Variant characterisation and clinical profile in a large cohort of patients with Ellis-van Creveld syndrome and a family with Weyers acrofacial dysostosis

BACKGROUND

Ellis-van Creveld syndrome (EvC) is a recessive disorder characterised by acromesomelic limb shortening, postaxial polydactyly, nail-teeth dysplasia and congenital cardiac defects, primarily caused by pathogenic variants in EVC or EVC2. Weyers acrofacial dysostosis (WAD) is an ultra-rare dominant condition allelic to EvC. The present work aimed to enhance current knowledge on the clinical manifestations of EvC and WAD and broaden their mutational spectrum.

METHODS

We conducted molecular studies in 46 individuals from 43 unrelated families with a preliminary clinical diagnosis of EvC and 3 affected individuals from a family with WAD and retrospectively analysed clinical data. The deleterious effect of selected variants of uncertain significance was evaluated by cellular assays.

MAIN RESULTS

We identified pathogenic variants in EVC/EVC2 in affected individuals from 41 of the 43 families with EvC. Patients from each of the two remaining families were found with a homozygous splicing variant in WDR35 and a de novo heterozygous frameshift variant in GLI3, respectively. The phenotype of these patients showed a remarkable overlap with EvC. A novel EVC2 C-terminal truncating variant was identified in the family with WAD. Deep phenotyping of the cohort recapitulated 'classical EvC findings' in the literature and highlighted findings previously undescribed or rarely described as part of EvC.

CONCLUSIONS

This study presents the largest cohort of living patients with EvC to date, contributing to better understanding of the full clinical spectrum of EvC. We also provide comprehensive information on the EVC/EVC2 mutational landscape and add GLI3 to the list of genes associated with EvC-like phenotypes.

Genetic and phenotypic findings in 34 novel Spanish patients with DDX3X neurodevelopmental disorder

DDX3X is a multifunctional ATP-dependent RNA helicase involved in several processes of RNA metabolism and in other biological pathways such as cell cycle control, innate immunity, apoptosis and tumorigenesis. Variants in DDX3X have been associated with a developmental disorder named intellectual developmental disorder, X-linked syndromic, Snijders Blok type (MRXSSB, MIM #300958) or DDX3X neurodevelopmental disorder (DDX3X-NDD). DDX3X-NDD is mainly characterized by intellectual disability, brain abnormalities, hypotonia and behavioral problems. Other common findings include gastrointestinal abnormalities, abnormal gait, speech delay and microcephaly. DDX3X-NDD is predominantly found in females who carry de novo variants in DDX3X. However, hemizygous pathogenic DDX3X variants have been also found in males who inherited their variants from unaffected mothers. To date, more than 200 patients have been reported in the literature. Here, we describe 34 new patients with a variant in DDX3X and reviewed 200 additional patients previously reported in the literature. This article describes 34 additional patients to those already reported, contributing with 25 novel variants and a deep phenotypic characterization. A clinical review of our cohort of DDX3X-NDD patients is performed comparing them to those previously published.

Lamb-Shaffer syndrome: 20 Spanish patients and literature review expands the view of neurodevelopmental disorders caused by SOX5 haploinsufficiency

Lamb-Shaffer Syndrome (LSS; OMIM #616803; ORPHA #313892; ORPHA #313884) is an infrequent genetic disorder that affects multiple aspects of human development especially those related to the development of the nervous system. LSS is caused by variants in the SOX5 gene. At the molecular level, SOX5 gene encodes for a transcription factor containing a High Mobility Group (HMG) DNA-Binding domain with relevant functions in brain development in different vertebrate species. Clinical features of Lamb-Shaffer syndrome may include intellectual disability, delayed speech and language development, attention deficits, hyperactivity, autism spectrum disorder, visual problems and seizures. Additionally, patients with the syndrome may present distinct facial dimorphism such as a wide mouth with full lips, small chin, broad nasal bridge, and deep-set eyes. Other physical features that have been reported in some patients include short stature, scoliosis, and joint hypermobility. Here, we report the clinical and molecular characterization of a Spanish LSS cohort of new 20 patients and review all the patients published so far which amount for 111 patients. The most frequent features included developmental delay, intellectual disability, visual problems, poor speech development and facial dysmorphic features. Strikingly, pain insensitivity and hypermetropia seems to be more frequent than previously reported, based on the frequency seen in the Spanish cohort. Eighty-three variants have been reported so far, single nucleotide variants (SNV) and copy number variants represent 47% and 53%, respectively, from the total of variants reported. Similarly to previous reports, the majority of the SNVs variants of the novel patients reported herein fall in the HMG domain of the protein. However, new variants, affecting other functional domains, were also detected. In conclusion, LLS is a rare genetic disorder mostly characterized by a wide range of developmental and neurological symptoms. Early diagnosis would allow to start of care programs, clinical follow up, prospective studies and appropriate genetic counseling, to promote clinical and social improvement to have profound lifelong benefits for patients and their families. Further research is needed to better understand the underlying mechanisms of the syndrome related to SOX5 haploinsufficiency.

Seven Additional Patients with SOX17 Related Pulmonary Arterial Hypertension and Review of the Literature

Pulmonary arterial hypertension (PAH) is an infrequent disorder characterized by high blood pressure in the pulmonary arteries. It may lead to premature death or the requirement for lung and/or heart transplantation. Genetics plays an important and increasing role in the diagnosis of PAH. Here, we report seven additional patients with variants in SOX17 and a review of sixty previously described patients in the literature. Patients described in this study suffered with additional conditions including large septal defects, as described by other groups. Collectively, sixty-seven PAH patients have been reported so far with variants in SOX17, including missense and loss-of-function (LoF) variants. The majority of the loss-of-function variants found in SOX17 were detected in the last exon of the gene. Meanwhile, most missense variants were located within exon one, suggesting a probable tolerated change at the amino terminal part of the protein. In addition, we reported two idiopathic PAH patients presenting with the same variant previously detected in five patients by other studies, suggesting a possible hot spot. Research conducted on PAH associated with congenital heart disease (CHD) indicated that variants in SOX17 might be particularly prevalent in this subgroup, as two out of our seven additional patients presented with CHD. Further research is still necessary to clarify the precise association between the biological pathway of SOX17 and the development of PAH.

Advancing pharmacogenetic testing in a tertiary hospital: a retrospective analysis after 10 years of activity

The field of pharmacogenetics (PGx) holds great promise in advancing personalized medicine by adapting treatments based on individual genetic profiles. Despite its benefits, there are still economic, ethical and institutional barriers that hinder its implementation in our healthcare environment. A retrospective analysis approach of anonymized data sourced from electronic health records was performed, encompassing a diverse patient population and evaluating key parameters such as prescribing patterns and test results, to assess the impact of pharmacogenetic testing. A head-to-head comparison with previously published activity results within the same pharmacogenetic laboratory was also conducted to contrast the progress made after 10 years. The analysis revealed significant utilization of pharmacogenetic testing in daily clinical practice, with 1,145 pharmacogenetic tests performed over a 1-year period and showing a 35% growth rate increase over time. Of the 17 different medical departments that sought PGx tests, the Oncology department accounted for the highest number, representing 58.47% of all genotyped patients. A total of 1,000 PGx tests were requested for individuals susceptible to receive a dose modification based on genotype, and 76 individuals received a genotype-guided dose adjustment. This study presents a comprehensive descriptive analysis of real-world data obtained from a public tertiary hospital laboratory specialized in pharmacogenetic testing, and presents data that strongly endorse the integration of pharmacogenetic testing into everyday clinical practice.

