Post-axial polydactyly type A2, overgrowth and autistic traits associated with a chromosome 13q31.3 microduplication encompassing miR-17-92 and GPC5

Genetic overview of postaxial polydactyly: Updated classification

Polydactyly or polydactylism, also known as a hyperdactyly, is a congenital limb defect with various morphologic phenotypes. Apart from physical and functional impairments, the presence of polydactyly is an indication of an underlying syndrome in the newborn. Usually, it follows as an autosomal dominant/recessive inheritance pattern with defects in the limb development's anteroposterior patterning. Although mutations in several genes have been associated with polydactyly; however, the exact underlying cause, pathways, and disease mechanisms are still unexplored, thus making it of multi-factorial origin. Polydactyly is divided into three subtypes; radial, ulnar, and central polydactyly. So far, 11 loci (PAPA1-PAPA11) and seven human genes have been reported to cause non-syndromic postaxial polydactyly in humans, including the ZNF141, GLI3, IQCE, GLI1, FAM92A1, KIAA0825, and DACH1. In this review, we discuss emerging evidences of clinical and molecular characterization of polydactyly types in term of the involvement of newly associated genes and loci for non-syndromic postaxial polydactyly, and how these might impact our understanding of the genetic mechanisms and molecular etiology involved in the cause of polydactyly.

Cartilage Homeostasis and Osteoarthritis

Healthy limb joints are important for maintaining health and attaining longevity. Endochondral ossification (the replacement of cartilage with bone, occurring during skeletal development) is essential for bone formation, especially in long-axis bones. In contrast to endochondral ossification, chondrocyte populations in articular cartilage persist and maintain joint tissue into adulthood. Articular cartilage, a connective tissue consisting of chondrocytes and their surrounding extracellular matrices, plays an essential role in the mechanical cushioning of joints in postnatal locomotion. Osteoarthritis (OA) pathology relates to disruptions in the balance between anabolic and catabolic signals, that is, the loss of chondrocyte homeostasis due to aging or overuse of cartilages. The onset of OA increases with age, shortening a person's healthy life expectancy. Although many people with OA experience pain, the mainstay of treatment is symptomatic therapy, and no fundamental treatment has yet been established. To establish regenerative or preventative therapies for cartilage diseases, further understanding of the mechanisms of cartilage development, morphosis, and homeostasis is required. In this review, we describe the general development of cartilage and OA pathology, followed by a discussion on anabolic and catabolic signals in cartilage homeostasis, mainly microRNAs.

Partial Trisomy 13q/Monosomy 3p Resulting from a Paternal Reciprocal 3p;13q Translocation in a Boy with Facial Dysmorphism and Hypertrophic Cardiomyopathy

Individuals with 3p deletion show a great clinical variability. Apparently, a 1.5-Mb terminal deletion, including the CRBN and CNTN4 genes, is sufficient to cause this syndrome. Partial trisomy 13q is a rare chromosomal abnormality with a variable phenotypic expression, but in most cases, patients have a phenotype resembling complete trisomy 13. The aim of the present study is to describe a 9-month-old Mexican male patient with 3p deletion/13q duplication and a novel clinical finding. He presented with facial dysmorphism and multiple congenital alterations. Echocardiogram revealed cardiac insufficiency with hypertrophic cardiomyopathy and pulmonary hypertension, not previously reported. Karyotype from the patient and his father were 46,XY,add(3)(p26) and 46,XY,t(3;13), respectively. Microarray assay of the proband exhibited an approximately 2.6-Mb loss at terminal 3p26.3 and a 27.7-Mb gain of the long arm in terminal chromosome 13 at q31.1q34. A chromosomal imbalance with a partial trisomy 13q31.1q34 and monosomy 3p26.3 of paternal origin were detected. Microarray assay of both parents were normal. The proband has a cardiomyopathy not previously reported. These data enrich the spectrum of clinical manifestations in 3p deletion/3q duplication chromosomopathy.

MicroRNAs in cartilage development and dysplasia

Small regulatory microRNAs (miRNAs) post-transcriptionally suppress gene expression. MiRNAs expressed in skeletal progenitor cells and chondrocytes regulate diverse aspects of cellular function and thus skeletal development. In this review, we discuss the role of miRNAs in skeletal development, particularly focusing on those whose physiological roles were revealed in vivo. Deregulation of miRNAs is found in multiple acquired diseases such as cancer; however congenital diseases caused by mutations in miRNA genes are very rare. Among those are mutations in miR-140 and miR-17~92 miRNAs which cause skeletal dysplasias. We also discuss pathological mechanisms underlining these skeletal dysplasias.

