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De novo DDX3X missense variants in males appear viable and contribute to syndromic intellectual disability
Abstract
DDX3X (Xp11.4) encodes a DEAD‐box RNA helicase that escapes X chromosome inactivation. Pathogenic variants in DDX3X have been shown to cause X‐linked intellectual disability (ID) (MRX102, MIM: 300958). The phenotypes associated with DDX3X variants are heterogeneous and include brain and behavioral abnormalities, microcephaly, hypotonia, and movement disorders and/or spasticity. The majority of DDX3X variants described are de novo mutations in females with ID. In contrast, most male DDX3X variants are inherited from an unaffected mother, with one documented exception being a recently identified de novo splice site variant. It has been suggested, therefore, that DDX3X exerts its effects through haploinsufficiency in females, and that affected males carry hypomorphic alleles that retain partial function. Given the lack of male de novo DDX3X variants, loss‐of‐function variants in this gene are suspected to be male lethal. Through whole‐exome sequencing, we identified three unrelated males with hemizygous missense DDX3X variants and ID. All three variants were confirmed by Sanger sequencing, with two established as de novo. In silico analyses were supportive of pathogenicity. We report the male phenotypes and compare them to phenotypes observed in previously reported male and female patients. In conclusion, we propose that de novo DDX3X variants are not necessarily male lethal and should be considered as a cause of syndromic ID in both males and females.
... The majority of genetic defects in DDX3X syndrome are de novo variants in the DDX3X gene, particularly in females (8,9). Only a few de novo DDX3X gene mutations have been detected in males (10). Unlike many X-linked genes, DDX3X escapes X-inactivation in females. ...
... In this regard, variance in the clinical presentation of different cases is thought to vary according to X-inactivation patterns, even in twins and siblings (11). DDX3X syndrome is the consequence of a de novo mutation within a DDX3X gene at conception, which can be inherited but not frequently (6,(9)(10)(11)(12). According to recent findings from multiple cohorts, the DDX3X gene has the highest proportion of missense variants identified among other autosomal dominant de novo monogenic rare neurodevelopmental disorders (2). ...
... The most common psychopathological expression of DDX3X de novo variants is developmental delay in both genders (6,9,10,13). To date, a total of 848 reported cases (809 females and 39 males) exist worldwide (14). ...
... The DDX3X syndrome is caused by a spontaneous mutation within the DDX3X gene at conception [7][8][9]. This RD can be inherited; however, it does not happen frequently [4,7,10]. Analyzed data from multiple large cohort studies indicates that the DDX3X gene has the highest proportion of missense variants identified among other autosomal dominant de novo monogenic RNDDs [11]. ...
... DDX3X de novo variants cause developmental delays (DD) both in females, as first proven in a large cohort study in 2015, as well as in males [7], as confirmed later in 2018 [4,10,12]. The gene-based prevalence of de novo mutations was estimated in a 2022 paper by extrapolating data from the number of neurodevelopmental disorders (NDDs) cohort cases [11]. ...
... A more detailed study of these behaviors is needed in future research. [9][10][11][12]15,19,23,24,26]. ...
(1) Background: Identification of typical behavioral manifestations in patients with DEAD-Box Helicase 3 X-linked gene (DDX3X) variants plays a crucial role in accurately diagnosing and managing the syndrome. The objective of this paper was to carry out a review of medical and public databases and assess the behavioral features of the DDX3X syndrome (DDX3X), with a particular focus on psycho-pathological symptoms. (2) Methods: An extensive computerized search was conducted in various databases, including PubMed, Medline Complete, Science Direct, Scopus, and Web of Science. Specific keywords and Medical Subject Headings were used to ensure the inclusion of relevant studies. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were applied to assess the methodological quality of the manuscripts. (3) Results: Only nine papers out of the 272 assessed met the inclusion criteria. These articles revealed various psycho-pathological manifestations in patients with the DDX3X syndrome. Intellectual disability (ID) or developmental disability (DD), speech delay, autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), generalized anxiety disorder (GAD), self-injurious behaviors (SIBs), sensory symptoms and sleep disturbance were demonstrated to be the most common psycho-pathological behavior manifestations. (4) Conclusions: Patients with the DDX3X syndrome manifest a wide spectrum of psycho-pathological symptoms. A comprehensive investigation of these symptoms in patients is essential for early diagnosis and effective therapy.
... De novo mutations in the RNA helicase, DDX3X, are one of the leading causes of ID in females and underlie DDX3X syndrome (Beal et al., 2019;Lennox et al., 2020;Scala et al., 2019;Snijders Blok et al., 2015;Wang et al., 2018). DDX3X is X-linked, which likely explains the preponderance of female cases; although an increasing number of de novo and inherited DDX3X mutations are found in males (Kellaris et al., 2018;Nicola et al., 2019). While DDX3X syndrome is characterized by ID, these individuals also commonly present with muscle tone and gait abnormalities, language deficits, abnormal brain MRIs (particularly white matter loss and corpus callosum defects), and many are diagnosed with ASD (Johnson-Kerner et al., 1993;Lennox et al., 2020;Tang et al., 2021). ...
... While the vast majority of individuals with DDX3X syndrome are females, males can harbor either maternally inherited or de novo DDX3X mutations (Kellaris et al., 2018;Nicola et al., 2019). Thus, as males only have a single copy of Ddx3x, we predicted that loss of Ddx3x in males would (multi-colored); Figure 1B adapted from Figure 1A and B from Hoye and Silver, 2021. ...
... While the vast majority of DDX3X syndrome individuals are female, an increasing number of male individuals have been identified (Kellaris et al., 2018;Nicola et al., 2019), comprising ~5% of all cases ( ddx3x. org). ...
Mutations in the RNA helicase, DDX3X, are a leading cause of Intellectual Disability and present as DDX3X syndrome, a neurodevelopmental disorder associated with cortical malformations and autism. Yet, the cellular and molecular mechanisms by which DDX3X controls cortical development are largely unknown. Here, using a mouse model of Ddx3x loss-of-function we demonstrate that DDX3X directs translational and cell cycle control of neural progenitors, which underlies precise corticogenesis. First, we show brain development is sensitive to Ddx3x dosage; complete Ddx3x loss from neural progenitors causes microcephaly in females, whereas hemizygous males and heterozygous females show reduced neurogenesis without marked microcephaly. In addition, Ddx3x loss is sexually dimorphic, as its paralog, Ddx3y, compensates for Ddx3x in the developing male neocortex. Using live imaging of progenitors, we show that DDX3X promotes neuronal generation by regulating both cell cycle duration and neurogenic divisions. Finally, we use ribosome profiling in vivo to discover the repertoire of translated transcripts in neural progenitors, including those which are DDX3X-dependent and essential for neurogenesis. Our study reveals invaluable new insights into the etiology of DDX3X syndrome, implicating dysregulated progenitor cell cycle dynamics and translation as pathogenic mechanisms.
... Recently, de novo mutations in DDX3X were reported to be a common cause of intellectual disability in humans (https://ddx3x.org) (Dikow et al., 2017;Kellaris et al., 2018;Lennox et al., 2020;Nicola et al., 2019;Snijders Blok et al., 2015;Wang et al., 2018). These mutations were found primarily in females, and there are strong indications that some of them lead to embryonic lethality in males (Nicola et al., 2019;Snijders Blok et al., 2015). ...
