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1.
Acta Derm Venereol ; 103: adv5758, 2023 06 05.
Article in English | MEDLINE | ID: mdl-37272364

ABSTRACT

Cafe-au-lait macules are the most distinctive clinical finding in neurofibromatosis type I. The aim of this prospective study of Greek children diagnosed with neurofibromatosis type I was to describe the dermatological phenotype and to analyse the characteristics of cafe-au-lait macules and their association with genotype. Pigment intensity and melatonin content of cafe-au-lait macules were measured with a narrowband spectrophotometer. A total of 63 children aged 6 months to 16 years old were studied. Mean melanin content varied, both among patients, and within each patient (p < 0.001). Females had a higher number of cafe-au-lait macules than did males (p = 0.025), and the melanin content of cafe-au-lait macules was lower in females than males (p < 0.001). Patients with protein-truncating variants in the neurofibromatosis type I gene had higher melanin content of cafe-au-lait macules than other types of genetic variants t (55) = 2.196, p = 0.032. Plexiform neurofibromas were also detected in the majority of patients with protein- truncating variants, while juvenile xanthogranulomas were detected equally in patients with protein-truncating and non-protein-truncating variants. In conclusion, cafe-au-lait macules with high melatonin content are associated with patients carrying non-protein-truncating variants. Therefore, measurement of cafe-au-lait macule pigment intensity might provide useful information for initial assessment of patients with neurofibromatosis type I and the severity of their future phenotype.


Subject(s)
Melatonin , Neurofibromatosis 1 , Male , Female , Humans , Neurofibromatosis 1/diagnosis , Neurofibromatosis 1/genetics , Melanins , Prospective Studies , Greece , Cafe-au-Lait Spots/diagnosis , Cafe-au-Lait Spots/genetics , Genotype
2.
J Assist Reprod Genet ; 39(6): 1341-1349, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35338417

ABSTRACT

PURPOSE: To investigate whether preimplantation genetic testing for aneuploidy (PGT-A) improves the clinical outcome in patients with advanced maternal age (AMA), recurrent miscarriages (RM), and recurrent implantation failure (RIF). METHODS: Retrospective cohort study from a single IVF center and a single genetics laboratory. One hundred seventy-six patients undergoing PGT-A were assigned to three groups: an AMA group, an RM group, and a RIF group. Two hundred seventy-nine patients that did not undergo PGT-A were used as controls and subgrouped similarly to the PGT-A cohort. For the PGT-A groups, trophectoderm biopsy was performed and array comparative genomic hybridization was used for PGT-A. Clinical outcomes were compared with the control groups. RESULTS: In the RM group, we observed a significant decrease of early pregnancy loss rates in the PGT-A group (18.1% vs 75%) and a significant increase in live birth rate per transfer (50% vs 12.5%) and live birth rate per patient (36% vs 12.5%). In the RIF group, a statistically significant increase in the implantation rate per transfer (69.5% vs 33.3%) as well as the live birth rate per embryo transfer (47.8% vs 19%) was observed. In the AMA group, a statistically significant reduction in biochemical pregnancy loss was observed (3.7% vs 31.5%); however, live birth rates per embryo transfer and per patient were not significantly higher than the control group. CONCLUSION: Our results agree with recently published studies, which suggest caution in the universal application of PGT-A in women with infertility. Instead, a more personalized approach by choosing the right candidates for PGT-A intervention should be followed.


Subject(s)
Abortion, Habitual , Preimplantation Diagnosis , Abortion, Habitual/diagnosis , Abortion, Habitual/genetics , Aneuploidy , Comparative Genomic Hybridization , Female , Fertilization in Vitro/methods , Genetic Testing/methods , Humans , Pregnancy , Pregnancy Rate , Preimplantation Diagnosis/methods , Retrospective Studies
3.
EMBO Rep ; 20(3)2019 03.
Article in English | MEDLINE | ID: mdl-30665945

ABSTRACT

Genome-wide studies in tumor cells have indicated that chromatin-modifying proteins are commonly mutated in human cancers. The lysine-specific methyltransferase 2C (KMT2C/MLL3) is a putative tumor suppressor in several epithelia and in myeloid cells. Here, we show that downregulation of KMT2C in bladder cancer cells leads to extensive changes in the epigenetic status and the expression of DNA damage response and DNA repair genes. More specifically, cells with low KMT2C activity are deficient in homologous recombination-mediated double-strand break DNA repair. Consequently, these cells suffer from substantially higher endogenous DNA damage and genomic instability. Finally, these cells seem to rely heavily on PARP1/2 for DNA repair, and treatment with the PARP1/2 inhibitor olaparib leads to synthetic lethality, suggesting that cancer cells with low KMT2C expression are attractive targets for therapies with PARP1/2 inhibitors.