A de novo 13q31.3 microduplication encompassing the miR-17 ~ 92 cluster results in features mirroring those associated with Feingold syndrome 2

Hemizygosity of the MIR17HG gene encoding the miR-17 ~ 92 cluster is associated with Feingold syndrome 2 characterized by intellectual disability, skeletal abnormalities, short stature, and microcephaly. Here, we report on a female with a de novo 13q31.3 microduplication encompassing MIR17HG but excluding GPC5. She presented developmental delay, skeletal and digital abnormalities, and features such as tall stature and macrocephaly mirroring those of Feingold syndrome 2 patients. The limited extent of the proband's rearrangement to the miR cluster and the corresponding normal expression level of the neighboring GPC5 in her cells, together with previously described data on affected individuals of two families carrying overlapping duplications of the miR-17 ~ 92 cluster that comprise part of GPC5, who likewise presented macrocephaly, developmental delay, as well as skeletal, digital and stature abnormalities, allow to define a new syndrome due to independent microduplication of the miR-17 ~ 92 cluster.

Spatio-Temporal Expression and Functional Analysis of miR-206 in Developing Orofacial Tissue

BACKGROUND

Development of the mammalian palate is dependent on precise, spatiotemporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs, function as crucial modulators of cell and tissue differentiation, regulating expression of key downstream genes.

OBSERVATIONS

Our laboratory has previously identified several developmentally regulated miRNAs, including miR-206, during critical stages of palatal morphogenesis. The current study reports spatiotemporal distribution of miR-206 during development of the murine secondary palate (gestational days 12.5-14.5).

RESULT AND CONCLUSION

Potential cellular functions and downstream gene targets of miR-206 were investigated using functional assays and expression profiling, respectively. Functional analyses highlighted potential roles of miR-206 in governing TGFß- and Wnt signaling in mesenchymal cells of the developing secondary palate. In addition, altered expression of miR-206 within developing palatal tissue of TGFß3-/- fetuses reinforced the premise that crosstalk between this miRNA and TGFß3 is crucial for secondary palate development.

Identifying Genomic Variations in Monozygotic Twins Discordant for Autism Spectrum Disorder Using Whole-Genome Sequencing

Autism spectrum disorder (ASD) presents a set of childhood neurodevelopmental disorders with impairments in social communication and restricted, repetitive, and stereotyped patterns of behavior. Here, based on the whole-genome sequencing (WGS) data of three monozygotic twins discordant for ASD, we explored multiple patient-specific genetic variations and prioritized a list of ASD risk genes. Our results identified DVMT (discordant variation in monozygotic twin) observed in at least two twin pairs, including 14,310 SNPs, 2,425 indels, and 16,735 CNVs, referring to a total of 2,174 genes, and 37 of these were covered by all three types of variations. Gene ontology (GO) enrichment analysis of biological processes for 2,174 genes showed that the majority of these genes were related to neurodevelopmental processes. In addition, functional network analysis showed that there was a strong functional relevance between 37 genes covered by all three types of variations. In conclusion, for the first time, we conducted a comprehensive scan of genomic differences between monozygotic twins discordant for ASD, providing researchers with in-depth directions. It may also provide effective strategies for clinical treatment of individuals affected by ASD.

Identification of miR-22-3p, miR-92a-3p, and miR-137 in peripheral blood as biomarker for schizophrenia

MicroRNAs (miRNAs) are a class of endogenous and non-coding single-stranded RNAs with length of about 22 nucleotides, and many are evolutionarily conserved. Although postmortem brain samples provide direct evidence of miRNA dysregulation within the brain, peripheral tissue samples can be obtained from living subjects and have the potential to yield biomarkers that could be used as diagnostic tools. To verify and detect additional miRNAs differentially expressed in peripheral blood and further explore their diagnostic value and function for schizophrenia, we performed a next-generation sequencing approach in combination with a literature search to select appropriate miRNAs. We then used real-time quantitative polymerase chain reaction (RT-qPCR) to identify miRNAs expressed aberrantly in schizophrenia. Binary regression analysis identified miR-22-3p, miR-92a-3p, and miR-137. Analysis of receiver operating characteristics (ROC) indicated that these three miRNAs could be used in combination as a biomarker for schizophrenia. Bioinformatic analyses of these genes and gene ontology (GO) enrichment revealed that the combination of miR-22-3p, miR-92a-3p, and miR-137 was closely associated with synaptic structure and function, which play important roles in the etiology and pathophysiology of schizophrenia.