... (Dikow et al., 2017;Kellaris et al., 2018;Lennox et al., 2020;Nicola et al., 2019;Snijders Blok et al., 2015;Wang et al., 2018). These mutations were found primarily in females, and there are strong indications that some of them lead to embryonic lethality in males (Nicola et al., 2019;Snijders Blok et al., 2015). Most of these mutations were predicted to result in decreased DDX3X activity, and the defects in female patients may be caused by haploinsufficiency or dominant-negative effects of the mutants; partial X inactivation of the DDX3X gene may also contribute to the phenotypes (Garieri et al., 2018;Lennox et al., 2020;Snijders Blok et al., 2015). ...
... Patients with DDX3X mutations display various defects in central nervous system (CNS) development, including intellectual disability, autism spectrum disorder, microcephaly, and corpus callosum hypoplasia. Most patients also have craniofacial disorders, ranging from mild dysmorphic facial features to severe oral-facial clefts (Dikow et al., 2017;Kellaris et al., 2018;Lennox et al., 2020;Nicola et al., 2019;Snijders Blok et al., 2015;Wang et al., 2018). Other common symptoms include congenital heart diseases, pigment defects, and hearing/visual impairment (Snijders Blok et al., 2015;Wang et al., 2018); a recent report also suggests that these patients have high rates of neuroblastoma, a rare NC-derived childhood tumor (Lennox et al., 2020). ...
Mutations in the RNA helicase DDX3 have emerged as a frequent cause of intellectual disability in humans. Because many patients carrying DDX3 mutations have additional defects in craniofacial structures and other tissues containing neural crest (NC)-derived cells, we hypothesized that DDX3 is also important for NC development. Using Xenopus tropicalis as a model, we show that DDX3 is required for normal NC induction and craniofacial morphogenesis by regulating AKT kinase activity. Depletion of DDX3 decreases AKT activity and AKT-dependent inhibitory phosphorylation of GSK3β, leading to reduced levels of β-catenin and Snai1, two GSK3β substrates that are critical for NC induction. DDX3 function in regulating these downstream signaling events during NC induction is likely mediated by RAC1, a small GTPase whose translation depends on the RNA helicase activity of DDX3. These results suggest an evolutionarily conserved role of DDX3 in NC development by promoting AKT activity, and provide a potential mechanism for the NC-related birth defects displayed by patients harboring mutations in DDX3 and its downstream effectors in this signaling cascade.
... Most male DDX3X variants were inherited from the unaffected mother whereas female DDX3X variants were de novo mutations. This fact suggests that events of DDX3X variants occur through haploinsufficiency in female patients and partial function of DDX3X is kept in male patients (Nicola et al., 2019). The phenotype of DDX3X variants is heterogeneous including psychomotor retardation (100%), brain anomalies (90%), congenital heart anomalies (71%), characteristic facies (68%), and hypotonia (68%) (Nicola et al., 2019). ...
... This fact suggests that events of DDX3X variants occur through haploinsufficiency in female patients and partial function of DDX3X is kept in male patients (Nicola et al., 2019). The phenotype of DDX3X variants is heterogeneous including psychomotor retardation (100%), brain anomalies (90%), congenital heart anomalies (71%), characteristic facies (68%), and hypotonia (68%) (Nicola et al., 2019). Here we report a case of a Japanese girl with psychomotor retardation caused by a novel DDX3X variant, who also exhibited severe constipation and recurrent paralytic ileus. ...
... We described a patient with developmental delay, severe constipation and recurrent paralytic ileus. The features of facial dysmorphism or psychomotor retardation were the same when previously gastroesophageal reflux has been reported (Nicola et al., 2019). We believe that this is an important case to expand the phenotype caused by DDX3X variants. ...
Mutations in DDX3X have recently been identified as a common cause of intellectual disability and congenital anomalies. DDX3X (Xp11.4) encodes the DEAD box RNA helicase that plays an important role in gene regulation, apoptosis, and oncogenesis.
Here, we report a case of 6-year-old Japanese girl with a novel variant (NM_001193416.3: c.1574A > G; p.(Tyr525Cys), who exhibited psychomotor retardation, severe constipation, and a recurrent paralytic ileus. This is the second report of severe gastrointestinal symptoms being associated with this disease. This report expands the phenotype caused by DDX3X variants and reveals an important clinical aspect for patients and medical staff.
... To characterize DDX3X variants in intellectual disability and to explore the likely association between the phenotype and DDX3X gene variants, we performed a systematic literature search in the PubMed database, the Human Gene Mutation Database (HGMD), the Online Mendelian Inheritance in Man (OMIM) and the China National Knowledge Infrastructure (CNKI) databases for publications using "intellectual disability" or "developmental delay" and "DDX3X" as the keywords (until January 9th, 2020). In addition to our patient, we identified 96 patients with DDX3X variants reported previously (10,(13)(14)(15)(16)(17)(18)(19). We excluded four patients reported in a single publication and one fetus from further analysis since all comprehensive clinical presentations were unavailable (17,18). ...
... nl/name-checker). Finally, we summarized the clinical and genetic characteristics of the remaining 91 patients reported in 10 publications (10,(13)(14)(15)(16)(18)(19)(20)(21)(22); the proportion of females was ∼89% (81/91), and only 10 male patients have been described. The findings are presented in Table 1 ...
... De novo patterns occurred in all female patients, and two of the de novo variants (c.573_575delCAT/p.I191del and c.1805G>A/p.R602Q) are mosaic in the proband, with allele fractions of 21% and 14%, respectively (18). Eight unique variants were identified in 10 male patients, including three de novo variants (15,18), four maternally inherited variants (10,13,18), and one variant with unknown parental status (c.1702C>T/p.P568S) (15). The pathogenicity of these maternally inherited variants was determined by functional testing, which suggested partial loss of function of DDX3X as the most likely pathogenic mechanism (10,13). ...
De novo DDX3X variants account for 1%–3% of intellectual disability (ID) in females and have been occasionally reported in males. Here, we report a female patient with severe ID and various other features, including epilepsy, movement disorders, behavior problems, sleep disturbance, precocious puberty, dysmorphic features, and hippocampus atrophy. With the use of family-based exome sequencing, we identified a de novo pathogenic variant (c.1745dupG/p.S583*) in the DDX3X gene. However, our patient did not present hypotonia, which is considered a frequent clinical manifestation associated with DDX3X variants. While hand stereotypies and sleep disturbance have been occasionally associated with the DDX3X spectrum, hippocampus atrophy has not been reported in patients with DDX3X-related ID. The investigation further expands the phenotype spectrum for DDX3X variants with syndromic intellectual disability, which might help to improve the understanding of DDX3X-related intellectual disability or developmental delay.
... Несмотря на то, что ген, ответственный за возникновение заболевания, локализован на Х-хромосоме, основное количество описанных к настоящему времени больных -женского пола. Существуют описания лишь несколько больных мальчиков с мутациями в гене DDX3X, возникшими de novo [9]. Показано, что появление клинических симптомов у женщин-гетерозиготных носительниц мутации обусловлено несбалансированной лайонизацией, в результате которой неактивной становится Х-хромосома, не несущая мутантный ген. ...