Subject(s)
DNA Repair , DNA-Binding Proteins/metabolism , Neoplasms/enzymology , Neoplasms/pathology , Animals , Base Sequence , Cell Line, Tumor , DNA Damage/genetics , DNA Methylation/drug effects , DNA Methylation/genetics , DNA Repair/genetics , DNA-Binding Proteins/genetics , Down-Regulation/drug effects , Down-Regulation/genetics , Enhancer Elements, Genetic/genetics , Gene Expression Regulation, Neoplastic/drug effects , Genomic Instability/drug effects , Genomic Instability/genetics , Homologous Recombination/genetics , Humans , Male , Mice, SCID , Neoplasms/genetics , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Poly(ADP-ribose) Polymerases/metabolism , Promoter Regions, Genetic/genetics
4.
Blood Cells Mol Dis ; 76: 32-39, 2019 05.
Article in English | MEDLINE | ID: mdl-30709626

ABSTRACT

The potential use of patient-specific induced pluripotent stem cells (hiPSCs) in the study and treatment of hematological diseases requires the setup of efficient and safe protocols for hiPSC generation. We aimed to adopt a reprogramming method for large-scale production of integration-free patient-specific hiPSC-lines in our stem cell processing laboratory, which supports a pediatric hematopoietic stem cell transplant unit located at a tertiary care children's hospital. We describe our 5-year experience in generation of hiPSC-lines from human bone marrow-derived mesenchymal stromal cells (BM-MSCs) using synthetic mRNAs encoding reprogramming factors. We generated hiPSC-lines from pediatric patients with ß-Thalassemia, Sickle Cell Anemia, Blackfan-Diamond Anemia, Severe Aplastic Anemia, DOCK8 Immunodeficiency and 1 healthy control. After optimization of the reprogramming procedure, average reprogramming efficiency of BM-MSCs was 0.29% (range 0.25-0.4). The complete reprogramming process lasted 14-16 days. Three to five hiPSC-colonies per sample were selected, expanded to 5 culture passages and then frozen. The whole procedure took an average time of 1.8 months (range 1.6-2.2). The hiPSC-lines expressed embryonic stem cell markers and exhibited pluripotency. This mRNA reprogramming method can be applicable in a hematopoietic stem cell culture lab setting and would be useful for the clinical translation of patient-specific hiPSCs.


Subject(s)
Cellular Reprogramming/drug effects , Hematologic Diseases/therapy , Induced Pluripotent Stem Cells/cytology , Mesenchymal Stem Cells/cytology , RNA, Messenger/pharmacology , Child , Hematopoietic Stem Cell Transplantation , Humans , Methods , Precision Medicine/methods , RNA, Messenger/chemical synthesis , Time Factors
5.
Neuropediatrics ; 50(1): 61-63, 2019 02.
Article in English | MEDLINE | ID: mdl-30541163

ABSTRACT

X-linked myotubular myopathy (XLMTM) is a rare inherited neuromuscular disorder associated with mutations in the MTM1 gene on the Xq28 region. We report a severely affected girl with XLMTM, caused by maternally inherited 661 kb Xq28 microduplication identified by chromosomal microarray analysis and confirmed also on DNA from muscle biopsy with a custom-designed X-chromosome-specific microarray. X-inactivation analysis revealed a skewed inactivation pattern on the proband's muscle biopsy. Muscle biopsy histopathology was indicative of increased variability in fiber diameter, marked and diffuse endomysial proliferation of adipose and connective tissues, as well as predominance of type 1 fibers.


