Ciliary Genes Are Down-Regulated in Bronchial Tissue of Primary Ciliary Dyskinesia Patients

Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous disease characterized by recurrent respiratory tract infections, sinusitis, bronchiectasis and male infertility. The pulmonary phenotype in PCD is caused by the impaired motility of cilia in the respiratory epithelium, due to ultrastructural defects of these organelles. We hypothesized that defects of multi-protein ciliary complexes should be reflected by gene expression changes in the respiratory epithelium. We have previously found that large group of genes functionally related to cilia share highly correlated expression pattern in PCD bronchial tissue. Here we performed an explorative analysis of differential gene expression in the bronchial tissue from six PCD patients and nine non-PCD controls, using Illumina HumanRef-12 Whole Genome BeadChips. We observed 1323 genes with at least 2-fold difference in the mean expression level between the two groups (t-test p-value <0.05). Annotation analysis showed that the genes down-regulated in PCD biopsies (602) were significantly enriched for terms related to cilia, whereas the up-regulated genes (721) were significantly enriched for terms related to cell cycle and mitosis. We assembled a list of human genes predicted to encode ciliary proteins, components of outer dynein arms, inner dynein arms, radial spokes, and intraflagellar transport proteins. A significant down-regulation of the expression of genes from all the four groups was observed in PCD, compared to non-PCD biopsies. Our data suggest that a coordinated down-regulation of the ciliome genes plays an important role in the molecular pathomechanism of PCD

Movement disorders associated with chromosomal aberrations diagnosed in adult patients

Introduction. Chromosomal aberrations are rare but important causes of various movement disorders. In cases of movement disorders associated with dysmorphic features, multiorgan involvement and/or intellectual disability, the identification of causative chromosomal aberrations should be considered. Aim of the study. The purpose of this article was to summarise clinical findings in six patients with dystonia and two with parkinsonism and identified chromosomal aberrations in a single-centre prospective study. Materials and methods. 15 adult patients with dystonia or parkinsonism were referred to array comparative genomic hybridisation (aCGH) testing from our Department of Neurology between 2014 and 2019. Additionally, one patient had a karyotype examination. Detailed clinical, psychological and radiological diagnostics were performed in each case. Results. Chromosomal aberrations were identified in six patients with dystonia and two with parkinsonism. Two patients were identified with aberrations associated with de Grouchy syndrome. We also reported generalised dystonia in patients with deletion in 3q26.31 and duplication in 3p26.3, as well as dystonia and hypoacusis in a patient with duplication in Xq26.3. One patient was diagnosed with duplication in 21q21.1. Early-onset parkinsonism was a manifestation of deletion in the 2q24.1 region. Late onset parkinsonism was also present in the patient with the most severe aberrations (duplication 1q21.1q44; deletion 10p15.3p15.1; deletion 10q11.21). Conclusions. Dystonia and parkinsonism are possible manifestations of chromosomal aberrations. Chromosomal aberrations should be excluded in patients with early-onset movement disorders and concomitant dysmorphic features and/or intellectual disability. It is important to include this cause of movement disorders in future classifications. aCGH can be a valuable diagnostic tool in the evaluation of movement disorder aetiology

Implementation of Exome Sequencing in Prenatal Diagnosis and Impact on Genetic Counseling: The Polish Experience

This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing.Background: Despite advances in routine prenatal cytogenetic testing, most anomalous fetuses remain without a genetic diagnosis. Exome sequencing (ES) is a molecular technique that identifies sequence variants across protein-coding regions and is now increasingly used in clinical practice. Fetal phenotypes differ from postnatal and, therefore, prenatal ES interpretation requires a large amount of data deriving from prenatal testing. The aim of our study was to present initial results of the implementation of ES to prenatal diagnosis in Polish patients and to discuss its possible clinical impact on genetic counseling. Methods: In this study we performed a retrospective review of all fetal samples referred to our laboratory for ES from cooperating centers between January 2017 and June 2021. Results: During the study period 122 fetuses were subjected to ES at our institution. There were 52 abnormal ES results: 31 in the group of fetuses with a single organ system anomaly and 21 in the group of fetuses with multisystem anomalies. The difference between groups was not statistically significant. There were 57 different pathogenic or likely pathogenic variants reported in 33 different genes. The most common were missense variants. In 17 cases the molecular diagnosis had an actual clinical impact on subsequent pregnancies or other family members. Conclusions: Exome sequencing increases the detection rate in fetuses with structural anomalies and improves genetic counseling for both the affected couple and their relatives.This research was funded by the Ministry of Health, granted to the Center of Postgradu- ate Medical Education, Poland, grant number Minigrant-501-1-106-44-20/MG4 to J.B., and by the National Science Centre, Poland, grant number Miniatura 2—Dec2018/02/X/NZ2/00709 to D.M.info:eu-repo/semantics/publishedVersio