Snijders Blok-Campeau Syndrome: Description of 20 Additional Individuals with Variants in CHD3 and Literature Review

Snijders Blok-Campeau syndrome (SNIBCPS, OMIM# 618205) is an extremely infrequent disease with only approximately 60 cases reported so far. SNIBCPS belongs to the group of neurodevelopmental disorders (NDDs). Clinical features of patients with SNIBCPS include global developmental delay, intellectual disability, speech and language difficulties and behavioral disorders like autism spectrum disorder. In addition, patients with SNIBCPS exhibit typical dysmorphic features including macrocephaly, hypertelorism, sparse eyebrows, broad forehead, prominent nose and pointed chin. The severity of the neurological effects as well as the presence of other features is variable among subjects. SNIBCPS is caused likely by pathogenic and pathogenic variants in CHD3 (Chromodomain Helicase DNA Binding Protein 3), which seems to be involved in chromatin remodeling by deacetylating histones. Here, we report 20 additional patients with clinical features compatible with SNIBCPS from 17 unrelated families with confirmed likely pathogenic/pathogenic variants in CHD3. Patients were analyzed by whole exome sequencing and segregation studies were performed by Sanger sequencing. Patients in this study showed different pathogenic variants affecting several functional domains of the protein. Additionally, none of the variants described here were reported in control population databases, and most computational predictors suggest that they are deleterious. The most common clinical features of the whole cohort of patients are global developmental delay (98%) and speech disorder/delay (92%). Other frequent features (51-74%) include intellectual disability, hypotonia, hypertelorism, abnormality of vision, macrocephaly and prominent forehead, among others. This study expands the number of individuals with confirmed SNIBCPS due to pathogenic or likely pathogenic variants in CHD3. Furthermore, we add evidence of the importance of the application of massive parallel sequencing for NDD patients for whom the clinical diagnosis might be challenging and where deep phenotyping is extremely useful to accurately manage and follow up the patients.

Identifying biomarkers of treatment response to ciclosporin in atopic dermatitis through multiomic predictive modelling: DERMATOMICS study protocol

INTRODUCTION

There is a need to optimise the management of atopic dermatitis (AD), improving the efficacy of treatments and reducing the toxicity associated with them. Although the efficacy of ciclosporine (CsA) in the treatment of AD has been thoroughly documented in the literature, the optimal dose has not been yet established. The use of multiomic predictive models of treatment response could optimise CsA therapy in AD.

METHODS AND ANALYSIS

The study is a low-intervention phase 4 trial to optimise the treatment of patients with moderate-severe AD requiring systemic treatment. The primary objectives are to identify biomarkers that could allow for the selection of responders and non-responders to first-line treatment with CsA and to develop a response prediction model to optimise the CsA dose and treatment regimen in responding patients based on these biomarkers. The study is divided into two cohorts: the first comprised of patients starting treatment with CsA (cohort 1), and the second, of patients already receiving or who have received CsA therapy (cohort 2).

ETHICS AND DISSEMINATION

The study activities began following authorisation by the Spanish Regulatory Agency (AEMPS) and the Clinical Research Ethics Committee of La Paz University Hospital approval. Trial results will be submitted for publication in an open access peer-reviewed medical speciality-specific publication.Trial registration of this study can be located at the EU Clinical Trials Register, available from https://euclinicaltrials.eu/search-for-clinical-trials/?lang=en. Our clinical trial was registered in the website before the enrolment of the first patient complying with European regulations. EU Clinical Trials Register is a primary registry according the WHO. Once our trial was included in a primary and official registry, in order to extend the accessibility to our research, we also registered it retrospectively in clinicaltrials.gov; however, this is not mandatory as per our regulation.

TRIAL REGISTRATION NUMBER

NCT05692843.

Prognostic Impact of Dihydropyrimidine Dehydrogenase Germline Variants in Unresectable Non-Small Cell Lung Cancer Patients Treated with Platin-Based Chemotherapy

Platin-based chemotherapy is the standard treatment for patients with non-small cell lung cancer (NSCLC). However, resistance to this therapy is a major obstacle in successful treatment. In this study, we aimed to investigate the impact of several pharmacogenetic variants in patients with unresectable NSCLC treated with platin-based chemotherapy. Our results showed that DPYD variant carriers had significantly shorter progression-free survival and overall survival compared to DPYD wild-type patients, whereas DPD deficiency was not associated with a higher incidence of high-grade toxicity. For the first time, our study provides evidence that DPYD gene variants are associated with resistance to platin-based chemotherapy in NSCLC patients. Although further studies are needed to confirm these findings and explore the underlying mechanisms of this association, our results suggest that genetic testing of DPYD variants may be useful for identifying patients at a higher risk of platin-based chemotherapy resistance and might be helpful in guiding future personalized treatment strategies in NSCLC patients.

Clinical Heterogeneity and Different Phenotypes in Patients with SETD2 Variants: 18 New Patients and Review of the Literature

SETD2 belongs to the family of histone methyltransferase proteins and has been associated with three nosologically distinct entities with different clinical and molecular features: Luscan-Lumish syndrome (LLS), intellectual developmental disorder, autosomal dominant 70 (MRD70), and Rabin-Pappas syndrome (RAPAS). LLS [MIM #616831] is an overgrowth disorder with multisystem involvement including intellectual disability, speech delay, autism spectrum disorder (ASD), macrocephaly, tall stature, and motor delay. RAPAS [MIM #6201551] is a recently reported multisystemic disorder characterized by severely impaired global and intellectual development, hypotonia, feeding difficulties with failure to thrive, microcephaly, and dysmorphic facial features. Other neurologic findings may include seizures, hearing loss, ophthalmologic defects, and brain imaging abnormalities. There is variable involvement of other organ systems, including skeletal, genitourinary, cardiac, and potentially endocrine. Three patients who carried the missense variant p.Arg1740Gln in SETD2 were reported with a moderately impaired intellectual disability, speech difficulties, and behavioral abnormalities. More variable findings included hypotonia and dysmorphic features. Due to the differences with the two previous phenotypes, this association was then named intellectual developmental disorder, autosomal dominant 70 [MIM 620157]. These three disorders seem to be allelic and are caused either by loss-of-function, gain-of-function, or missense variants in the SETD2 gene. Here we describe 18 new patients with variants in SETD2, most of them with the LLS phenotype, and reviewed 33 additional patients with variants in SETD2 that have been previously reported in the scientific literature. This article offers an expansion of the number of reported individuals with LLS and highlights the clinical features and the similarities and differences among the three phenotypes associated with SETD2.