... Однако клинические проявления варьируют также в пределах одного аминокислотного остатка. Так, среди описанных в литературе ранее вариантов нуклеотидной последовательности p.Pro568Leu [1], p.Pro568Ser [9] и p.Pro568Arg, клиническая картина сходна по тяжести в первом и третьем случае соответственно, во втором случае больным яв-ляется мальчик, что говорит о менее значительном нарушении функции белка. Это можно объяснить тем, что лейцин и аргинин являются крупными разветвленными аминокислотами и, заменяя в белке самую маленькую аминокислоту пролин, могут нарушать конформацию геликазного домена, которая и приводит к потере функции белка. ...
... У родителей мутаций не выявлено, следовательно, она возникла de novo. Данная нуклеотидная замена не была описана как патогенная, однако ранее в том же аминокислотном остатке описан патогенный вариант p.Pro568Ser у больного мужского пола[9] и p. Pro568Leu у больной женского пола[1]. К сожалению, авторам не удалось установить происхождение мутации: de novo или унаследованной. ...
Введение. Х-сцепленная умственная отсталость 102‑го типа, обусловленная мутациями в гене DDX3X, – один из наиболее распространенных моногенных вариантов интеллектуального дефицита у лиц женского пола.
Цель исследования – описание клинико-генетических характеристик лиц женского пола в России с умственной отсталостью 102‑го типа, обусловленных вновь выявленными мутациями.
Материалы и методы. Диагноз умственной отсталости 102‑го типа устанавливался на основании особенности клинических проявлений и выявленной мутации в гене DDX3X по результатам секвенирования экзома нового поколения и последующего подтверждения выявленных вариантов автоматическим секвенированием по Сэнгеру.
Результаты. Представлено описание клинико-генетических характеристик 2 больных женского пола с Х-сцепленной умствен- ной отсталостью 102‑го типа, обусловленной вновь выявленными мутациями с.1703С>G и c.113A>G (NM_001193416) в гене DDX3X в гетерозиготном состоянии. Описаны новые особенности фенотипа. Предположен механизм возникновения клинико-генетических корреляций, который может быть использован как прогностический маркер развития заболевания.
Заключение. Описаны клинико-генетические характеристики 2 больных с мутациями в гене DDX3X, нарушающими аминокислотную последовательность различных белковых регионов, с различной тяжестью клинических проявлений. Полученные результаты могут свидетельствовать в пользу существования зависимости выраженности фенотипа от локализации и характера мутаций в гене и обусловливают актуальность проведения дальнейших исследований, направленных на поиск клинико-генетических корреляций.
... Recently, de novo mutations in DDX3X were reported to be a common cause of intellectual disability in humans (https://ddx3x.org) (Dikow et al., 2017;Kellaris et al., 2018;Lennox et al.;Nicola et al., 2019;Snijders Blok et al., 2015;Wang et al., 2018). ...
... These mutations were found primarily in females, and there are strong indications that some of them lead to embryonic lethality in males (Nicola et al., 2019;Snijders Blok et al., 2015). Most of these mutations were predicted to result in decreased DDX3X activity, and the defects in female patients may be caused by haploinsufficiency or dominantnegative effects of the mutants; partial X inactivation of the DDX3X gene may also contribute to the phenotypes (Garieri et al., 2018;Lennox et al.;Snijders Blok et al., 2015). ...
... Patients with DDX3X mutations display various defects in central nervous system (CNS) development, including intellectual disability, autism spectrum disorder, microcephaly, and corpus callosum hypoplasia. Most patients also have craniofacial disorders, ranging from mild dysmorphic facial features to severe oral-facial clefts (Dikow et al., 2017;Kellaris et al., 2018;Lennox et al.;Nicola et al., 2019;Snijders Blok et al., 2015;Wang et al., 2018). Other common symptoms include congenital heart diseases, pigment defects, and hearing/visual impairment (Snijders Blok et al., 2015;Wang et al., 2018); a recent report also suggests that these patients have high rates of neuroblastoma, a rare NC-derived childhood tumor (Lennox et al.). ...
Mutations in the RNA helicase DDX3 have emerged as a frequent cause of intellectual disability in humans. Because many patients carrying DDX3 mutations have additional defects in craniofacial structures and other tissues containing neural crest (NC)-derived cells, we hypothesized that DDX3 is also important for NC development. Using Xenopus tropicalis as a model, we show that DDX3 is required for normal NC induction and craniofacial morphogenesis by regulating AKT kinase activity. Depletion of DDX3 decreases AKT activity and AKT-dependent inhibitory phosphorylation of GSK3β, leading to reduced levels of β-catenin and Snai1, two GSK3β substrates that are critical for NC induction. DDX3 function in regulating these downstream signaling events during NC induction is likely mediated by RAC1, a small GTPase whose translation depends on the RNA helicase activity of DDX3. These results suggest an evolutionarily conserved role of DDX3 in NC development by promoting AKT activity, and provide a potential mechanism for the NC-related birth defects displayed by patients harboring mutations in DDX3 and its downstream effectors in this signaling cascade.
... Most of the described variants are predicted to lead to loss of protein function ( [2,7]. Conversely, only 10 male patients have been described so far, suggesting a lethal effect in most fetal cases [1,[7][8][9]. Six of them harbored maternally inherited missense variants, two carried de novo missense variants, and one carried a de novo splice site variant. The mode of inheritance in one patient harboring a missense variant was not confirmed [1,[7][8][9]. ...
... Six of them harbored maternally inherited missense variants, two carried de novo missense variants, and one carried a de novo splice site variant. The mode of inheritance in one patient harboring a missense variant was not confirmed [1,[7][8][9]. Regardless of gender, most DDX3X patients carry missense variants affecting the ATP-binding or C-terminal helicase domains, similarly to those identified in our patients, without a clear genotype-phenotype correlation [2,7,10]. ...
... Facial dysmorphisms are common, including clinical features of Toriello-Carey syndrome [2,7,8]. Interestingly, the existence of sex-specific phenotypes has been hypothesized [9]. Although all reported male patients have ID and global DD, and most of them suffer from movement disorders, they exhibit peculiar phenotypic features. ...
De novo DDX3X variants account for 1–3% of syndromic intellectual disability (ID) in females and have been occasionally reported in males. Furthermore, somatic DDX3X variants occur in several aggressive cancers, including medulloblastoma. We report three unrelated females with severe ID, dysmorphic features, and a common brain malformative pattern characterized by malformations of cortical development, callosal dysgenesis, basal ganglia anomalies, and midbrain–hindbrain malformations. A pilocytic astrocytoma was incidentally diagnosed in Patient 1 and trigonocephaly was found in Patient 2. With the use of family based whole exome sequencing (WES), we identified three distinct de novo variants in DDX3X. These findings expand the phenotypic spectrum of DDX3X-related disorders, demonstrating unique neuroradiological features resembling those of the tubulinopathies, and support a role for DDX3X in neuronal development. Our observations further suggest a possible link between germline DDX3X variants and cancer development.
... MRXSSB is a rare, X-linked neurodevelopmental disorder that manifests during the early stages of development. Complete loss of function mutations, for example, frameshift and splice site mutation, seems to be associated with dominant inheritance, whereas the missense mutation is associated with recessive inheritance (Nicola et al., 2019). MRXSSB shows variable characteristics, including mild to severe intellectual disability, hypertonia, microcephaly, seizures, a number of movement disorders including spasticity, dyskinesia and stiff-legged, visual abnormalities and various dysmorphisms (Nicola et al., 2019;Boitnott et al., 2021). ...