The classical genetic and genomic approach to the pathogenesis of primary ciliary dyskinesia

Trilharen (of cilia) zijn sterk gedifferentieerde structuren die specifieke cellulaire functies vervullen, zoals voortbeweging, waarneming van omgevingssignalen, of het geleidelijk naar buiten werken van de slijmlaag in de luchtwegen. Positionering van organen in het lichaam is deels ook afhankelijk van de werking van trilharen. Primaire ciliaire dyskinesie (PCD) is een erfelijke aandoening die gepaard gaat met een verminderde beweeglijkheid van de trilharen. Doordat hierdoor de luchtwegen worden aangetast, ontstaan er blijvende verwijdingen van de luchtwegen (bronchiën), aangeduid als bronchiëctasie en een chronische bijholteontsteking. Er bestaat ook een stoornis van de beweeglijkheid van de trilharen waarbij de organen in spiegelbeeld gepositioneerd zijn (situs inversus); deze noemt men wel het syndroom van Kartagener. In dit proefschrift wordt onderzoek gepresenteerd gericht op het ontrafelen van de oorzaak van PCD middels klassieke genetische en genomische studies. Het klassieke genetische onderzoek maakt gebruik van koppelingsonderzoek (linkage analyse). Dit onderzoek richt zich op het vinden van een ziektegen met behulp van zogenaamde genetische markers waarbij de overerving van het ziektegen dat de ziekte veroorzaakt, eenzelfde overervingspatroon volgt als de DNA marker. In hoofdstuk 2 wordt koppelingsonderzoek in 70 families met PCD beschreven. In deze studie is de aanname gedaan dat patiënten met het syndroom van Kartagener genetisch gezien andere afwijkingen hebben dan patiënten met PCD. Het hele erfelijke materiaal van 52 families met het syndroom van Kartagener is bekeken met 462 microstalliet markers. Eenzelfde studie is gedaan in 18 families met PCD. Deze studie suggereerde dat genen op chromosoom 15q24-q25 betrokken zijn bij het syndroom van Kartagener (LOD score 4.34). Motile cilia are small cellular projectiles that by synchronized beating propel fluid over the tissues. Cilia generate the flow of mucus and cerebrospinal fluid in the respiratory tract and in the brain, respectively, whereas in the Fallopian tubes cilia help to move the ovum toward the uterus. Flagella, built on a similar to cilia scheme, provide motility to spermatozoa. The motility of cilia plays an important role in initial left-right symmetry breaking event during embryogenesis. Primary ciliary dyskinesia (PCD) is a rare genetic disorder caused by mutations in genes functionally related to cilia motility. Lack of ciliary beating leads to recurrent respiratory tract infections and bronchiectasis because of defective mucociliary clearance. Kinetic dysfunction of the sperm tails causes infertility. Due to immotility of cilia on the embryonic node, left-right determination is randomized causing situs inversus in approximately half of the patients. PCD is inherited, in most of the cases, as autosomal recessive trait. The genetic heterogeneity of the disease is very high. Mutations in eleven genes have been identified in PCD patients so far. Despite this, large majority of cases remain unexplained on the molecular level. High genetic heterogeneity in conjunction with low diversity of the clinical phenotype makes difficult cloning of new genes by means of linkage analysis. Cilia are build of multiprotein complexes controlled by hundreds or even thousands of genes which makes selection of disease candidate genes a difficult task.

Deep Learning-Based Analysis of Face Images as a Screening Tool for Genetic Syndromes

Approximately 4% of the world’s population suffers from rare diseases. A vast majority of these disorders have a genetic background. The number of genes that have been linked to human diseases is constantly growing, but there are still genetic syndromes that remain to be discovered. The diagnostic yield of genetic testing is continuously developing, and the need for testing is becoming more significant. Due to limited resources, including trained clinical geneticists, patients referred to clinical genetics units must be accurately selected. Around 30–40% of genetic disorders are associated with specific facial characteristics called dysmorphic features. As part of our research, we analyzed the performance of classifiers based on deep learning face recognition models in detecting dysmorphic features. We tested two classification problems: a multiclass problem (15 genetic disorders vs. controls) and a two-class problem (disease vs. controls). In the multiclass task, the best result reached an accuracy level of 84%. The best accuracy result in the two-class problem reached 96%. More importantly, the binary classifier detected disease features in patients with diseases that were not previously present in the training dataset. The classifier was able to generalize differences between patients and controls, and to detect abnormalities without information about the specific disorder. This indicates that a screening tool based on deep learning and facial recognition could not only detect known diseases, but also detect patients with diseases that were not previously known. In the future, this tool could help in screening patients before they are referred to the genetic unit