Adult experiences in Beckwith-Wiedemann syndrome

Beckwith-Wiedemann syndrome (BWS) is an overgrowth and epigenetic disorder caused by changes on chromosome 11p15. The primary features requiring management in childhood include macroglossia, omphalocele, lateralized overgrowth, hyperinsulinism, and embryonal tumors. Management guidelines have not been developed for adults with BWS and there have been few studies to assess the clinical needs of these patients. Furthermore, there have been few studies on the psychosocial implications of BWS in children or adults. Here, we present a descriptive summary of data gathered from two separate adult BWS cohorts. The first, a patient-based survey cohort, includes self-reported health information and recollections about BWS experiences, while the second provides results of a medical record-based assessment from patients in an overgrowth registry. Results highlight the clinical features and medical issues affecting two large independent cohorts of adults with BWS while noting similarities. Open-ended questions asked of the survey cohort yielded themes to guide future qualitative studies. Finally, the study demonstrated the reliability of patient-reported data and the utility of international partnerships in this context.

Borazine Promoted Growth of Highly Oriented Thin Films

We report on a phenomenon, where thin films sputter-deposited on single-crystalline Al₂O₃(0001) substrates exposed to borazine─a precursor commonly used for the synthesis of hexagonal boron nitride layers─are more highly oriented than those grown on bare Al₂O₃(0001) under the same conditions. We observed this phenomenon in face-centered cubic Pd, body-centered cubic Mo, and trigonal Ta₂C thin films grown on Al₂O₃(0001). Interestingly, intermittent exposure to borazine during the growth of Ta₂C thin films on Ta₂C yields better crystallinity than direct deposition of monolithic Ta₂C. We attribute these rather unusual results to a combination of both enhanced adatom mobilities on, and epitaxial registry with, surfaces exposed to borazine during the deposition. We expect that our approach can potentially help improve the crystalline quality of thin films deposited on a variety of substrates.

Utility of CYP2D6 copy number variants as prognostic biomarker in localized anal squamous cell carcinoma

BACKGROUND

Anal squamous cell carcinoma (ASCC) is an infrequent tumor whose treatment has not changed since the 1970s. The aim of this study is the identification of biomarkers allowing personalized treatments and improvement of therapeutic outcomes.

METHODS

Forty-six paraffin tumor samples from ASCC patients were analyzed by whole-exome sequencing. Copy number variants (CNVs) were identified and their relation to disease-free survival (DFS) was studied and validated in an independent retrospective cohort of 101 ASCC patients from the Multidisciplinary Spanish Digestive Cancer Group (GEMCAD). GEMCAD cohort proteomics allowed assessing the biological features of these tumors.

RESULTS

On the discovery cohort, the median age was 61 years old, 50% were males, stages I/II/III: 3 (7%)/16 (35%)/27 (58%), respectively, median DFS was 33 months, and overall survival was 45 months. Twenty-nine genes whose duplication was related to DFS were identified. The most representative was duplications of the CYP2D locus, including CYP2D6, CYP2D7P, and CYP2D8P genes. Patients with CYP2D6 CNV had worse DFS at 5 years than those with two CYP2D6 copies (21% vs. 84%; p < .0002, hazard ratio [HR], 5.8; 95% confidence interval [CI], 2.7-24.9). In the GEMCAD validation cohort, patients with CYP2D6 CNV also had worse DFS at 5 years (56% vs. 87%; p = .02, HR = 3.6; 95% CI, 1.1-5.7). Mitochondria and mitochondrial cell-cycle proteins were overexpressed in patients with CYP2D6 CNV.

CONCLUSIONS

Tumor CYP2D6 CNV identified patients with a significantly worse DFS at 5 years among localized ASCC patients treated with 5-fluorouracil, mitomycin C, and radiotherapy. Proteomics pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets for these high-risk patients.

PLAIN LANGUAGE SUMMARY

Anal squamous cell carcinoma is an infrequent tumor whose treatment has not been changed since the 1970s. However, disease-free survival in late staged tumors is between 40% and 70%. The presence of an alteration in the number of copies of CYP2D6 gene is a biomarker of worse disease-free survival. The analysis of the proteins in these high-risk patients pointed out mitochondria and mitochondrial cell-cycle genes as possible therapeutic targets. Therefore, the determination of the number of copies of CYP2D6 allows the identification of anal squamous carcinoma patients with a high-risk of relapse that could be redirected to a clinical trial. Additionally, this study may be useful to suggest new treatment strategies to increase current therapy efficacy.

Impact of dose adjustment of fluoropyrimidines on toxicity in patients with DPD-deficient colorectal cancer: A single-center experience

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Background: Fluoropyrimidines (FPs) are the chemotherapy backbone for most patients with CRC. FPs are metabolized by dihydropyrimidine dehydrogenase (DPD). Current guidelines recommend measuring DPD activity before chemotherapy administration to adjust the initial dose and thus prevent high-grade toxicity. However, the clinical impact of this strategy is still understudied. We aim to study the efficacy and toxicity of FPs dose modifications according to DPD activity in patients with CRC. Methods: We retrospectively identified all the CRC cancer patients treated with FPs between January 2017 and July 2021 and with DPD activity assessment at Hospital Universitario La Paz, Madrid, Spain. Clinical characteristics and tolerability were collected. Two cohorts were stablished according to its DPD activity, patients with a normal DPD metabolism (DPD wild-type patients) and patients with a diminished metabolism of FPs (DPD deficient patients). Results: A total of 249 CRC patients were included in this study. Sixteen patients (6,4%) were DPD deficient, and 15 of them (94%) received initially 50% of the recommended standard dosing of FPs (increasing to 75% in following cycles if well tolerated) according to guidelines. Forty percent of non-DPD deficiency started FPs at 75% of the standard initial dose due to frailty. Two toxic deaths were observed in the DPD-wild-type cohort, none in the DPD deficient cohort. Clinico-pathological characteristics of patients and their toxicity according to each cohort are depicted in the table. No significant differences in G3/4 toxicity between both groups (40% and 37% in the DPD-wild-type and DPD-deficient cohort, respectively). Diarrhea G3/4 was numerically more present in the DPD-deficient group (25% vs 12%, respectively). Conclusions: Overall, DPD genotype-guided FP treatment in DPD deficient patients with CRC may prevent high-grade toxicity. Diarrhea might still be higher in this group despite dose modifications, so careful surveillance and early treatment should be considered in these patients. [Table: see text]

A large, ten-generation family with autosomal dominant preaxial polydactyly/triphalangeal thumb: Historical, clinical, genealogical, and molecular studies

We present a large, ten-generation family of 273 individuals with 84 people having preaxial polydactyly/triphalangeal thumb due to a pathogenic variant in the zone of polarizing activity regulatory sequence (ZRS) within the exon 5 of LMBR1. The causative change maps to position 396 of the ZRS, located at position c.423 + 4909C > T (chr7:156791480; hg38; LMBR1 ENST00000353442.10; rs606231153 NG_009240.2) in the intron 5 of LMBR1. The first affected individual with the disorder was traced back to mid-1700, when some settlers and workers established in Cervera de Buitrago, a small village about 82 km North to Madrid. Clinical and radiological studies of most of the affected members have been performed for 42 years (follow-up of the family by LFGA). Molecular studies have confirmed a pathogenic variant in the ZRS that segregates in this family. To the best of our knowledge, this is the largest family with preaxial polydactyly/triphalangeal thumb reported so far.