Subject(s)
Chromosome Duplication/genetics , Chromosomes, Human, X/genetics , Myopathies, Structural, Congenital/diagnosis , Myopathies, Structural, Congenital/genetics , Child , Female , Humans
6.
Am J Hum Genet ; 97(6): 922-32, 2015 Dec 03.
Article in English | MEDLINE | ID: mdl-26637982

ABSTRACT

We describe an X-linked genetic syndrome associated with mutations in TAF1 and manifesting with global developmental delay, intellectual disability (ID), characteristic facial dysmorphology, generalized hypotonia, and variable neurologic features, all in male individuals. Simultaneous studies using diverse strategies led to the identification of nine families with overlapping clinical presentations and affected by de novo or maternally inherited single-nucleotide changes. Two additional families harboring large duplications involving TAF1 were also found to share phenotypic overlap with the probands harboring single-nucleotide changes, but they also demonstrated a severe neurodegeneration phenotype. Functional analysis with RNA-seq for one of the families suggested that the phenotype is associated with downregulation of a set of genes notably enriched with genes regulated by E-box proteins. In addition, knockdown and mutant studies of this gene in zebrafish have shown a quantifiable, albeit small, effect on a neuronal phenotype. Our results suggest that mutations in TAF1 play a critical role in the development of this X-linked ID syndrome.


Subject(s)
Developmental Disabilities/genetics , Histone Acetyltransferases/genetics , Intellectual Disability/genetics , Neurodegenerative Diseases/genetics , TATA-Binding Protein Associated Factors/genetics , Transcription Factor TFIID/genetics , Adolescent , Animals , Child , Child, Preschool , Developmental Disabilities/metabolism , Developmental Disabilities/pathology , Disease Models, Animal , E-Box Elements , Facies , Family , Gene Expression Regulation , Histone Acetyltransferases/metabolism , Humans , Infant , Inheritance Patterns , Intellectual Disability/metabolism , Intellectual Disability/pathology , Male , Mutation , Neurodegenerative Diseases/metabolism , Neurodegenerative Diseases/pathology , Pedigree , Phenotype , Signal Transduction , TATA-Binding Protein Associated Factors/metabolism , Transcription Factor TFIID/metabolism , Young Adult , Zebrafish
7.
Reproduction ; 154(6): 777-788, 2017 12.
Article in English | MEDLINE | ID: mdl-28916718

ABSTRACT

Paternal contributions to the zygote are thought to extend beyond delivery of the genome and paternal RNAs have been linked to epigenetic transgenerational inheritance in different species. In addition, sperm-egg fusion activates several downstream processes that contribute to zygote formation, including PLC zeta-mediated egg activation and maternal RNA clearance. Since a third of the preimplantation developmental period in the mouse occurs prior to the first cleavage stage, there is ample time for paternal RNAs or their encoded proteins potentially to interact and participate in early zygotic activities. To investigate this possibility, a bespoke next-generation RNA sequencing pipeline was employed for the first time to characterise and compare transcripts obtained from isolated murine sperm, MII eggs and pre-cleavage stage zygotes. Gene network analysis was then employed to identify potential interactions between paternally and maternally derived factors during the murine egg-to-zygote transition involving RNA clearance, protein clearance and post-transcriptional regulation of gene expression. Our in silico approach looked for factors in sperm, eggs and zygotes that could potentially interact co-operatively and synergistically during zygote formation. At least five sperm RNAs (Hdac11, Fbxo2, Map1lc3a, Pcbp4 and Zfp821) met these requirements for a paternal contribution, which with complementary maternal co-factors suggest a wider potential for extra-genomic paternal involvement in the developing zygote.


Subject(s)
Computer Simulation , Models, Genetic , RNA, Messenger/genetics , Sperm-Ovum Interactions , Spermatozoa/physiology , Zygote/physiology , Animals , Computational Biology , Databases, Genetic , Female , Gene Expression Profiling , Gene Expression Regulation, Developmental , Gene Regulatory Networks , Male , Mice , Mice, Inbred C57BL , Pregnancy , RNA Processing, Post-Transcriptional , RNA Stability , RNA, Messenger/metabolism , RNA, Messenger, Stored/genetics , RNA, Messenger, Stored/metabolism , Signal Transduction , Spermatozoa/metabolism , Transcription, Genetic , Zygote/metabolism
8.
Pediatr Res ; 82(2): 253-260, 2017 Aug.
Article in English | MEDLINE | ID: mdl-28422950

