accurately as possible and to ignore a potential distractor that could appear either before, at the same time, or after the target. Response times (RTs) were collected, and indices of alerting (i.e., reactivity to warning signals), distraction, and interruption (i.e., reactivity to signals appearing during attentive processing) were computed. RESULTS: The amplitude of the indices differed between the groups, F(2, 76) = 3.1, p < .05. No difference was found with alerting (p > .85) or distraction (p > .84), but the interruption index was higher in the NF1 group than the controls (p < .043). CONCLUSIONS: Elementary components on which more complex attention processes are based are not all ok in NF1. It is suggested that overreactivity to and longer inspection of visual signals occurring outside the current focus of attention characterizes NF1 and that this might be partially responsible for focus of attention instability and lower interference resistance in NF1.

Correlation between pre- or postoperative MRI findings and cerebellar sequelae in patients with medulloblastomas.

INTRODUCTION: Immediate and delayed cerebellar dysfunction may be expected after surgical resection of a medulloblastoma. We investigated whether pre-operative and delayed post-operative MRI may correlate with such sequelae. MATERIAL AND METHODS: The data of 31 patients in continuous complete remission after removal of medulloblastoma, irradiation and chemotherapy, were retrospectively reviewed. Magnetic Resonance Imaging (MRI) was analyzed for the following items: preoperative MRI (ratio of the surface of the tumor/posterior fossa, presence of ventricular dilatation or tonsilar hernia, involvement of the dentate nucleus) and delayed post-operative MRI (amount of cerebellar parenchyma removed, degree of cerebellar atrophy, presence of T1 hypointense regions in remaining cerebellar area and removal of region containing dentate nucleus). These data were correlated with immediate and long-term cerebellar syndrome and daily life repercussions. RESULTS: On preoperative MRI, the ratio of the surface of the tumor/posterior fossa and the presence of tonsilar hernia were significantly correlated with long-term sequelae on speech (respectively P = 0.027 and P = 0.05). Initial supratentorial ventricular dilatation was correlated with ability to sustain adequately daily tasks (P = 0.002). On delayed MRI, cerebellar atrophy was inversely correlated with ability to sustain daily tasks (P = 0.002). Hypointense T1 territory in remaining cerebellar parenchyma significantly correlated with immediate post-operative cerebellar syndrome (P = 0.01) and showed a tendency for post-operative mutism (P = 0.087) but was not correlated with any long-term sequelae. CONCLUSION: Increased cranial pressure on initial MRI and cerebellar atrophy detected on subsequent MRI studies correlated with immediate and long-term cerebellar sequelae.

[Usefulness of systematic brain magnetic resonance imaging in children with neurofibromatosis type 1]. / La réalisation systématique de l'imagerie par résonance magnétique cérébrale a-t-elle un intérêt chez l'enfant atteint de neurofibromatose de type 1?

BACKGROUND AND AIM: The aim of this study was to evaluate the usefulness of systematic screening of asymptomatic neurofibromatosis type 1 (NF1) children with magnetic resonance imaging (MRI). PATIENTS AND METHODS: We retrospectively reviewed the MRIs of children diagnosed with NF1 disease according to the National Institutes of Health criteria, who had been followed for at least 1 year by the department of pediatric neurology (Lyon, France). Brain MRI was systematically performed in asymptomatic patients under 6 years of age. RESULTS: One hundred patients with a median follow-up of 3.7 years (range, 1-8.6 years) were reviewed. Brain MRI was performed in a total of 94 children. Nine optic pathway gliomas were detected in symptomatic patients. Six children had symptoms caused by the tumor. Gliomas remained stable in 10 patients; 1 symptomatic glioma in an 8-year-old girl required treatment. Spontaneous regression was seen in 1 patient. CONCLUSION: Our results suggest that MRI screening of asymptomatic children to detect optic pathway gliomas does not improve the therapeutic decision and should not be performed systematically. We suggest further investigation in collaboration with the French NF Network.

Acute renal dysfunction after cardiac surgery with cardiopulmonary bypass is associated with plasmatic IL6 increase.

BACKGROUND: Acute renal dysfunction (ARD) is common after cardiac surgery with cardiopulmonary bypass (CPB). CPB results in a sudden systemic inflammatory response. Systemic and local pro-inflammatory cytokines synthesis has been linked with sub-clinical renal injury, especially tubular lesions. Therefore, we sought to assess the systemic synthesis pro-inflammatory cytokines and its association with perioperative ARD after cardiac surgery with CPB. METHODS: Sixty-two patients undergoing cardiac surgery with CPB were prospectively included. Four groups of patients were defined according to blood creatinine increase: no ARD (less than 25% increase), faint ARD (25-50% increase), moderate ARD (50-100% increase), severe ARD (more than 100% increase). RESULTS: Within the 48 post-operative hours was ARD observed as no dysfunction (41.9%), faint (32.2%), moderate (16.1%), severe (9.6%). One patient had to undergo a dialysis. Pre-operative characteristics were homogenous between the four groups excepted the left ventricle ejection fraction. ARD was associated with a low urinary output with high sodium excretion fraction. Significant increase of IL-6 level occurred when patients underwent a severe ARD despite no significant differences for the CRP and TNF-alpha concentrations. CONCLUSION: Severe acute renal dysfunction after cardiac surgery with CPB is associated with a significant increased IL-6 systemic production.

Reactivity to visual signals and the cerebellar vermis: Evidence from a rare case with rhombencephalosynapsis.

The modulatory role of the cerebellum was investigated in a case with rhombencephalosynapsis (RS), a rare dysplasia characterized by the absence of the cerebellar vermis. The visual psychophysical task involved localizing a target and ignoring a distractor appearing either before, at the same time as, or after the target. It allowed us to assess reactivity to warning signals, distraction, and reactivity to signals appearing during attentive processing. Compared with a control sample, the patient exhibited greater reactivity to warning signals and difficulties interrupting attentive processing, whereas distraction was not increased. Complementary analyses showed that these deficits did not reflect just delayed development of attentional processes. These results suggest that the cerebellum modulates responsiveness and commands attentional/exploratory flexibility in response to sensory signals.