... Complete loss of function mutations, for example, frameshift and splice site mutation, seems to be associated with dominant inheritance, whereas the missense mutation is associated with recessive inheritance (Nicola et al., 2019). MRXSSB shows variable characteristics, including mild to severe intellectual disability, hypertonia, microcephaly, seizures, a number of movement disorders including spasticity, dyskinesia and stiff-legged, visual abnormalities and various dysmorphisms (Nicola et al., 2019;Boitnott et al., 2021). DDX3X being a ubiquitous protein, its expression has been observed to be abundant in brain tissues during developmental stages. ...
... Kellaris et al. [3] proposed that hypomorphic DDX3X variants may be viable in hemizygous males and do not cause clinical phenotype in female carriers. However, few de novo DDX3X mutations have been identified in males [4]. Although these male patients share many of the clinical features with affected females, some distinct clinical phenotypes can depend on the gender of the patient and on the pathogenicity of the variant. ...
... Despite the ubiquitous expression of the DDX3X protein, high expression levels are detected in all the cortical layers of the embryonic brain, consistent with its crucial role in cortical development during neurogenesis [10] and, as a consequence, DDX3X mutations are reported to impact on neuronal function [4]. In particular, defective neurite outgrowth and neural progenitor differentiation/migration could account for brain malformations and the consequent characteristic clinical phenotypes of the DDX3X syndrome [5]. ...
Background
De novo pathogenic variants in the DDX3X gene are reported to account for 1–3% of unexplained intellectual disability (ID) in females, leading to the rare disease known as DDX3X syndrome (MRXSSB, OMIM #300958). Besides ID, these patients manifest a variable clinical presentation, which includes neurological and behavioral defects, and abnormal brain MRIs.
Case presentation
We report a 10-year-old girl affected by delayed psychomotor development, delayed myelination, and polymicrogyria (PMG). We identified a novel de novo missense mutation in the DDX3X gene (c.625C > G) by whole exome sequencing (WES). The DDX3X gene encodes a DEAD-box ATP-dependent RNA-helicase broadly implicated in gene expression through regulation of mRNA metabolism. The identified mutation is located just upstream the helicase domain and is suggested to impair the protein activity, thus resulting in the altered translation of DDX3X-dependent mRNAs. The proband, presenting with the typical PMG phenotype related to the syndrome, does not show other clinical signs frequently reported in presence of missense DDX3X mutations that are associated with a most severe clinical presentation. In addition, she has brachycephaly, never described in female DDX3X patients, and macroglossia, that has never been associated with the syndrome.
Conclusions
This case expands the knowledge of DDX3X pathogenic variants and the associated DDX3X syndrome phenotypic spectrum.
... Kellaris et al. [3] proposed that hypomorphic DDX3X variants may be viable in hemizygous males and do not cause clinical phenotype in female carriers. However, few de novo DDX3X mutations have been identi ed in males [4]. Although these male patients share many of the clinical features with affected females, some distinct clinical phenotypes can depend on the gender of the patient and on the pathogenicity of the variant. ...
... Despite the ubiquitous expression of the DDX3X protein, high expression levels are detected in all the cortical layers of the embryonic brain, consistent with its crucial role in cortical development during neurogenesis [10] and, as a consequence, DDX3X mutations are reported to impact on neuronal function [4]. In particular, defective neurite outgrowth and neural progenitor differentiation/migration could account for brain malformations and the consequent characteristic clinical phenotypes of the DDX3X syndrome [11]. ...
Background: De novo pathogenic variants in the DDX3X gene are reported to account for 1–3% of unexplained intellectual disability (ID) in females, leading to the rare disease known as DDX3X syndrome (MRXSSB, OMIM #300958). Besides ID, these patients manifest a variable clinical presentation, which includes neurological and behavioral defects, and abnormal brain MRIs.
Case presentation: We report a 10-year-old girl affected by delayed psychomotor development, delayed myelination, and polymicrogyria (PMG). We identified a novel de novo missense mutation in the DDX3X gene (c.C625G) by exome sequencing. The DDX3X gene encodes a DEAD-box ATP-dependent RNA-helicase broadly implicated in gene expression through regulation of mRNA metabolism. The identified mutation is located just upstream the helicase domain and is suggested to impair the protein activity, thus resulting in the altered translation of DDX3X-dependent mRNAs. The proband, presenting with the typical PMG phenotype related to the syndrome, does not show other clinical signs frequently reported in presence of missense DDX3X mutations that are associated with a most severe clinical presentation. In addition, she has brachycephaly, never described in female DDX3X patients, and macroglossia, that has never been associated with the syndrome.
Conclusions: This case expands the knowledge of DDX3X pathogenic variants and the associated DDX3X syndrome phenotypic spectrum.
... X-linked mental retardation-102 (MRX102; MIM: 300958) has been described in patients with variants of DDX3X at Xp11.4 which encodes a DEAD-box RNA helicase [9,10]. DDX3X plays an important role in transcription, splicing, transport of RNA, and translation, and works as a key regulator in the Wnt/β-catenin signaling pathway [11,12]. ...
... However, further details were not described [19]. Nearly all published DDX3X variants resulting in MRX102 so far are de novo and are proved "damaging in biology" [9]. MRX102 has not been previously confused with ataxic CP until now. ...
Background:
Cerebral palsy (CP) is a non-progressive disorder of movement and posture due to a static insult to the brain. In CP, the depth of investigation is guided by the patients' medical history and their clinical examination. Magnetic resonance imaging (MRI) has a high yield and is widely used for investigation in CP.
Case presentation:
In this paper, we report a novel DDX3X variant in a girl afflicted with the X-linked mental retardation-102 (MRX102). The girl had been misdiagnosed with CP in her early life based on a comprehensive clinical evaluation and associated clinical features, such as developmental delay, reduced activities of the arms and legs, and abnormal brain MRI. Subsequently, whole-exome sequencing was applied to better distinguish between CP and actual MRX102 with similar characteristics.
Conclusions:
We report on a de novo heterozygous DDX3X variant mimicking cerebral palsy and suggest a thorough and conscientious review during diagnosis of CP.
... Heterozygous, germline, missense mutations that disrupt DDX3X RNA helicase function account for up to 3% of intellectual disability in human females and cause hindbrain developmental defects very similar to those that we observed in female Blbp-Cre +/À ;Ddx3x Flx/Flx mice (Dikow et al., 2017;Lennox et al., 2020;Nicola et al., 2019;Scala et al., 2019;Snijders Blok et al., 2015). Thus, Ddx3x deletion from the mouse brain phenocopies DDX3X loss-of-function mutations in humans. ...
... It is important to note that although our mouse models delete Ddx3x, human medulloblastomas contain mainly heterozygous missense mutations in the gene (Northcott et al., 2019). However, evidence suggests that these alterations are likely to be functionally equivalent: developmental defects in Blbp-Cre +/À ;Ddx3x Flx/Flx mice are strikingly similar to those seen in humans with de novo, heterozygous, germline DDX3X mutations; several missense mutations observed in humans with developmental defects are identical to those observed in medulloblastoma; and these mutations have been shown to impair RNA helicase activity and be functionally equivalent to knockout of Ddx3x in the developing forebrain (Dikow et al., 2017;Lennox et al., 2020;Nicola et al., 2019;Scala et al., 2019;Snijders Blok et al., 2015). Furthermore, a common feature of DDX3X mutations associated with both developmental defects and medulloblastoma, is their capacity to sequester DDX3X within stress granules: the greater the degree of sequestration, the more severe the phenotype (Lennox et al., 2020;Valentin-Vega et al., 2016). ...