A Clinical Review of Generalized Overgrowth Syndromes in the Era of Massively Parallel Sequencing

The overgrowth syndromes are important to diagnose, not just for accurate genetic counseling, but also for knowledge surrounding cancer surveillance and prognosis. There has been a recent expansion in the number of genes associated with a mendelian overgrowth phenotype, so this review updates previous classifications of overgrowth syndromes. We also describe a clinical and molecular approach to the investigation of individuals presenting with overgrowth. This review aims to assist the clinical diagnosis of generalized overgrowth syndromes by outlining the salient features of well-known overgrowth syndromes alongside the many syndromes that have been discovered and classified more recently. We provide key clinical "handles" to aid clinical diagnosis and a list of genes to aid with panel design when using next generation sequencing, which we believe is frequently needed due to the overlapping phenotypic features seen between overgrowth syndromes.

Neural Glycosylphosphatidylinositol-Anchored Proteins in Synaptic Specification

Glycosylphosphatidylinositol (GPI)-anchored proteins are a specialized class of lipid-associated neuronal membrane proteins that perform diverse functions in the dynamic control of axon guidance, synaptic adhesion, cytoskeletal remodeling, and localized signal transduction, particularly at lipid raft domains. Recent studies have demonstrated that a subset of GPI-anchored proteins act as critical regulators of synapse development by modulating specific synaptic adhesion pathways via direct interactions with key synapse-organizing proteins. Additional studies have revealed that alteration of these regulatory mechanisms may underlie various brain disorders. In this review, we highlight the emerging role of GPI-anchored proteins as key synapse organizers that aid in shaping the properties of various types of synapses and circuits in mammals.

MicroRNA Profiling during Craniofacial Development: Potential Roles for Mir23b and Mir133b

Defects in mid-facial development, including cleft lip/palate, account for a large number of human birth defects annually. In many cases, aberrant gene expression results in either a reduction in the number of neural crest cells (NCCs) that reach the frontonasal region and form much of the facial skeleton or subsequent failure of NCC patterning and differentiation into bone and cartilage. While loss of gene expression is often associated with developmental defects, aberrant upregulation of expression can also be detrimental. microRNAs (miRNAs) are a class of non-coding RNAs that normally repress gene expression by binding to recognition sequences located in the 3′ UTR of target mRNAs. miRNAs play important roles in many developmental systems, including midfacial development. Here, we take advantage of high throughput RNA sequencing (RNA-seq) from different tissues of the developing mouse midface to interrogate the miRs that are expressed in the midface and select a subset for further expression analysis. Among those examined, we focused on four that showed the highest expression level in in situ hybridization analysis. Mir23b and Mir24.1 are specifically expressed in the developing mouse frontonasal region, in addition to areas in the perichondrium, tongue musculature and cranial ganglia. Mir23b is also expressed in the palatal shelves and in anterior epithelium of the palate. In contrast, Mir133b and Mir128.2 are mainly expressed in head and trunk musculature. Expression analysis of mir23b and mir133b in zebrafish suggests that mir23b is expressed in the pharyngeal arch, otic vesicle, and trunk muscle while mir133b is similarly expressed in head and trunk muscle. Functional analysis by overexpression of mir23b in zebrafish leads to broadening of the ethmoid plate and aberrant cartilage structures in the viscerocranium, while overexpression of mir133b causes a reduction in ethmoid plate size and a significant midfacial cleft. These data illustrate that miRs are expressed in the developing midface and that Mir23b and Mir133b may have roles in this developmental process.

miRNAs in Bone Development

Skeletal development is a multistage process during which mesenchymal progenitor cells undergo proliferation and differentiation and subsequently give rise to bone and cartilage forming cells. Each step is regulated by various transcription factors and signaling molecules. microRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression. Several in vivo and in vitro studies have shown that miRNAs play significant roles in skeletal development. Identifying their functions may give insights into the treatment of developmental disorders of the skeleton. This review summarizes miRNAs that have been shown to participate in various stages of skeletal development by targeting crucial factors.