Gene expression studies in cells from primary ciliary dyskinesia patients identify 208 potential ciliary genes

Cilia are small cellular projections that either act as sensors (primary cilia) or propel fluid over the epithelia of various organs (motile cilia). The organellum has gained much attention lately because of its involvement in a group of human diseases called ciliopathies. Primary ciliary dyskinesia (PCD) is an autosomal recessive ciliopathy caused by mutations in cilia motility genes. The disease is characterized by recurrent respiratory tract infections due to the lack of an efficient mucociliary clearance. We performed whole-genome gene expression profiling in bronchial biopsies from PCD patients. We used the quality threshold clustering algorithm to identify groups of genes that revealed highly correlated RNA expression patterns in the biopsies. The largest cluster contained 372 genes and was significantly enriched for genes related to cilia. The database and literature search showed that 164 genes in this cluster were known cilia genes, strongly indicating that the remaining 208 genes were likely to be new cilia genes. The tissue expression pattern of the 208 new cilia genes and the 164 known genes was consistent with the presence of motile cilia in a given tissue. The analysis of the upstream promotor sequences revealed evidence for RFX transcription factors binding site motif in both subgroups. Based on the correlated expression patterns in PCD-affected tissues, we identified 208 genes that we predict to be involved in cilia biology. Our predictions are based directly on the human material and not on model organisms. This list of genes provides candidate genes for PCD and other ciliopathies

Sequence analysis of 21 genes located in the Kartagener syndrome linkage region on chromosome 15q

Primary ciliary dyskinesia (PCD) is a rare genetic disorder, which shows extensive genetic heterogeneity and is mostly inherited in an autosomal recessive fashion. There are four genes with a proven pathogenetic role in PCD. DNAH5 and DNAI1 are involved in 28 and 10% of PCD cases, respectively, while two other genes, DNAH11 and TXNDC3, have been identified as causal in one PCD family each. We have previously identified a 3.5cM (2.82 Mb) region on chromosome 15q linked to Kartagener syndrome (KS), a subtype of PCD characterized by the randomization of body organ positioning. We have now refined the KS candidate region to a 1.8Mb segment containing 18 known genes. The coding regions of these genes and three neighboring genes were subjected to sequence analysis in seven KS probands, and we were able to identify 60 single nucleotide sequence variants, 35 of which resided in mRNA coding sequences. However, none of the variations alone could explain the occurrence of the disease in these patients

Self-esteem in the deaf who have become cochlear implant users as adults.

OBJECTIVE:Self-esteem is a good predictor of mental health and is crucial for well-being and psychological functioning. It is especially important in situations where there are potential mental health problems, such as in people suffering from hearing loss or total deafness. This study aims to gauge the level of self-esteem in adults with hearing problems, in particular those who, in adulthood, had received a cochlear implant (CI). The subjects had different onset (pre-lingual/post-lingual) and amount (deafness/partial deafness) of hearing loss, and their current level of self-esteem was compared to that of the general population. The association of self-esteem with other deafness-related variables (e.g. satisfaction with their CI or whether they also used a hearing aid) and sociodemographic factors was also investigated. METHODS:Data were obtained from questionnaires mailed to patients who, when adult, had received a CI. The subjects were divided into four subgroups: subjects with pre-lingual deafness, post-lingual deafness, pre-lingual partial deafness, and post-lingual partial deafness. To evaluate their self-esteem, the Rosenberg Self-Esteem Scale (RSES) was used. For data on sociodemographic status and information related to deafness and CI, we used our own Information Inquiry form. For statistical analysis of the results, we compared means (t-test, ANOVA), investigated correlations, and applied linear regression. RESULTS:The self-esteem of deaf and partially deaf CI users was significantly lower than in the general population, especially for post-lingually deafened subjects. The only factor related to deafness and CIs that explained self-esteem was self-rated satisfaction with the CI-meaning that higher satisfaction was associated with higher self-esteem. The major sociodemographic factor that explained self-esteem was marital/partnership status (being in a relationship was helpful). Also men had higher self-esteem than women. Those with higher levels of education, and those working or studying, had higher self-esteem than those who did not. RSES was found to have a single-factor structure. CONCLUSION:Deafness and partial deafness appear to be risk factors for lower self-esteem, a finding that rehabilitation, medical, educational, and employment communities should be made aware of. Medical intervention in the form of a CI supplies the person with improved hearing, but it is not a panacea: their self-esteem is still vulnerable, and reinforcement of self-esteem is an aspect that professionals should focus on. Psychological, psycho-educational, and psychotherapeutic interventions have important roles to play for CI recipients