DEAD-Box Helicase 3 X-Linked (DDX3X) is frequently mutated in the Wingless (WNT) and Sonic hedghog (SHH) subtypes of medulloblastoma—the commonest malignant childhood brain tumor, but whether DDX3X functions as a medulloblastoma oncogene or tumor suppressor gene is not known. Here, we show that Ddx3x regulates hindbrain patterning and development by controlling Hox gene expression and cell stress signaling. In mice predisposed to Wnt- or Shh medulloblastoma, Ddx3x sensed oncogenic stress and suppressed tumor formation. WNT and SHH medulloblastomas normally arise only in the lower and upper rhombic lips, respectively. Deletion of Ddx3x removed this lineage restriction, enabling both medulloblastoma subtypes to arise in either germinal zone. Thus, DDX3X is a medulloblastoma tumor suppressor that regulates hindbrain development and restricts the competence of cell lineages to form medulloblastoma subtypes.
... Multiple types of de novo variants have been identified in affected females, including nonsense, frameshift, missense and splice site variants. In contrast to the numerous reported females with DDX3X-related NDD, only a small number of reports on males with rare hemizygous DDX3X variants have been published [7,18,19]. All of these males have missense or splice site variants, either maternally inherited or de novo. ...
DDX3X -related neurodevelopmental disorder is one of the most common monogenic causes of intellectual disability in females, with currently >1000 females diagnosed worldwide. In contrast, reports on affected males with DDX3X variants are scarce. The limited knowledge on this X-linked disorder in males hinders the interpretation of hemizygous DDX3X variants in clinical practice. In this study, we present a new cohort of 19 affected males (from 17 unrelated families) with (possibly) disease-causing DDX3X variants, for whom we collected clinical and molecular data. Additionally, we reviewed the existing literature on 13 males with DDX3X variants. The phenotype in males is diverse, including intellectual disability, speech/language delays, behavioural challenges and structural brain abnormalities. The vast majority of males have missense variants, including two recurrent variants (p.(Arg351Gln) and p.(Arg488Cys)). No truncating variants have been reported, consistent with the presumed embryonic lethality of complete loss-of-function of DDX3X in males. In our novel cohort, 6/17 variants are de novo in the affected male and 3/17 variants are de novo in the mother. This study provides significant insights in the genetic and phenotypic spectrum of males with DDX3X variants, by presenting the data of a combined cohort ( n = 32) of novel and published individuals. Our data show that variants in DDX3X can cause an X-linked neurodevelopmental disorder in males, with unaffected or mildly affected carrier females. These findings will aid the interpretation of hemizygous missense variants in DDX3X and can guide clinical management and counselling, in particular with regard to recurrence risks in the respective families.
... DDX3X is located on the X chromosome, and the majority of affected individuals with DDX3X syndrome are females. Notably, a growing number of males have been identified suggesting that some DDX3X mutations may be tolerated in males [12,15,16]. Beyond neurodevelopment, missense mutations in DDX3X also cause diverse cancers including medulloblastoma [17][18][19][20]. ...
De novo mutations in the RNA binding protein DDX3X cause neurodevelopmental disorders including DDX3X syndrome and autism spectrum disorder. Amongst ~200 mutations identified to date, half are missense. While DDX3X loss of function is known to impair neural cell fate, how the landscape of missense mutations impacts neurodevelopment is almost entirely unknown. Here, we integrate transcriptomics, proteomics, and live imaging to demonstrate clinically diverse DDX3X missense mutations perturb neural development via distinct cellular and molecular mechanisms. Using mouse primary neural progenitors, we investigate four recurrently mutated DDX3X missense variants, spanning clinically severe (2) to mild (2). While clinically severe mutations impair neurogenesis, mild mutations have only a modest impact on cell fate. Moreover, expression of severe mutations leads to profound neuronal death. Using a proximity labeling screen in neural progenitors, we discover DDX3X missense variants have unique protein interactors. We observe notable overlap amongst severe mutations, suggesting common mechanisms underlying altered cell fate and survival. Transcriptomic analysis and subsequent cellular investigation highlights new pathways associated with DDX3X missense variants, including upregulated DNA Damage Response. Notably, clinically severe mutations exhibit excessive DNA damage in neurons, associated with increased cytoplasmic DNA:RNA hybrids and formation of stress granules. These findings highlight aberrant RNA metabolism and DNA damage in DDX3X-mediated neuronal cell death. In sum our findings reveal new mechanisms by which clinically distinct DDX3X missense mutations differentially impair neurodevelopment.
... Given the distinct morphological and catalytic phenotypes observed in our hollow mutants, we questioned whether these mutants may be correlated more strongly with DDX3X-related diseases than the diffuse mutants. We examined the cBio Portal database 46 and ten studies of DDX3X-related neurodevelopmental disorder (NDD) 4,25,26,[47][48][49][50][51][52][53] . We counted the number of patient samples in which the mutations appeared (and mutations within three amino acids). ...
Mutations in the RNA helicase DDX3X, implicated in various cancers and neurodevelopmental disorders, often impair RNA unwinding and translation. However, the mechanisms underlying the impairment and the differential interactions of DDX3X mutants with wild-type (WT) X-linked DDX3X and Y-linked homolog DDX3Y remain elusive. This study reveals that specific DDX3X mutants more frequently found in disease form distinct hollow condensates in cells. Using a combined structural, biochemical, and single-molecule microscopy study, we show that reduced ATPase and RNA release activities contribute to condensate formation and these catalytic deficits result from inhibiting the catalytic cycle at multiple steps. Proteomic investigations further demonstrate that these hollow condensates sequester WT DDX3X/DDX3Y and other proteins crucial for diverse signaling pathways. WT DDX3X enhances the dynamics of heterogeneous mutant/WT hollow condensates more effectively than DDX3Y. These findings offer valuable insights into the catalytic defects of specific DDX3X mutants and their differential interactions with wild-type DDX3X and DDX3Y, potentially explaining sex biases in disease.
... ;https://doi.org/10.1101https://doi.org/10. /2024 In 46,XY males, rare constitutional (germline) mutations in DDX3X cause a neurodevelopmental disorder ('DDX3X syndrome') (Kellaris et al. 2018;Nicola et al. 2019). By contrast, constitutional mutations of DDX3Y in 46,XY males cause a surprisingly subtle phenotype. ...