Regulating Craniofacial Development at the 3' End: MicroRNAs and Their Function in Facial Morphogenesis

Defects in craniofacial development represent a majority of observed human birth defects, occurring at a rate as high as 1:800 live births. These defects often occur due to changes in neural crest cell (NCC) patterning and development and can affect non-NCC-derived structures due to interactions between NCCs and the surrounding cell types. Proper craniofacial development requires an intricate array of gene expression networks that are tightly controlled spatiotemporally by a number of regulatory mechanisms. One of these mechanisms involves the action of microRNAs (miRNAs), a class of noncoding RNAs that repress gene expression by binding to miRNA recognition sequences typically located in the 3' UTR of target mRNAs. Recent evidence illustrates that miRNAs are crucial for vertebrate facial morphogenesis, with changes in miRNA expression leading to facial birth defects, including some in complex human syndromes such as 22q11 (DiGeorge Syndrome). In this review, we highlight the current understanding of miRNA biogenesis, the roles of miRNAs in overall craniofacial development, the impact that loss of miRNAs has on normal development and the requirement for miRNAs in the development of specific craniofacial structures, including teeth. From these studies, it is clear that miRNAs are essential for normal facial development and morphogenesis, and a potential key in establishing new paradigms for repair and regeneration of facial defects.

MicroRNA and Posttranscriptional Dysregulation in Psychiatry

Psychiatric syndromes, including schizophrenia, mood disorders, and autism spectrum disorders, are characterized by a complex range of symptoms, including psychosis, depression, mania, and cognitive deficits. Although the mechanisms driving pathophysiology are complex and remain largely unknown, advances in the understanding of gene association and gene networks are providing significant clues to their etiology. In recent years, small noncoding RNA molecules known as microRNA (miRNA) have emerged as potential players in the pathophysiology of mental illness. These small RNAs regulate hundreds of target transcripts by modifying their stability and translation on a broad scale, influencing entire gene networks in the process. There is evidence to suggest that numerous miRNAs are dysregulated in postmortem neuropathology of neuropsychiatric disorders, and there is strong genetic support for association of miRNA genes and their targets with these conditions. This review presents the accumulated evidence linking miRNA dysregulation and dysfunction with schizophrenia, bipolar disorder, major depressive disorder, and autism spectrum disorders and the potential of miRNAs as biomarkers or therapeutics for these disorders. We further assess the functional roles of some outstanding miRNAs associated with these conditions and how they may be influencing the development of psychiatric symptoms.

MicroRNAs involved in bone formation

During skeletal development, mesenchymal progenitor cells undergo a multistage differentiation process in which they proliferate and become bone- and cartilage-forming cells. This process is tightly regulated by multiple levels of regulatory systems. The small non-coding RNAs, microRNAs (miRNAs), post-transcriptionally regulate gene expression. Recent studies have demonstrated that miRNAs play significant roles in all stages of bone formation, suggesting the possibility that miRNAs can be novel therapeutic targets for skeletal diseases. Here, we review the role and mechanism of action of miRNAs in bone formation. We discuss roles of specific miRNAs in major types of bone cells, osteoblasts, chondrocytes, osteoclasts, and their progenitors. Except a few, the current knowledge about miRNAs in bone formation has been obtained mainly by in vitro studies; further validation of these findings in vivo is awaited. We also discuss about several miRNAs of particular interest in the light of future therapies of bone diseases.

Short stature, digit anomalies and dysmorphic facial features are associated with the duplication of miR-17 ~ 92 cluster

MicroRNAs (miRNAs) are key regulators of gene expression, playing important roles in development, homeostasis, and disease. Recent experimental evidence indicates that mutation or deregulation of the MIR17HG gene (miR-17 ~ 92 cluster) contributes to the pathogenesis of a variety of human diseases, including cancer and congenital developmental defects. We report on a 9-year-old boy who presented with developmental delay, autism spectrum disorder, short stature, mild macrocephaly, lower facial weakness, hypertelorism, downward slanting palpebral fissures, brachydactyly, and clinodactyly. SNP-microarray analysis revealed 516 kb microduplication at 13q31.3 involving the entire MIR17HG gene encoding the miR-17 ~ 92 polycistronic miRNA cluster, and the first five exons of the GPC5 gene. Family study confirmed that the microduplication was maternally inherited by the proband and one of his five half-brothers; digit and other skeletal anomalies were exclusive to the family members harboring the microduplication.

This case represents the smallest reported microduplication to date at 13q31.3 and provides evidence supporting the important role of miR-17 ~ 92 gene dosage in normal growth and skeletal development. We postulate that any dosage abnormality of MIR17HG, either deletion or duplication, is sufficient to interrupt skeletal developmental pathway, with variable outcome from growth retardation to overgrowth.