Genetic variants associated with steatohepatitis and liver fibrosis in HIV-infected patients with NAFLD

Background and aims: Nonalcoholic fatty liver disease (NAFLD) is a common cause of liver damage in people living with HIV (PLWHIV). Several studies have investigated candidate genes for susceptibility to NAFLD and to steatohepatitis. PNPLA3, TM6SF2, and MBOAT7-TMC4 have been reported to be associated with elevated ALT levels and the histologic parameters of nonalcoholic steatohepatitis and severity of fibrosis. Our objective was to analyze the relationship between PNPLA3, TM6SF2, and MBOAT7-TMC4 and steatosis, steatohepatitis, and liver fibrosis in PLWHIV with NAFLD.

Method: A cohort of PLWHIV with persistently elevated aminotransferase levels and suspected NAFLD who underwent liver biopsy and determination of genetic variants was assessed at two large centers in Spain. All participants included in the current study were genotyped for rs738409 (PNPLA3), rs58542926 (TM6SF2), and rs641738 (MBOAT7-TMC4).

Results: The study population comprised PLWHIV who were on stable antiretroviral therapy [7.7% women; median age, 49.3 years (44–53.4)]. The median CD4 count was 829 (650–980), 60% had metabolic syndrome, and 18.5% were diabetic. The median BMI was 28.9 (25.5–30.8). Patients with liver steatosis (any grade) vs. nonsteatosis tended to harbor the PNPLA3 G allele variant [57.6% vs. 16.7% (p = 0.09)], but not TM6SF2 or MBOAT7-TMC4 variants. However, those with steatohepatitis vs. nonsteatohepatitis significantly more frequently had the PNPLA3 G allele variant [69.4% vs. 39.1% (p < 0.05)] and the MBOAT7-TMC4 A allele variant [75% vs. 42% (p < 0.05)]. In our cohort, the TM6SF2 gene variant was not associated with steatosis or steatohepatitis. The PNPLA3 G allele variant was associated with steatohepatitis [OR 4.9 (1.3–18); p 0.02] and liver fibrosis [OR 4.3 (1.1–17.4); p 0.04], and the MBOAT7-TMC4 A allele variant was associated with steatohepatitis [OR 6.6 (1.6–27.6); p 0.01].

Conclusion: The PNPLA3 G allele variant and MBOAT7-TMC4 A allele variant were associated with steatohepatitis and liver fibrosis in PLWHIV with persistently elevated aminotransferases and NAFLD. We recommend routine genotyping for PNPLA3 and MBOAT7-TMC4 in PLWHIV with NAFLD to identify those at higher risk of progression.

Clinical Spectrum and Tumour Risk Analysis in Patients with Beckwith-Wiedemann Syndrome Due to CDKN1C Pathogenic Variants

Beckwith-Wiedemann syndrome spectrum (BWSp) is an overgrowth disorder caused by imprinting or genetic alterations at the 11p15.5 locus. Clinical features include overgrowth, macroglossia, neonatal hypoglycaemia, omphalocele, hemihyperplasia, cleft palate, and increased neoplasm incidence. The most common molecular defect observed is hypomethylation at the imprinting centre 2 (KCNQ1OT1:TSS DMR) in the maternal allele, which accounts for approximately 60% of cases, although CDKN1C pathogenic variants have been reported in 5-10% of patients, with a higher incidence in familial cases. In this study, we examined the clinical and molecular features of all cases of BWSp identified by the Spanish Overgrowth Registry Initiative with pathogenic or likely pathogenic CDKN1C variants, ascertained by Sanger sequencing or next-generation sequencing, with special focus on the neoplasm incidence, given that there is scarce knowledge of this feature in CDKN1C-associated BWSp. In total, we evaluated 21 cases of BWSp with CDKN1C variants; 19 were classified as classical BWS according to the BWSp scoring classification by Brioude et al. One of our patients developed a mediastinal ganglioneuroma. Our study adds evidence that tumour development in patients with BWSp and CDKN1C variants is infrequent, but it is extremely relevant to the patient's follow-up and supports the high heterogeneity of BWSp clinical features associated with CDKN1C variants.

Synergistic effect of antimetabolic and chemotherapy drugs in triple-negative breast cancer

The triple-negative breast cancer (TNBC) subtype comprises approximately 15% of all breast cancers and is associated with poor long-term outcomes. Classical chemotherapy remains the standard of treatment, with toxicity and resistance being major limitations. TNBC is a high metabolic group, and antimetabolic drugs are effective in inhibiting TNBC cell growth. We analyzed the combined effect of chemotherapy and antimetabolic drug combinations in MDA-MB-231, MDA-MB-468 and HCC1143 human TNBC cell lines. Cells were treated with each drug or with drug combinations at a range of concentrations to establish the half-maximal inhibitory concentrations (IC₅₀). The dose-effects of each drug or drug combination were calculated, and the synergistic or antagonistic effects of drug combinations were defined. Chemotherapy and antimetabolic drugs exhibited growth inhibitory effects on TNBC cell lines. Antimetabolic drugs targeting the glycolysis pathway had a synergistic effect with chemotherapy drugs, and antiglycolysis drug combinations also had a synergistic effect. The use of these drug combinations could lead to new therapeutic strategies that reduce chemotherapy drug doses, decreasing their toxic effect, or that maintain the doses but enhance their efficacy by their synergistic effect with other drugs.

Even violins can cry: specifically vocal emotional behaviours also drive the perception of emotions in non-vocal music

A wealth of theoretical and empirical arguments have suggested that music triggers emotional responses by resembling the inflections of expressive vocalizations, but have done so using low-level acoustic parameters (pitch, loudness, speed) that, in fact, may not be processed by the listener in reference to human voice. Here, we take the opportunity of the recent availability of computational models that allow the simulation of three specifically vocal emotional behaviours: smiling, vocal tremor and vocal roughness. When applied to musical material, we find that these three acoustic manipulations trigger emotional perceptions that are remarkably similar to those observed on speech and scream sounds, and identical across musician and non-musician listeners. Strikingly, this not only applied to singing voice with and without musical background, but also to purely instrumental material.

This article is part of the theme issue ‘Voice modulation: from origin and mechanism to social impact (Part I)’.

Analytical validation of a laboratory-development multigene pharmacogenetic assay

OBJECTIVE

The implementation of pharmacogenetics (PGx) in clinical practice is an essential tool for personalized medicine. However, clinical laboratories must validate their procedures before being used to perform PGx studies in patients, in order to confirm that they are adequate for the intended purposes.

METHODS

We designed a validation process for our in-house pharmacogenetic PCR-based method assay.

RESULTS

The concordance to reference, repeatability and reproducibility was 100%. Sensitivity and specificity were 100% for the detection of variant diplotypes in CYP2C9, CYP3A5, TPMT, DPYD and UGT1A1 genes. The sensitivity was lower in the detection of CYP2C19 variants due to a limitation in the design that prevents the detection of CYP2C19 *2/*10 diplotype.

CONCLUSIONS

The success of implementing clinical pharmacogenetic testing into routine clinical practice is dependent on the precision of genotyping. Limitations must be bearing in mind to guarantee the quality of PGx assays in clinical laboratory practice. We provided objective evidence that the necessary requirements in our laboratory-development assay were fulfilled.