The Y-linked gene DDX3Y and its X-linked homolog DDX3X survived the evolution of the human sex chromosomes from ordinary autosomes. DDX3X encodes a multi-functional RNA helicase, with mutations causing developmental disorders and cancers. We find that, among X-linked genes with surviving Y homologs, DDX3X is extraordinarily dosage-sensitive. Studying cells of individuals with sex chromosome aneuploidy, we observe that when the number of Y chromosomes increases, DDX3X transcript levels fall; conversely, when the number of X chromosomes increases, DDX3Y transcript levels fall. In 46,XY cells, CRISPRi knockdown of either DDX3X or DDX3Y causes transcript levels of the homologous gene to rise. In 46,XX cells, chemical inhibition of DDX3X protein activity elicits an increase in DDX3X transcript levels. Thus, perturbation of either DDX3X or DDX3Y expression is buffered – by negative cross-regulation of DDX3X and DDX3Y in 46,XY cells, and by negative auto-regulation of DDX3X in 46,XX cells. DDX3X - DDX3Y cross-regulation is mediated through mRNA destabilization – as shown by metabolic labeling of newly transcribed RNA – and buffers total levels of DDX3X and DDX3Y protein in human cells. We infer that post-transcriptional auto-regulation of the ancestral (autosomal) DDX3 gene transmuted into auto- and cross-regulation of DDX3X and DDX3Y as these sex-linked genes evolved from ordinary alleles of their autosomal precursor.
... Statistically significant differences of sex chromosme complement (XX vs XY), gonadal phenotype (Sry-vs Sry+) and the interaction of sex chromosome complement with gonadal phenotype (interaction) are indicated as follows: * p < 0.05, ** p < 0.01, *** p < 0.001, ns, not significant difference. accumulative number of new observations that are detecting the implication of sex chromosome genes on pathological conditions of the nervous system [29,[35][36][37][38][39][40][41][42][43][44], it will be essential to explore the potential link between sex chromosome genes, alterations in neurosteroid levels, and brain pathology in future studies. For instance, the identification of an influence of sex chromosome genes on the levels of steroids that are altered in bipolar disorder and contribute to maniac episodes [45] may potentially result in the identification of a new avenue for therapeutic interventions. ...
... We are the first to report on education in a cohort of participants with DDX3X-NDD, finding that two thirds of participants attended specialist schools, while one-third attended mainstream school. Previous case reports of three males with DDX3X variants who had moderate to severe ID attended specialist schools (Nicola et al., 2019). Further examination of educational support needs for school-aged children is warranted to inform recommendations for access to tailored supports (e.g., modified lessons, specialist staff and/or equipment/technology). ...
Pathogenic variants in DDX3X are associated with neurodevelopmental disorders. Communication impairments are commonly reported, yet specific speech and language diagnoses have not been delineated, preventing prognostic counseling and targeted therapies. Here, we characterized speech and language in 38 female individuals, aged 1.69–24.34 years, with pathogenic and likely pathogenic DDX3X variants (missense, n = 13; nonsense, n = 12; frameshift, n = 7; splice site, n = 3; synonymous, n = 2; deletion, n = 1). Standardized speech, language, motor, social, and adaptive behavior assessments were administered. All participants had gross motor deficits in infancy (34/34), and fine motor deficits were common throughout childhood (94%; 32/34). Intellectual disability was reported in 86% (24/28) of participants over 4 years of age. Expressive, receptive, and social communication skills were, on average, severely impaired. However, receptive language was significantly stronger than expressive language ability. Over half of the assessed participants were minimally verbal (66%; 22/33; range = 2 years 2 months–24 years 4 months; mean = 8 years; SD = 6 years) and augmented speech with sign language, gestures, or digital devices. A quarter of the cohort had childhood apraxia of speech (25%; 9/36). Despite speech and language impairments, social motivation was a relevant strength. Many participants used augmentative and alternative communication (AAC), underscoring the need for early, tailored, and comprehensive AAC intervention.
... Clinical manifestations of DDX3X-related disorders (DDX3X-RD) include ID, hypotonia and behavioral problems such as autism spectrum disorder (ASD), attention-de cit/hyperactivity disorder (ADHD) and hyperactivity, self-injurious behavior, poor impulse control or aggression in females 1,2, 5-8 and males 9,10 . ...
We report two series of individuals with DDX3X variations, one (48 individuals) from physicians and one (44 individuals) from caregivers. These two series include several symptoms in common, with fairly similar distribution, which suggests that caregivers’ data are close to physicians’ data. For example, both series identified early childhood symptoms that were not previously described: feeding difficulties, mean walking age and age at first words. Each of the two datasets provide complementary knowledge. We confirmed that symptoms are similar to those in the literature and provide more details on feeding difficulties. Caregivers considered that the symptom attention-deficit/hyperactivity disorder was most worrisome. Both series also reported sleep disturbance. Recently, anxiety has been reported in individuals with DDX3X variants. We strongly suggest that attention-deficit/hyperactivity disorder, anxiety and sleep disorders need to be treated. In addition, we demonstrate preliminary evidence of a mild genome-wide DNA methylation profile in patients carrying mutations in DDX3X .
... Mutated forms of Ddx3x have been detected in different cancer types and are associated with intellectual disability (DDX3X syndrome), brain malformations, autism and epilepsy [108,169,170]. Most DDX3X syndrome individuals are female, an observation leading to the idea that the Y-linked homolog DDX3Y can compensate for DDX3X loss and contribute to milder phenotypes in males carrying DDX3X mutations [171,172]. Complete loss of Ddx3x in a conditional knockout (Ddx3x-cKO) mouse model led to microcephaly only in females, which might suggest that expression of the Y-linked homolog Ddx3y explains why Ddx3x-cKO male mice are phenotypically milder than Ddx3x-cKO females [173]. In addition, loss of one versus two Ddx3x copies caused vastly different corticogenesis phenotypes: Ddx3x-cKO females presented profound apoptosis in neural progenitors and neurons in the developing neocortex, whereas heterozygous females and Ddx3x-cKO males had impaired neurogenesis without cell death. ...
For many decades to date, neuroendocrinologists have delved into the key contribution of gonadal hormones to the generation of sex differences in the developing brain and the expression of sex-specific physiological and behavioral phenotypes in adulthood. However, it was not until recent years that the role of sex chromosomes in the matter started to be seriously explored and unveiled beyond gonadal determination. Now we know that the divergent evolutionary process suffered by X and Y chromosomes has determined that they now encode mostly dissimilar genetic information and are subject to different epigenetic regulations, characteristics that together contribute to generate sex differences between XX and XY cells/individuals from the zygote throughout life. Here we will review and discuss relevant data showing how particular X- and Y-linked genes and epigenetic mechanisms controlling their expression and inheritance are involved, along with or independently of gonadal hormones, in the generation of sex differences in the brain.
... Around 848 individuals have been identified (https://ddx3x.org/). In general, DDX3X-related ID is more common in females with de novo variants and less common in males, who usually inherited from unaffected heterozygous mothers except few cases of de novo male patients (Snijders Blok et al., 2015;Wang et al., 2018;Nicola et al., 2019;Tang et al., 2021). Moreover, there are phenotypic differences in females with DDX3X variants. ...