ABSTRACT

BackroundMicrocephaly can either be isolated or it may coexist with other neurological entities and/or multiple congenital anomalies, known as syndromic microcephaly. Although many syndromic cases can be classified based on the characteristic phenotype, some others remain uncertain and require further investigation. The present study describes the application of array-comparative genomic hybridization (array-CGH) as a diagnostic tool for the study of patients with clinically unknown syndromic microcephaly.MethodsFrom a cohort of 210 unrelated patients referred with syndromic microcephaly, we applied array-CGH analysis in 53 undiagnosed cases. In all the 53 cases except one, previous standard karyotype was negative. High-resolution 4 × 180K and 1 × 244K Agilent arrays were used in this study.ResultsIn 25 out of the 53 patients with microcephaly among other phenotypic anomalies, array-CGH revealed copy number variations (CNVs) ranging in size between 15 kb and 31.6 Mb. The identified CNVs were definitely causal for microcephaly in 11/53, probably causal in 7/53, and not causal for microcephaly in 7/53 patients. Genes potentially contributing to brain deficit were revealed in 16/53 patients.ConclusionsArray-CGH contributes to the elucidation of undefined syndromic microcephalic cases by permitting the discovery of novel microdeletions and/or microduplications. It also allows a more precise genotype-phenotype correlation by the accurate definition of the breakpoints in the deleted/duplicated regions.


Subject(s)
Comparative Genomic Hybridization/methods , Microcephaly/genetics , Child , Cohort Studies , Female , Humans , Karyotyping , Male , Syndrome
9.
Birth Defects Res A Clin Mol Teratol ; 106(7): 536-41, 2016 Jul.
Article in English | MEDLINE | ID: mdl-26969897

ABSTRACT

BACKGROUND: Antley-Bixler syndrome (ABS) is an exceptionally rare craniosynostosis syndrome that can be accompanied by disordered steroidogenesis, and is mainly caused by mutations in the POR gene, inherited in an autosomal recessive manner. Here we report the prenatal and postmortem findings of three sibling fetuses with ABS as a result of compound heterozygosity of a paternal submicroscopic deletion and a maternal missense mutation in the POR gene. METHODS: Prenatal ultrasound and postmortem examination were performed in three sibling fetuses with termination of pregnancy at 22, 23, and 17 weeks of gestation, respectively. Molecular analysis of fetus 2 and 3 included (a) bidirectional sequencing of exon 8 of the POR gene after amplification of the specific locus by polymerase chain reaction, to detect single nucleotide variants (SNVs) and (b) high resolution comparative genomic hybridization (CGH) positive single nucleotide polymorphism array CGH (aCGH) analysis to detect copy number variants (CNVs), copy neutral areas of loss of heterozygosity and uniparental disomy. RESULTS: The diagnosis of ABS was suggested by the postmortem examination findings. The combination of the POR gene molecular analysis and aCGH revealed a compound heterozygous genotype of a maternal SNV (p.A287P) and a paternal CNV (NC_000007.13:g.(?_75608488)_(75615534_?)del). CONCLUSION: To the best of our knowledge, these sibling fetuses add to the few reported cases of ABS, caused by a combination of a SNV and a CNV in the POR gene. The detailed description of the pathologic and radiographic findings of second trimester fetuses affected with ABS adds novel knowledge concerning the early ABS phenotype, in lack of previous relevant reports. Birth Defects Research (Part A) 106:536-541, 2016. © 2016 Wiley Periodicals, Inc.


Subject(s)
Antley-Bixler Syndrome Phenotype , Chromosome Deletion , Cytochrome P-450 Enzyme System/genetics , Fetus , Heterozygote , Siblings , Antley-Bixler Syndrome Phenotype/diagnostic imaging , Antley-Bixler Syndrome Phenotype/genetics , Female , Fetus/abnormalities , Fetus/diagnostic imaging , Humans , Male
10.
Am J Med Genet A ; 164A(3): 666-70, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24375959