Individual Tree Segmentation Method Based on Mobile Backpack LiDAR Point Clouds

Individual tree (IT) segmentation is crucial for forest management, supporting forest inventory, biomass monitoring or tree competition analysis. Light detection and ranging (LiDAR) is a prominent technology in this context, outperforming competing technologies. Aerial laser scanning (ALS) is frequently used for forest documentation, showing good point densities at the tree-top surface. Even though under-canopy data collection is possible with multi-echo ALS, the number of points for regions near the ground in leafy forests drops drastically, and, as a result, terrestrial laser scanners (TLS) may be required to obtain reliable information about tree trunks or under-growth features. In this work, an IT extraction method for terrestrial backpack LiDAR data is presented. The method is based on DBSCAN clustering and cylinder voxelization of the volume, showing a high detection rate (∼90%) for tree locations obtained from point clouds, and low commission and submission errors (accuracy over 93%). The method includes a sensibility assessment to calculate the optimal input parameters and adapt the workflow to real-world data. This approach shows that forest management can benefit from IT segmentation, using a handheld TLS to improve data collection productivity.

Tenorio syndrome: Description of 14 novel cases and review of the clinical and molecular features

Tenorio syndrome (TNORS) (OMIM #616260) is a relatively recent disorder with very few cases described so far. Clinical features included macrocephaly, intellectual disability, hypotonia, enlarged ventricles and autoimmune diseases. Molecular underlying mechanism demonstrated missense variants and a large deletion encompassing RNF125, a gene that encodes for an U3 ubiquitin ligase protein. Since the initial description of the disorder in six patients from four families, several new patients were diagnosed, adding more evidence to the clinical spectrum. In this article, we described 14 additional cases with deep phenotyping and make an overall review of all the cases with pathogenic variants in RNF125. Not all patients presented with overgrowth, but instead, most patients showed a common pattern of neurodevelopmental disease, macrocephaly and/or large forehead. Segregation analysis showed that, though the variant was inherited in some patients from an apparently asymptomatic parent, deep phenotyping suggested a mild form of the disease in some of them. The mechanism underlying the development of this disease is not well understood yet and the report of further cases will help to a better understanding and clinical characterization of the syndrome.

Schuurs-Hoeijmakers Syndrome (PACS1 Neurodevelopmental Disorder): Seven Novel Patients and a Review

Schuurs–Hoeijmakers syndrome (SHMS) or PACS1 Neurodevelopmental disorder is a rare disorder characterized by intellectual disability, abnormal craniofacial features and congenital malformations. SHMS is an autosomal dominant hereditary disease caused by pathogenic variants in the PACS1 gene. PACS1 is a trans-Golgi-membrane traffic regulator that directs protein cargo and several viral envelope proteins. It is upregulated during human embryonic brain development and has low expression after birth. So far, only 54 patients with SHMS have been reported. In this work, we report on seven new identified SHMS individuals with the classical c.607C > T: p.Arg206Trp PACS1 pathogenic variant and review clinical and molecular aspects of all the patients reported in the literature, providing a summary of clinical findings grouped as very frequent (≥75% of patients), frequent (50–74%), infrequent (26–49%) and rare (less than ≤25%).

Novel TNIP2 and TRAF2 Variants Are Implicated in the Pathogenesis of Pulmonary Arterial Hypertension

Background: Pulmonary arterial hypertension (PAH) is a rare disease characterized by pulmonary vascular remodeling and right heart failure. Specific genetic variants increase the incidence of PAH in carriers with a family history of PAH, those who suffer from certain medical conditions, and even those with no apparent risk factors. Inflammation and immune dysregulation are related to vascular remodeling in PAH, but whether genetic susceptibility modifies the PAH immune response is unclear. TNIP2 and TRAF2 encode for immunomodulatory proteins that regulate NF-κB activation, a transcription factor complex associated with inflammation and vascular remodeling in PAH. Methods: Two unrelated families with PAH cases underwent whole-exome sequencing (WES). A custom pipeline for variant prioritization was carried out to obtain candidate variants. To determine the impact of TNIP2 and TRAF2 in cell proliferation, we performed an MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay on healthy lung pericytes transfected with siRNA specific for each gene. To measure the effect of loss of TNIP2 and TRAF2 on NF-kappa-beta (NF-κB) activity, we measured levels of Phospho-p65-NF-κB in siRNA-transfected pericytes using western immunoblotting. Results: We discovered a novel missense variant in the TNIP2 gene in two affected individuals from the same family. The two patients had a complex form of PAH with interatrial communication and scleroderma. In the second family, WES of the proband with PAH and primary biliary cirrhosis revealed a de novo protein-truncating variant in the TRAF2. The knockdown of TNIP2 and TRAF2 increased NF-κB activity in healthy lung pericytes, which correlated with a significant increase in proliferation over 24 h. Conclusions: We have identified two rare novel variants in TNIP2 and TRAF2 using WES. We speculate that loss of function in these genes promotes pulmonary vascular remodeling by allowing overactivation of the NF-κB signaling activity. Our findings support a role for WES in helping identify novel genetic variants associated with dysfunctional immune response in PAH.

[Improved office blood pressure control by automatic delayed-reading oscillometric device]

INTRODUCTION

Office blood pressure (BP) measurement is a recommended procedure, although the out-of-office BP measurements are increasingly used.

OBJECTIVE

To know the degree of BP control by clinical measurement.

MATERIAL AND METHODS

During November 2019 demographic and clinical data, office attended systolic BP (SBP) and diastolic BP (DBP) measured with an automatic device with delayed reading and, if performed, data from ambulatory BP monitoring (ABPM) were collected.

RESULTS

102 patients (67 men) were included, with a mean age of 64.9 years, 30% diabetic and 34% with cardiovascular complications. 70% had a controlled hypertesion (<140/90 mmHg) by office BP, the mean SBP was 131 ± 16.5 mmHg and the DBP was 73 ± 9.5 mmHg. Old age and diabetes were associated with uncontrolled hypertension. Thirty three patients had ABPM data, which allowed them to be classified according to the 24-hour BP into: 30% true normotension, 9% white-coat hypertension, 15% sustained hypertension, and 45% masked hypertension.

CONCLUSION

The use of automatic devices reduces the white-coat phenomenon, improving the % of patients with office BP controlled. However, this is not confirmed outside the clinic, showing the importance of ABPM in the evaluation of hypertension control. Office BP measurement is useful in patients initial assessment and also provides educational aspects, although the methodology must be optimized to define its clinical role.