Skewed XCI plays an important role in the phenotypic heterogeneities of many X-linked disorders, even involving in diseases caused by XCI-escaping genes. DDX3X-related intellectual disability is more common in females and less common in males, who usually inherit from unaffected heterozygous mothers. As an X inactivation (XCI) escaping gene, the role of skewed XCI in the phenotype of DDX3X mutant female is unknown. Here we reported a DDX3X: c.694_711dup18 de novo heterozygous mutation in a female with intellectual disability on the maternal X chromosome on the basis of SNPs detected by PCR-sanger sequencing. AR assay revealed that the maternal mutant X chromosome was extremely inactivated in the proband. Using RNA sequencing and whole-exome sequencing, we quantified allelic read counts and allele-specific expression, and confirmed that the mutant X chromosome was inactive. Further, we verified that the mutant DDX3X allele had a lower expression level by RNA sequencing and RT-PCR, and the normal and mutated DDX3X expression accounted for respectively 70% and 30% of total. In conclusion, we found a symptomatic female with extreme skewing XCI in the DDX3X mutant allele. It was discovered that XCI in the mutant allele was insufficient to reverse the phenotype of DDX3X-related neurodevelopmental disorder. It contributed to a better understanding of the role of skewed XCI in phenotypic differences, which can aid in the genetic counseling and prenatal diagnosis of disorders in females with DDX3X defects.
... DDX3X loss-of-function variants are one of the more common single-gene causes of ID, affecting an estimated 1-3% of females with unexplained ID (Snijders- Blok et al., 2015;Wang et al., 2018) and more rarely affecting males (Nicola et al., 2019). As availability of genetic testing increases, numbers of individuals diagnosed with DDX3X variants are likely to rise considerably. ...
DDX3X variants are a common cause of intellectual disability (ID) in females, and have been associated with autism spectrum disorder and emotional-behavioural difficulties. In this study, we compared phenotypic data for 23 females with DDX3X variants, to 23 females with ID and other genetic diagnoses. We found a wide range of adaptive, social and emotional function within the DDX3X group. Autism characteristics did not differ between DDX3X and comparison groups, while levels of anxiety and self-injurious behaviour (SIB) were significantly higher in the DDX3X group. Within the DDX3X group, adaptive function, autism characteristics, anxiety and SIB scores were positively correlated, with evidence for group-specific associations with SIB. Future work is warranted to explore the multilevel mechanisms contributing to social and emotional development in individuals with DDX3X variants.
... Less common dysmorphic facial features include telecanthus, short palpebral fissures, epicanthal folds, smooth and/or long philtrum, thin upper vermilion, high-arched palate, micrognathia and large, protruding or low-set ears [64,66]. In male patients, the syndrome is characterized by intellectual disability and can also include neurological abnormalities such as behavior problems and movement disorder, brachycephaly, macrocephaly, facial dysmorphisms, strabismus, bifid uvula, nuchal thickening, pulmonary stenosis, cardiac anomalies, visual impairment and hearing loss [63,67,68] (Table 1). ...
Cranial neural crest (NC) cells delaminate from the neural folds in the forebrain to the hindbrain during mammalian embryogenesis and migrate into the frontonasal prominence and pharyngeal arches. These cells generate the bone and cartilage of the frontonasal skeleton, among other diverse derivatives. RNA-binding proteins (RBPs) have emerged as critical regulators of NC and craniofacial development in mammals. Conventional RBPs bind to specific sequence and/or structural motifs in a target RNA via one or more RNA-binding domains to regulate multiple aspects of RNA metabolism and ultimately affect gene expression. In this review, we discuss the roles of RBPs other than core spliceosome components during human and mouse NC and craniofacial development. Where applicable, we review data on these same RBPs from additional vertebrate species, including chicken, Xenopus and zebrafish models. Knockdown or ablation of several RBPs discussed here results in altered expression of transcripts encoding components of developmental signaling pathways, as well as reduced cell proliferation and/or increased cell death, indicating that these are common mechanisms contributing to the observed phenotypes. The study of these proteins offers a relatively untapped opportunity to provide significant insight into the mechanisms underlying gene expression regulation during craniofacial morphogenesis.
... Some missense/in-frame mutations are associated with more severe phenotypes (3). Only a few affected males-all carrying missense mutations-have been identified (1,3,12,13). These males often inherit the mutations from their mothers, who appear asymptomatic. ...
Background
Mutations in the X-linked gene DDX3X account for ∼2% of intellectual disability in females, often co-morbid with behavioral problems, motor deficits, and brain malformations. DDX3X encodes an RNA helicase with emerging functions in corticogenesis and synaptogenesis.
Methods
We generated a Ddx3x haploinsufficient mouse (Ddx3x+/- females) with construct validity for DDX3X loss-of-function mutations. We used standardized batteries to assess developmental milestones and adult behaviors, as well as magnetic resonance imaging and immunostaining of cortical projection neurons to capture early postnatal changes in brain development.
Results
Ddx3x+/- females show physical, sensory, and motor delays that evolve into behavioral anomalies in adulthood, including hyperactivity, anxiety-like behaviors, cognitive impairments in specific tasks (e.g., contextual fear memory but not novel object recognition memory) and motor deficits. Motor function declines with age but not if mice were previously exposed to behavioral training. Developmental and behavioral changes are associated with a reduction in brain volume, with some regions (e.g., cortex and amygdala) disproportionally affected. Cortical thinning is accompanied by defective cortical lamination, indicating that Ddx3x regulates the balance of glutamatergic neurons in the developing cortex.
Conclusions
These data shed new light on the developmental mechanisms driving DDX3X syndrome and support face validity of this novel pre-clinical mouse model.
... Most of the identified DDX3X variants are in females; it is assumed that males carrying a very deleterious DDX3X variant do not survive to term, a finding confirmed in mouse models [17]. Surviving male patients carry missense variants that are thought to act as hypomorphic alleles [19,20]. Because DDX3X variants appear to be very penetrant, all variants that have been identified in females to date are de novo. ...
Background
DDX3X syndrome is a recently identified genetic disorder that accounts for 1–3% of cases of unexplained developmental delay and/or intellectual disability (ID) in females, and is associated with motor and language delays, and autism spectrum disorder (ASD). To date, the published phenotypic characterization of this syndrome has primarily relied on medical record review; in addition, the behavioral dimensions of the syndrome have not been fully explored.
Methods
We carried out multi-day, prospective, detailed phenotyping of DDX3X syndrome in 14 females and 1 male, focusing on behavioral, psychological, and neurological measures. Three participants in this cohort were previously reported with limited phenotype information and were re-evaluated for this study. We compared results against population norms and contrasted phenotypes between individuals harboring either (1) protein-truncating variants or (2) missense variants or in-frame deletions.
Results
Eighty percent (80%) of individuals met criteria for ID, 60% for ASD and 53% for attention-deficit/hyperactivity disorder (ADHD). Motor and language delays were common as were sensory processing abnormalities. The cohort included 5 missense, 3 intronic/splice-site, 2 nonsense, 2 frameshift, 2 in-frame deletions, and one initiation codon variant. Genotype–phenotype correlations indicated that, on average, missense variants/in-frame deletions were associated with more severe language, motor, and adaptive deficits in comparison to protein-truncating variants.
Limitations
Sample size is modest, however, DDX3X syndrome is a rare and underdiagnosed disorder.
Conclusion
This study, representing a first, prospective, detailed characterization of DDX3X syndrome, extends our understanding of the neurobehavioral phenotype. Gold-standard diagnostic approaches demonstrated high rates of ID, ASD, and ADHD. In addition, sensory deficits were observed to be a key part of the syndrome. Even with a modest sample, we observe evidence for genotype–phenotype correlations with missense variants/in-frame deletions generally associated with more severe phenotypes.