ABSTRACT

Constitutional microdeletions affecting 3q13.2q13.31 are rare and attempts for genotype-phenotype correlations have only recently been made in a cohort of 28 patients. The major phenotypic features of this rare syndrome are hypotonia, developmental delay, and facial anomalies. In this study, we report on a male infant with a novel reciprocal 3.671 Mb microduplication at the genomic region 3q13.2q13.31 associated with dysmorphic features and multiple congenital anomalies. The current patient was investigated by high-resolution array comparative genomic hybridization (aCGH). This is the first report of a microduplication 3q13.2q13.31 that shares a lot of common clinical features with those carrying the microdeletion. The 3q13.2q13.31 duplicated region in our patient contains nine dosage sensitive genes, amongst them the genes ATG3, CCDC80, KIAA2018, NAA50, ZDHHC23, DRD3, ZBTB20, GAP43, LSAMP. As it is the case for many other well-described reciprocal deletion/duplication syndromes, some have very different clinical features (Williams-Beuren deletion syndrome, WBS/WBS triplication) [Somerville et al. (2005); N Engl J Med 353:1694-1701], while others share similar phenotypic features (22q11.2 microdeletion/microduplication) [Portnoi (2009); Eur J Med Genet 52:88-93]. In conclusion, we describe the main phenotypic features of a possibly novel microduplication 3q13.2q13.31 syndrome. Additionally five of the dosage-sensitive genes and BOC gene are suggested to be responsible for the main phenotypic features. Evaluation of multiple patients with the microduplication is needed for full delineation of this syndrome.


Subject(s)
Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/genetics , Chromosome Duplication , Chromosomes, Human, Pair 2 , Chromosomes, Human, Pair 3 , Comparative Genomic Hybridization , Genetic Association Studies , Humans , Infant , Male , Phenotype
11.
Cureus ; 16(8): e67792, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39323708

ABSTRACT

Cystic fibrosis (CF) is a hereditary disease with great genetic complexity as not all mutations are disease-causing and genotype doesn't always predict phenotype. This case involves a child with CF and genotype F508del/CFTRdup1_11. The CFTRdup1_11 duplication was not reported previously, and genetic counseling was based on reports describing the clinical course of people carrying smaller duplications of the same area combined with F508del. The predicted clinical presentation was CF with pancreatic insufficiency. However, the case presented has so far shown no clinical symptoms and has borderline sweat chloride concentrations.

12.
Genes (Basel) ; 15(8)2024 Aug 10.
Article in English | MEDLINE | ID: mdl-39202413

ABSTRACT

The human 16p11.2 chromosomal region is rich in segmental duplications which mediate the formation of recurrent CNVs. CNVs affecting the 16p11.2 region are associated with an increased risk for developing neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia, and intellectual disability (ID), as well as abnormal body weight and head circumference and dysmorphic features, with marked phenotypic variability and reduced penetrance. CNVs affecting the 16p11.2 region mainly affect a distal interval of ~220 Kb, between Breakpoints 2 and 3 (BP2-BP3), and a proximal interval of ~593 Kb (BP4-BP5). Here, we report on 15 patients with recurrent 16p11.2 rearrangements that were identified among a cohort of 1600 patients (0.9%) with neurodevelopmental disorders. A total of 13 deletions and two duplications were identified, of which eight deletions included the proximal 16p11.2 region (BP4-BP5) and five included the distal 16p11.2 region (BP2-BP3). Of the two duplications that were identified, one affected the proximal and one the distal 16p11.2 region; however, both patients had additional CNVs contributing to phenotypic severity. The features observed and their severity varied greatly, even between patients within the same family. This article aims to further delineate the clinical spectrum of patients with 16p11.2 recurrent rearrangements in order to aid the counselling of patients and their families.


Subject(s)
Chromosomes, Human, Pair 16 , Intellectual Disability , Phenotype , Humans , Chromosomes, Human, Pair 16/genetics , Male , Female , Child , Adolescent , Child, Preschool , Intellectual Disability/genetics , Intellectual Disability/pathology , DNA Copy Number Variations , Chromosome Deletion , Adult , Autism Spectrum Disorder/genetics , Autism Spectrum Disorder/pathology , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/pathology , Chromosome Aberrations , Young Adult
13.
Genes (Basel) ; 15(8)2024 Aug 02.
Article in English | MEDLINE | ID: mdl-39202375

ABSTRACT

Alport syndrome (AS) is a hereditary glomerulopathy due to pathogenic variants in COL4A3, COL4A4, and COL4A5. Treatment with Renin-Angiotensin-Aldosterone System (RAAS) inhibitors can delay progression to end stage renal disease (ESRD). From 2018 until today, we performed Whole Exome Sequencing (WES) in 19 patients with AS phenotype with or without positive family history. Fourteen of these patients were children. Genetic testing was extended to family members at risk. All patients received a genetic diagnosis of AS: five X-linked AS (XLAS) males, five X-linked AS (XLAS) females, six autosomal dominant AS (ADAS), and one autosomal recessive AS (ARAS). After cascade screening four XLAS males and eight XLAS females, six ADAS and three ARAS heterozygotes were added to our initial results. Fifteen patients were eligible to start treatment with RAAS inhibitors after their diagnosis. All XLAS female patients, ARAS heterozygotes, and ADAS have been advised to be followed up, so that therapeutic intervention can begin in the presence of microalbuminuria. Genetic diagnosis of AS ensures early therapeutic intervention and appropriate follow up to delay progression to chronic kidney disease, especially in thet pediatric population.