Introduction of Deep Learning in Thermographic Monitoring of Cultural Heritage and Improvement by Automatic Thermogram Pre-Processing Algorithms

The monitoring of heritage objects is necessary due to their continuous deterioration over time. Therefore, the joint use of the most up-to-date inspection techniques with the most innovative data processing algorithms plays an important role to apply the required prevention and conservation tasks in each case study. InfraRed Thermography (IRT) is one of the most used Non-Destructive Testing (NDT) techniques in the cultural heritage field due to its advantages in the analysis of delicate objects (i.e., undisturbed, non-contact and fast inspection of large surfaces) and its continuous evolution in both the acquisition and the processing of the data acquired. Despite the good qualitative and quantitative results obtained so far, the lack of automation in the IRT data interpretation predominates, with few automatic analyses that are limited to specific conditions and the technology of the thermographic camera. Deep Learning (DL) is a data processor with a versatile solution for highly automated analysis. Then, this paper introduces the latest state-of-the-art DL model for instance segmentation, Mask Region-Convolution Neural Network (Mask R-CNN), for the automatic detection and segmentation of the position and area of different surface and subsurface defects, respectively, in two different artistic objects belonging to the same family: Marquetry. For that, active IRT experiments are applied to each marquetry. The thermal image sequences acquired are used as input dataset in the Mask R-CNN learning process. Previously, two automatic thermal image pre-processing algorithms based on thermal fundamentals are applied to the acquired data in order to improve the contrast between defective and sound areas. Good detection and segmentation results are obtained regarding state-of-the-art IRT data processing algorithms, which experience difficulty in identifying the deepest defects in the tests. In addition, the performance of the Mask R-CNN is improved by the prior application of the proposed pre-processing algorithms.

Development, behaviour and sensory processing in Marshall-Smith syndrome and Malan syndrome: phenotype comparison in two related syndromes

BACKGROUND

Ultrarare Marshall-Smith and Malan syndromes, caused by changes of the gene nuclear factor I X (NFIX), are characterised by intellectual disability (ID) and behavioural problems, although questions remain. Here, development and behaviour are studied and compared in a cross-sectional study, and results are presented with genetic findings.

METHODS

Behavioural phenotypes are compared of eight individuals with Marshall-Smith syndrome (three male individuals) and seven with Malan syndrome (four male individuals). Long-term follow-up assessment of cognition and adaptive behaviour was possible in three individuals with Marshall-Smith syndrome.

RESULTS

Marshall-Smith syndrome individuals have more severe ID, less adaptive behaviour, more impaired speech and less reciprocal interaction compared with individuals with Malan syndrome. Sensory processing difficulties occur in both syndromes. Follow-up measurement of cognition and adaptive behaviour in Marshall-Smith syndrome shows different individual learning curves over time.

CONCLUSIONS

Results show significant between and within syndrome variability. Different NFIX variants underlie distinct clinical phenotypes leading to separate entities. Cognitive, adaptive and sensory impairments are common in both syndromes and increase the risk of challenging behaviour. This study highlights the value of considering behaviour within developmental and environmental context. To improve quality of life, adaptations to environment and treatment are suggested to create a better person-environment fit.

Efficacité d’un traitement par lopinavir/ritonavir chez des patients hospitalisés pour pneumopathie précoce à SARS-CoV-2 : une étude rétrospective

Introduction

Actuellement, il n’existe pas de traitement antiviral spécifique pour la prise en charge des pneumopathies sévères à SARS-CoV-2. Le Haut Conseil de santé publique français a recommandé l’utilisation du lopinavir/ritonavir (LPV/RTV) qui a montré une efficacité in vitro contre ce virus. La charge virale atteignant son maximum dans la première semaine de l’infection, l’efficacité de ce traitement est probablement optimale s’il est administré pour des formes de pneumopathies précoces survenant au cours de cette première semaine.

Matériels et méthodes

Nous avons conduit une étude rétrospective à partir des données du dossier patient d’un hôpital de 350 lits, comparant 2 prises en charge des pneumopathies précoces à SARS-CoV-2 : soins de support (SDS) seuls versus SDS associés à un traitement par LPV/RTV (400 mg/100 mg) 2 fois par jour, à l’exclusion de tout autre traitement. Les patients âgés de 18 à 80 ans, hospitalisés pour pneumopathie précoce à SARS-CoV-2 avec PCR positive, en service médecine hors unité de soins intensifs (USI), ayant reçu au moins 48 h de traitement par LPV/RTV débuté dans les 10 jours à partir du début des symptômes ont été inclus dans l’analyse. Le critère de jugement principal était le transfert en USI. Les critères de jugement secondaires étaient : la mortalité hospitalière, la mortalité à j7, la survenue d’un syndrome de détresse respiratoire aigu, et la durée totale d’hospitalisation.

Résultats

Entre le 2 mars et le 12 avril 2020, 59 patients parmi les 225 (26 %) hospitalisés pour infection à SARS-CoV-2 étaient éligibles pour l’analyse. Vingt (34 %) avaient reçu un traitement par LPV/RTV + SDS et 39 (66 %) avaient reçu des SDS seuls. Le délai médian entre le début des symptômes et l’hospitalisation était de 4 jours (IQR [3–6]) et la durée médiane de traitement par LPV/RTV était de 6 jours, (IQR [5–7]). Les 2 groupes étaient comparables en termes de comorbidité (âge [médiane 56 ans, IQR (46–65)], sexe, IMC, diabète, insuffisance cardiaque et respiratoire). Dix patients ont été transférés en USI : 3/29 (15 %) dans le groupe LPV/RTV + SDS et 7/39 (18 %) dans le groupe traitement par SDS seuls (p = 0,37). La mortalité hospitalière était similaire (2 patients dans le groupe SDS seuls et aucun dans le groupe LPV/RTV + SDS, p = 0,4). Nous n’avons pas retrouvé de différence pour les autres critères de jugement. Dans le modèle de régression logistique incluant le sexe, l’âge, et la prise de LPV/RTV, aucun facteur n’était associé de manière significative à une réduction du transfert en USI.

Conclusion

L’utilisation de LPV/RTV dans les pneumopathies précoces à SARS-CoV-2 n’a pas diminué significativement le taux de passage en USI ni la mortalité hospitalière. Nos résultats justifient cependant que la stratégie d’administration précoce d’une thérapie antivirale soit évaluée dans le cadre d’un essai clinique randomisé plus important.

Development of Thermal Principles for the Automation of the Thermographic Monitoring of Cultural Heritage

The continuous deterioration of elements, with high patrimonial value over time, can only be mitigated or annulled through the application of techniques that facilitate the preventative detection of the possible agents of deterioration. InfraRed Thermography (IRT) is one of the most used techniques for this task. However, there are few IRT methodologies, which can automatically monitor the cultural heritage field, and are vitally important in eliminating the subjectivity in interpreting and accelerating the analysis process. In this work, a study is performed on a tessellatum layer of a mosaic to automatically: (i) Detect the first appearance of the thermal footprint of internal water, (ii) delimit the contours of the thermal footprint of internal water from its first appearance, and (iii) classify between harmful and non-harmful internal water. The study is based on the analysis of the temperature distribution of each thermal image. Five thermal images sequences are acquired during the simulation of different real situations, obtaining a set of promising results for the optimization of the thermographic inspection process, while discussing the following recommended steps to be taken in the study for future researches.

Growth Kinetics of Two-Dimensional Hexagonal Boron Nitride Layers on Pd(111)

Using in situ variable-temperature scanning tunneling microscopy (300-673 K) during chemical vapor deposition of two-dimensional hexagonal boron nitride (hBN) on Pd(111) from borazine precursor at pressures up to 10^-6 mbar, we identify the mechanisms leading to carpetlike uphill or downhill growth across the Pd steps. Deposition at a higher rate and lower temperature promotes uphill growth via preferential attachment at the ascending and descending step-edges, whereas a lower deposition rate and higher temperature lead to downhill growth via nucleation and growth of islands on Pd terraces. We attribute this unusual growth behavior to differences in temperature-dependent rates of hBN deposition at the steps versus on the Pd terraces. Our results illustrate how growth mechanisms can be activated by a pair of parameters (substrate temperature and partial pressure of borazine) and provide new insights into the mechanisms underlying carpetlike growth of hBN and other layered materials.