Subject(s)
Nephritis, Hereditary , Humans , Nephritis, Hereditary/genetics , Nephritis, Hereditary/diagnosis , Female , Male , Child , Child, Preschool , Adolescent , Genetic Testing/methods , Exome Sequencing , Collagen Type IV/genetics , Early Diagnosis , Infant , Mutation , Adult , Kidney Failure, Chronic/genetics , Kidney Failure, Chronic/diagnosis , Phenotype
14.
Pediatr Res ; 73(6): 772-6, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23481551

ABSTRACT

BACKGROUND: Congenital heart diseases (CHDs) are often associated with other congenital anomalies, dysmorphic features, and developmental delay, and only a few cases of chromosomal abnormalities are detected by conventional cytogenetic techniques. The microarray comparative genomic hybridization (CGH) analysis allows the identification of submicroscopic genomic rearrangements. METHODS: During the past 3 y, 55 of 330 patients referred for array CGH had CHD of unknown etiology plus at least one additional indication of abnormal chromosomal phenotype. High-resolution 1 × 244 K or 4 × 180 K Agilent arrays were used in this study (average resolution 7-13 kb). RESULTS: Copy-number variations were detected in 37 of 55 patients, and in 29 of 37 patients there were genes that have been associated with CHD. All 37 patients had at least one additional phenotypic abnormality: 30 of 37 had one or more other congenital anomalies, 23 of 37 had dysmorphic features, 16 of 37 had intellectual disability, 13 of 37 had abnormal magnetic resonance imaging, 10 of 37 had hypotonia, and 7 of 37 had seizures. In 9 of 55 patients, unexpected genomic rearrangements in relation to their phenotype were identified. CONCLUSION: In patients with CHD and at least one additional indication of abnormal chromosomal phenotype, array CGH analysis could detect possible submicroscopic chromosomal abnormalities and provide proper genetic counseling.


Subject(s)
Comparative Genomic Hybridization , Heart Defects, Congenital/diagnosis , Heart Defects, Congenital/genetics , Humans , Infant , Infant, Newborn , Syndrome
15.
Genes (Basel) ; 14(8)2023 07 25.
Article in English | MEDLINE | ID: mdl-37628571

ABSTRACT

Chromosomal microarray analysis (CMA) is considered a first-tier test for patients with developmental disabilities and congenital anomalies and is also routinely applied in prenatal diagnosis. The current consensus size cut-off for reporting copy number variants (CNVs) in the prenatal setting ranges from 200 Kb to 400 Kb, with the intention of minimizing the impact of variants of uncertain significance (VUS). Very limited data are currently available on the application of higher resolution platforms prenatally. The aim of this study is to investigate the feasibility and impact of applying high-resolution CMA in the prenatal setting. To that end, we report on the outcomes of applying CMA with a size cut-off of 20 Kb in 250 prenatal samples and discuss the findings and diagnostic yield and also provide follow-up for cases with variants of uncertain significance. Overall, 19.6% (49) showed one or more chromosomal abnormalities, with the findings classified as Pathogenic (P) or Likely Pathogenic (LP) in 15.6% and as VUS in 4%. When excluding the cases with known familial aberrations, the diagnostic yield was 12%. The smallest aberration detected was a 32 Kb duplication of the 16p11.2 region. In conclusion, this study demonstrates that prenatal diagnosis with a high-resolution aCGH platform can reliably detect smaller CNVs that are often associated with neurodevelopmental phenotypes while providing an increased diagnostic yield, regardless of the indication for testing, with only a marginal increase in the VUS incidence. Thus, it can be an important tool in the prenatal setting.