In Situ Variable-Temperature Scanning Tunneling Microscopy Studies of Graphene Growth Using Benzene on Pd(111)

Using a combination of in situ ultrahigh-vacuum variable-temperature scanning tunneling microscopy, ex situ Raman spectroscopy, and scanning electron microscopy, we investigated the growth of graphene using benzene on Pd(111) at temperatures up to 1100 K. Benzene adsorbs readily on Pd(111) at room temperature and forms an ordered superstructure upon annealing at 473 K. Exposure to benzene at 673 K enhances Pd step motion and yields primarily amorphous carbon upon cooling to room temperature. Monolayer graphene domains, 10-30 nm in size, appear during annealing this sample at 873 K. Dosing benzene at 1100 K results in graphene domains with varying degrees of crystallinity, while post-deposition annealing at 1100 K for 1200 s yields monolayer graphene domains larger than 150 × 150 nm². Our results, which indicate that graphene growth on Pd(111) using benzene requires deposition/annealing temperatures higher than 673 K, are in striking contrast with the reported growth of graphene using benzene at temperatures as low as 373 K on relatively inert Cu surfaces.

Further definition of the proximal 19p13.3 microdeletion/microduplication syndrome and implication of PIAS4 as the major contributor

The proximal 19p13.3 microdeletion/microduplication (prox19p13.3del/dup) syndrome is a recently described disorder with common clinical features including developmental delay, intellectual disability, speech delay, facial dysmorphic features with ear defects, anomalies of the hands and feet, umbilical hernia and hypotonia. While deletions are associated with macrocephaly, patients with duplications have microcephaly. The smallest region of overlap in multiple patients (113.5 kb) included three genes and one pseudogene, with a suggested major role of PIAS4 in determination of the phenotype and head size in these patients. Here, we refine the prox19p13.3del/dup with four additional patients: two with microdeletions, one with microduplication and one family with single-nucleotide nonsense variant in PIAS4. The patient with the PIAS4 loss of function variant displayed a phenotype quite similar to deletion patients -including the macrocephaly and many other core features of the syndrome. Patient's SNV was inherited from her mother who is similarly affected. Thus, our data indicate that PIAS4 is a major contributor to the proximal 19p13.3del/dup syndrome phenotype. In summary, we report the first patient with a pathogenic variant in PIAS4- and three additional rearrangements at the proximal 19p13.3 locus. These observations add further evidence about the molecular basis of this microdeletion/microduplication syndrome.

Payload for Contact Inspection Tasks with UAV Systems

This paper presents a payload designed to perform semi-autonomous contact inspection tasks without any type of positioning system external to the UAV, such as a global navigation satellite system (GNSS) or motion capture system, making possible inspection in challenging GNSS- denied sites. This payload includes two LiDAR sensors which measure the distance between the UAV and the target structure and their inner orientation angle. The system uses this information to control the approaching of the UAV to the structure and the contact between both, actuating over the pitch and yaw signals. This control is performed using a hybrid automaton with different states that represent all the possible UAV status during the inspection tasks. It uses different control strategies in each state. An ultrasonic gauge has been used as the inspection sensor of the payload to measure the thickness of a metallic sheet. The sensor requires a stable contact in order to collect reliable measurements. Several tests have been performed on the system, reaching accurate results which show it is able to maintain a stable contact with the target structure.

Road Environment Semantic Segmentation with Deep Learning from MLS Point Cloud Data

In the near future, the communication between autonomous cars will produce a network of sensors that will allow us to know the state of the roads in real time. Lidar technology, upon which most autonomous cars are based, allows the acquisition of 3D geometric information of the environment. The objective of this work is to use point clouds acquired by Mobile Laser Scanning (MLS) to segment the main elements of road environment (road surface, ditches, guardrails, fences, embankments, and borders) through the use of PointNet. Previously, the point cloud was automatically divided into sections in order for semantic segmentation to be scalable to different case studies, regardless of their shape or length. An overall accuracy of 92.5% has been obtained, but with large variations between classes. Elements with a greater number of points have been segmented more effectively than the other elements. In comparison with other point-by-point extraction and ANN-based classification techniques, the same success rates have been obtained for road surfaces and fences, and better results have been obtained for guardrails. Semantic segmentation with PointNet is suitable when segmenting the scene as a whole, however, if certain classes have more interest, there are other alternatives that do not need a high training cost.

A safety analysis of roundabouts and turbo roundabouts based on Petri nets

Objective: In this work, a roundabout and a turbo roundabout model are compared and previous modeling with continuous Petri nets and safety are analyzed through indicators of complexity. Petri nets are a graphic and mathematical representation that allow a faithful modeling of urban systems. Method: The methodology has been designed for the transformation of a real system to small subgraphs that represent the maneuvers in roundabouts, approximated as roads and lanes of incorporation. Places within the roundabout have been located and defined as continuous places from their influence and visibility toward adjacent conditions. The transitions have been modeled by time and inhibitory arcs, which represent priorities and areas where drivers must pay attention. The created networks represent a faithful model of vehicle flow trajectories in the roundabouts. Results: The methodology is applied to the same real road intersection. The case study is a recent transformation from roundabout to turbo roundabout. The roundabout network complexity is corroborated by a greater number of entries and exits that lead to each roundabout place (reflected in the maneuvers that can be performed) and a greater number of inhibiting arcs. In most of the turbo roundabout places, the driver's only option is reduced to occupying next place. The possibility of choosing between several places supposes a greater trajectory intersection and an increased time for decision making. The only situation where the complexity is the same between both systems is when a vehicle accesses the inner lane of the roundabout from the left lane on a single-lane road. The main maneuvers causing accidents have been modeled and their solution in a turbo roundabout is presented. Conclusions: The reduced complexity of the turbo roundabout is due to the strict limitations in lane changes, turning turbo roundabouts into a safer model: A lower number of possible movements that can be performed by drivers and a smaller number of trajectories with collision risk. Petri nets have proven to be perfectly applicable to the representation of traffic circular systems (such as roundabouts and turbo roundabouts) and to measure the complexity and security of the system.

Further delineation of Malan syndrome

Malan syndrome is an overgrowth disorder described in a limited number of individuals. We aim to delineate the entity by studying a large group of affected individuals. We gathered data on 45 affected individuals with a molecularly confirmed diagnosis through an international collaboration and compared data to the 35 previously reported individuals. Results indicate that height is > 2 SDS in infancy and childhood but in only half of affected adults. Cardinal facial characteristics include long, triangular face, macrocephaly, prominent forehead, everted lower lip, and prominent chin. Intellectual disability is universally present, behaviorally anxiety is characteristic. Malan syndrome is caused by deletions or point mutations of NFIX clustered mostly in exon 2. There is no genotype‐phenotype correlation except for an increased risk for epilepsy with 19p13.2 microdeletions. Variants arose de novo, except in one family in which mother was mosaic. Variants causing Malan and Marshall‐Smith syndrome can be discerned by differences in the site of stop codon formation. We conclude that Malan syndrome has a well recognizable phenotype that usually can be discerned easily from Marshall–Smith syndrome but rarely there is some overlap. Differentiation from Sotos and Weaver syndrome can be made by clinical evaluation only.