Subject(s)
Chromosome Aberrations , Prenatal Diagnosis , Female , Pregnancy , Humans , Microarray Analysis , Phenotype , Vitamins
16.
Cells ; 12(13)2023 06 30.
Article in English | MEDLINE | ID: mdl-37443790

ABSTRACT

Although MSCs grant pronounced potential for cell therapies, several factors, such as their heterogeneity restrict their use. To overcome these limitations, iMSCs (MSCs derived from induced pluripotent stem cells (iPSCs) have attracted attention. Here, we analyzed the transcriptome of MSCs, iPSCs and iMSCs derived from healthy individuals and osteoarthritis (OA) patients and explored miRNA-mRNA interactions during these transitions. We performed RNA-seq and gene expression comparisons and Protein-Protein-Interaction analysis followed by GO enrichment and KEGG pathway analyses. MicroRNAs' (miRNA) expression profile using miRarrays and differentially expressed miRNA's impact on regulating iMSCs gene expression was also explored. Our analyses revealed that iMSCs derivation from iPSCs favors the expression of genes conferring high proliferation, differentiation, and migration properties, all of which contribute to a rejuvenated state of iMSCs compared to primary MSCs. Additionally, our exploration of the involvement of miRNAs in this rejuvenated iMSCs transcriptome concluded in twenty-six miRNAs that, as our analysis showed, are implicated in pluripotency. Notably, the identified here interactions between hsa-let7b/i, hsa-miR-221/222-3p, hsa-miR-302c, hsa-miR-181a, hsa-miR-331 with target genes HMGA2, IGF2BP3, STARD4, and APOL6 could prove to be the necessary tools that will convey iMSCs into the ideal mean for cell therapy in osteoarthritis.


Subject(s)
MicroRNAs , Osteoarthritis , Humans , Transcriptome/genetics , MicroRNAs/metabolism , Cell Differentiation/genetics , Cell- and Tissue-Based Therapy , Osteoarthritis/genetics , Osteoarthritis/therapy
17.
J Mycol Med ; 33(1): 101326, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36272381

ABSTRACT

INTRODUCTION: The clinical spectrum of Aspergillus fumigatus diseases in cystic fibrosis (CF) patients, including allergic bronchopulmonary aspergillosis (ABPA) and Aspergillus fumigatus chronic colonization, has recently gained attention due to its association with the progression of lung disease. Our aim was to examine whether there is a difference on pathogenic variant frequencies of the CFTR gene between CF patients with ABPA and those with A. fumigatus chronic colonization. MATERIAL AND METHODS: Greek CF patients diagnosed with ABPA and/or A. fumigatus chronic colonization were grouped according to their CFTR genotype. Patients with "minimal" CFTR function were defined as carrying a combination of class I or II pathogenic variants, while patients with "residual" function as carrying at least one class III, IV, V or VI pathogenic variant. RESULTS: Fifty-four CF patients were included and all except one were defined as having "minimal" CFTR function. Among the 108 CFTR alleles, 69 (63.9%) of pathogenic variants belonged to class II, and 32 (29.6%) to class I. Five patients had a history of both ABPA and A. fumigatus chronic colonization. No significant difference was detected among patients diagnosed only with ABPA (n = 29) and those who had only a positive history of A. fumigatus chronic colonization (n = 20). The median age of ABPA diagnosis was significantly lower than the median age of A. fumigatus chronic colonization (P = 0.011), while no significant difference was detected on median FEV1% predicted. DISCUSSION: No significant differences were detected in the type of CFTR pathogenic variants among patients with ABPA and those with A. fumigatus colonization. Similar studies should be performed in larger CF populations of different ethnic origin to further confirm our results.


Subject(s)
Aspergillosis, Allergic Bronchopulmonary , Cystic Fibrosis , Humans , Aspergillus fumigatus/genetics , Aspergillosis, Allergic Bronchopulmonary/complications , Aspergillosis, Allergic Bronchopulmonary/epidemiology , Aspergillosis, Allergic Bronchopulmonary/genetics , Cystic Fibrosis/complications , Cystic Fibrosis/genetics , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Retrospective Studies , Greece/epidemiology
18.
Syst Biol Reprod Med ; 69(1): 3-19, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36576378