Clinical Implementation of Pharmacogenetic Testing in a Hospital of the Spanish National Health System: Strategy and Experience Over 3 Years

In 2014, we established a pharmacogenetics unit with the intention of facilitating the integration of pharmacogenetic testing into clinical practice. This unit was centered around two main ideas: i) individualization of clinical recommendations, and ii) preemptive genotyping in risk populations. Our unit is based on the design and validation of a single nucleotide polymorphism (SNP) microarray, which has allowed testing of 180 SNPs associated with drug response (PharmArray), and clinical consultation regarding the results. Herein, we report our experience in integrating pharmacogenetic testing into our hospital and we present the results of the 2,539 pharmacogenetic consultation requests received over the past 3 years in our unit. The results demonstrate the feasibility of implementing pharmacogenetic testing in clinical practice within a national health system.

mTOR mutations in Smith-Kingsmore syndrome: Four additional patients and a review

Smith-Kingsmore syndrome (SKS) OMIM #616638, also known as MINDS syndrome (ORPHA 457485), is a rare autosomal dominant disorder reported so far in 23 patients. SKS is characterized by intellectual disability, macrocephaly/hemi/megalencephaly, and seizures. It is also associated with a pattern of facial dysmorphology and other non-neurological features. Germline or mosaic mutations of the mTOR gene have been detected in all patients. The mTOR gene is a key regulator of cell growth, cell proliferation, protein synthesis and synaptic plasticity, and the mTOR pathway (PI3K-AKT-mTOR) is highly regulated and critical for cell survival and apoptosis. Mutations in different genes in this pathway result in known rare diseases implicated in hemi/megalencephaly with epilepsy, as the tuberous sclerosis complex caused by mutations in TSC1 and TSC2, or the PIK3CA-related overgrowth spectrum (PROS). We here present 4 new cases of SKS, review all clinical and molecular aspects of this disorder, as well as some characteristics of the patients with only brain mTOR somatic mutations.

Safety assessment on pedestrian crossing environments using MLS data

In the framework of infrastructure analysis and maintenance in an urban environment, it is important to address the safety of every road user. This paper presents a methodology for the evaluation of several safety indicators on pedestrian crossing environments using geometric and radiometric information extracted from 3D point clouds collected by a Mobile Mapping System (MMS). The methodology is divided in four main modules which analyze the accessibility of the crossing area, the presence of traffic lights and traffic signs, and the visibility between a driver and a pedestrian on the proximities of a pedestrian crossing. The outputs of the analysis are exported to a Geographic Information System (GIS) where they are visualized and can be further processed in the context of city management. The methodology has been tested on approximately 30 pedestrian crossings in cluttered urban environments of two different cities. Results show that MMS are a valid mean to assess the safety of a specific urban environment, regarding its geometric conditions. Remarkable results are presented on traffic light classification, with a global F-score close to 95%.

Molecular characterization of breast cancer cell response to metabolic drugs

Metabolic reprogramming is a hallmark of cancer. It has been described that breast cancer subtypes present metabolism differences and this fact enables the possibility of using metabolic inhibitors as targeted drugs in specific scenarios. In this study, breast cancer cell lines were treated with metformin and rapamycin, showing a heterogeneous response to treatment and leading to cell cycle disruption. The genetic causes and molecular effects of this differential response were characterized by means of SNP genotyping and mass spectrometry-based proteomics. Protein expression was analyzed using probabilistic graphical models, showing that treatments elicit various responses in some biological processes such as transcription. Moreover, flux balance analysis using protein expression values showed that predicted growth rates were comparable with cell viability measurements and suggesting an increase in reactive oxygen species response enzymes due to metformin treatment. In addition, a method to assess flux differences in whole pathways was proposed. Our results show that these diverse approaches provide complementary information and allow us to suggest hypotheses about the response to drugs that target metabolism and their mechanisms of action.

Expansion of a CD26low Effector TH Subset and Reduction in Circulating Levels of sCD26 in Stable Allergic Asthma in Adults

BACKGROUND AND OBJETIVE

The pathogenesis of asthma is dependent on the balance between regulatory and effector T cells, which display differential expression of CD25 and CD26. Therefore, alteration of circulating levels of sCD25 and sCD26 during allergic asthma could be conditioned by changes in leukocyte phenotype. Objectives: To analyze expression of CD25 and CD26 on T lymphocytes and their soluble derivatives (sCD25, sCD26) during stable phases of moderate-severe allergic asthma.

METHODS

Cross-sectional study with 2 adult cohorts of allergic asthmatics. Clinical, anthropometric, pulmonary, hematological, and biochemical parameters were measured. Phenotyping was performed with flow cytometry in both circulating and cultured leukocytes. Dipeptidyl peptidase 4 (DPP4) activity was assayed in culture supernatants.

RESULTS

In vitro studies revealed upregulation of CD26 on human T lymphocytes upon activation, especially under TH17-favoring conditions, and a correlation with soluble DPP4 activity (rs=0.641; P<.001). CD26 expression on lymphocytes was higher in asthmatics, while serum sCD26 was lower in women and patients. The latter finding could be associated with an expanded CD25low/CD26low/CD127low subset of effector CD4+ T cells in allergic asthma, with no changes in Treg percentages. However, women showed an increased Teff/Treg ratio, which could explain their greater susceptibility to asthma.

CONCLUSIONS

Allergic asthma causes an increment in CD25lowCD26low helper T cells detected in stable stages. These changes are mirrored in serum and should be considered in the light of the downmodulating role of CD26 in major chemokines related to the pathogenesis of asthma such as CCL11 (eotaxin), CCL5 (RANTES), and CXCL12a (SDF-1α).

In-frame Variants in FLNA Proximal Rod 1 Domain Associate With a Predominant Cardiac Valvular Phenotype

INTRODUCTION AND OBJECTIVES

X-linked cardiac valvular dysplasia is a rare form of male-specific congenital heart defect mainly characterized by myxomatous degeneration of the atrioventricular valves with variable hemodynamic consequences. It is caused by genetic defects in FLNA-encoded filamin A, a widely expressed actin-binding protein that regulates cytoskeleton organization. Filamin A loss of function has also been associated with often concurring neurologic and connective tissue manifestations, with mutations in the first half of the Rod 1 domain apparently expressing the full cardiac phenotype. We contribute to previous genotype-phenotype correlations with a multidisciplinary approach in a newly-described family.

METHODS

Cardiologic, dysmorphologic, and genetic evaluation of available members were complemented with transcriptional and X-chromosome inactivation studies.

RESULTS

A novel FLNA mutation c.1066-3C>G cosegregated with a male-expressed, apparently isolated, cardiac phenotype with no skewed X-inactivation pattern in female carriers. This variant was shown to result in an in-frame deletion of 8 amino acid residues near the N-terminal region of the protein.

CONCLUSIONS

A nonimprinted, partial loss of function of filamin A proximal Rod 1 domain seems to be the pathogenetic mechanism of cardiac valvular dysplasia, with some cases occasionally expressing associated extracardiac manifestations.