ABSTRACT

Increasing female age is accompanied by a corresponding fall in her fertility. This decline is influenced by a variety of factors over an individual's life course including background genetics, local environment and diet. Studying both coding and non-coding RNAs of the embryo could aid our understanding of the causes and/or effects of the physiological processes accompanying the decline including the differential expression of sub-cellular biomarkers indicative of various diseases. The current study is a post-hoc analysis of the expression of trophectoderm RNA data derived from a previous high throughput study. Its main aim is to determine the characteristics and potential functionalities that characterize long non-coding RNAs. As reported previously, a maternal age-related component is potentially implicated in implantation success. Trophectoderm samples representing the full range of maternal reproductive ages were considered in relation to embryonic implantation potential, trophectoderm transcriptome dynamics and reproductive maternal age. The long non-coding RNA (lncRNA) biomarkers identified here are consistent with the activities of embryo-endometrial crosstalk, developmental competency and implantation and share common characteristics with markers of neoplasia/cancer invasion. Corresponding genes for expressed lncRNAs were more active in the blastocysts of younger women are associated with metabolic pathways including cholesterol biosynthesis and steroidogenesis.


Subject(s)
Blastocyst , Embryo Implantation , Humans , Female , Maternal Age , Blastocyst/physiology , Embryo Implantation/genetics , Embryo, Mammalian , Endometrium/metabolism
19.
Genes (Basel) ; 14(7)2023 07 21.
Article in English | MEDLINE | ID: mdl-37510394

ABSTRACT

Whole-Exome Sequencing (WES) has proven valuable in the characterization of underlying genetic defects in most rare diseases (RDs). Copy Number Variants (CNVs) were initially thought to escape detection. Recent technological advances enabled CNV calling from WES data with the use of accurate and highly sensitive bioinformatic tools. Amongst 920 patients referred for WES, 454 unresolved cases were further analysed using the ExomeDepth algorithm. CNVs were called, evaluated and categorized according to ACMG/ClinGen recommendations. Causative CNVs were identified in 40 patients, increasing the diagnostic yield of WES from 50.7% (466/920) to 55% (506/920). Twenty-two CNVs were available for validation and were all confirmed; of these, five were novel. Implementation of the ExomeDepth tool promoted effective identification of phenotype-relevant and/or novel CNVs. Among the advantages of calling CNVs from WES data, characterization of complex genotypes comprising both CNVs and SNVs minimizes cost and time to final diagnosis, while allowing differentiation between true or false homozygosity, as well as compound heterozygosity of variants in AR genes. The use of a specific algorithm for calling CNVs from WES data enables ancillary detection of different types of causative genetic variants, making WES a critical first-tier diagnostic test for patients with RDs.


Subject(s)
Algorithms , Rare Diseases , Humans , Exome Sequencing , DNA Copy Number Variations/genetics , Data Analysis
20.
Expert Rev Mol Diagn ; 23(11): 999-1010, 2023.
Article in English | MEDLINE | ID: mdl-37754746

ABSTRACT

BACKGROUND: Persistent hyperCKemia results from muscle dysfunction often attributed to genetic alterations of muscle-related genes, such as the dystrophin gene (DMD). Retrospective assessment of findings from DMD analysis, in association with persistent HyperCKemia, was conducted. PATIENTS AND METHODS: Evaluation of medical records from 1354 unrelated cases referred during the period 1996-2021. Assessment of data concerning the detection of DMD gene rearrangements and nucleotide variants. RESULTS: A total of 730 individuals (657 cases, 569 of Greek and 88 of Albanian origins) were identified, allowing an overall estimation of dystrophinopathy incidence at ~1:3800 live male births. The heterogeneous spectrum of 275 distinct DMD alterations comprised exon(s) deletions/duplications, nucleotide variants, and rare events, such as chromosome translocation {t(X;20)}, contiguous gene deletions, and a fused gene involving the DMD and the DOCK8 genes. Ethnic-specific findings include a common founder variant in exon 36 ('Hellenic' variant). CONCLUSIONS: Some 50% of hyperCKemia cases were characterized as dystrophinopathies, highlighting that DMD variants may be considered the most common cause of hyperCKemia in Greece. Delineation of the broad genetic and clinical heterogeneity is fundamental for actionable public health decisions and theragnosis, as well as the establishment of guidelines addressing ethical considerations, especially related to the mild asymptomatic patient subgroup.


Subject(s)
Dystrophin , Muscular Dystrophy, Duchenne , Humans , Male , Dystrophin/genetics , Greece/epidemiology , Guanine Nucleotide Exchange Factors , Muscle Weakness , Muscular Dystrophy, Duchenne/diagnosis , Nucleotides , Retrospective Studies
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