... For example, polymicrogyria has not been detected in individuals with loss-of-function mutations but only in a subset of females with missense/in-frame mutations, and this group is more delayed developmentally (3). Only a few affected males-all carrying missense mutations-have been identified (1,3,15,16). These males often inherit the mutations from their mothers, who appear asymptomatic. ...
Background
Mutations in the X-linked gene DDX3X account for ~2% of intellectual disability in females, often co-morbid with behavioral problems, motor deficits, and brain malformations. DDX3X encodes an RNA helicase with emerging functions in corticogenesis and synaptogenesis.
Methods
We generated a Ddx3x haploinsufficient mouse ( Ddx3x +/− ) with construct validity for DDX3X loss-of-function mutations. We used standardized batteries to assess developmental milestones and adult behaviors, as well as magnetic resonance imaging and immunostaining of cortical projection neurons to capture early postnatal changes in brain development.
Results
Ddx3x +/− mice show physical, sensory, and motor delays that evolve into behavioral anomalies in adulthood, including hyperactivity, anxiety-like behaviors, cognitive impairments, and motor deficits. Motor function further declines with age. These behavioral changes are associated with a reduction in brain volume, with some regions (e.g., cortex and amygdala) disproportionally affected. Cortical thinning is accompanied by defective cortical lamination, indicating that Ddx3x regulates the balance of glutamatergic neurons in the developing cortex.
Conclusions
These data shed new light on the developmental mechanisms driving DDX3X syndrome and support face validity of this novel pre-clinical mouse model.
... These girls presented with ID, developmental delay, movement disorders, behavior problems, hypotonia and epilepsy [83]. Since this initial finding, more than 100 cases bearing pathogenic mutations in the DDX3X gene affected by variable degrees of neurodevelopmental delay have been identified, including several male patients [84][85][86][87][88]. In contrast with mutations identified in DDX6 and DHX30 (see below), NDD-associated mutations are spread across the DDX3X gene ( Figure 2). ...
Intellectual disability (ID) affects at least 1% of the population, and typically presents in the first few years of life. ID is characterized by impairments in cognition and adaptive behavior and is often accompanied by further delays in language and motor skills, as seen in many neurodevelopmental disorders (NDD). Recent widespread high-throughput approaches that utilize whole-exome sequencing or whole-genome sequencing have allowed for a considerable increase in the identification of these pathogenic variants in monogenic forms of ID. Notwithstanding this progress, the molecular and cellular consequences of the identified mutations remain mostly unknown. This is particularly important as the associated protein dysfunctions are the prerequisite to the identification of targets for novel drugs of these rare disorders. Recent Next-Generation sequencing-based studies have further established that mutations in genes encoding proteins involved in RNA metabolism are a major cause of NDD. Here, we review recent studies linking germ-line mutations in genes encoding factors mediating mRNA decay and regulators of translation , namely DCPS, EDC3, DDX6 helicase and ID. These RNA-binding proteins have well-established roles in mRNA decapping and/or translational repression, and the mutations abrogate their ability to remove 5 0 caps from mRNA, diminish their interactions with cofactors and stabilize subsets of transcripts. Additional genes encoding RNA helicases with roles in translation including DDX3X and DHX30 have also been linked to NDD. Given the speed in the acquisition, analysis and sharing of sequencing data, and the importance of post-transcriptional regulation for brain development, we anticipate mutations in more such factors being identified and functionally characterized.
... ASD is a heterogeneous group of neurodevelopmental disorders, characterized by early-onset deficits in social interaction and communication skills, together with restricted, repetitive behavior. Defects in DDX3X function in humans is associated with brain and behavioral abnormalities, microcephaly, facial dysmorphism, hypotonia, aggression and movement disorders and/or spasticity in female and probably in male [59,[76][77][78][79][80][81][82][83][84][85]. The finding of a sexual dimorphic autism related protein specifically in the striatum is of particular interest because defects in striatal circuitry are known to cause autism-like phenotypes [86]. ...
Genetic disruption of synaptic proteins results in a whole variety of human neuropsychiatric disorders including intellectual disability, schizophrenia or autism spectrum disorder (ASD). In a wide range of these so-called synaptopathies a sex bias in prevalence and clinical course has been reported. Using an unbiased proteomic approach, we analyzed the proteome at the interaction site of the pre- and postsynaptic compartment, in the prefrontal cortex, hippocampus, striatum and cerebellum of male and female adult C57BL/6J mice. We were able to reveal a specific repertoire of synaptic proteins in different brain areas as it has been implied before. Additionally, we found a region-specific set of novel synaptic proteins differentially expressed between male and female individuals including the strong ASD candidates DDX3X, KMT2C, MYH10 and SET. Being the first comprehensive analysis of brain region-specific synaptic proteomes from male and female mice, our study provides crucial information on sex-specific differences in the molecular anatomy of the synapse. Our efforts should serve as a neurobiological framework to better understand the influence of sex on synapse biology in both health and disease.
The Y-linked gene DDX3Y and its X-linked homolog DDX3X survived the evolution of the human sex chromosomes from ordinary autosomes. DDX3X encodes a multifunctional RNA helicase, with mutations causing developmental disorders and cancers. We find that, among X-linked genes with surviving Y homologs, DDX3X is extraordinarily dosage sensitive. Studying cells of individuals with sex chromosome aneuploidy, we observe that when the number of Y Chromosomes increases, DDX3X transcript levels fall; conversely, when the number of X Chromosomes increases, DDX3Y transcript levels fall. In 46,XY cells, CRISPRi knockdown of either DDX3X or DDX3Y causes transcript levels of the homologous gene to rise. In 46,XX cells, chemical inhibition of DDX3X protein activity elicits an increase in DDX3X transcript levels. Thus, perturbation of either DDX3X or DDX3Y expression is buffered: by negative cross-regulation of DDX3X and DDX3Y in 46,XY cells and by negative auto-regulation of DDX3X in 46,XX cells. DDX3X – DDX3Y cross-regulation is mediated through mRNA destabilization—as shown by metabolic labeling of newly transcribed RNA—and buffers total levels of DDX3X and DDX3Y protein in human cells. We infer that post-transcriptional auto-regulation of the ancestral (autosomal) DDX3X gene transmuted into auto- and cross-regulation of DDX3X and DDX3Y as these sex-linked genes evolved from ordinary alleles of their autosomal precursor.
Introduction and Methods
We report two series of individuals with DDX3X variations, one (48 individuals) from physicians and one (44 individuals) from caregivers.
Results
These two series include several symptoms in common, with fairly similar distribution, which suggests that caregivers' data are close to physicians' data. For example, both series identified early childhood symptoms that were not previously described: feeding difficulties, mean walking age, and age at first words.
Discussion
Each of the two datasets provides complementary knowledge. We confirmed that symptoms are similar to those in the literature and provides more details on feeding difficulties. Caregivers considered that the symptom attention‐deficit/hyperactivity disorder were most worrisome. Both series also reported sleep disturbance. Recently, anxiety has been reported in individuals with DDX3X variants. We strongly suggest that attention‐deficit/hyperactivity disorder, anxiety, and sleep disorders need to be treated.
Loss-of-function of DDX3X is a leading cause of neurodevelopmental disorders (NDD) in females. DDX3X is also a somatically mutated cancer driver gene proposed to have tumour promoting and suppressing effects. We perform saturation genome editing of DDX3X, testing in vitro the functional impact of 12,776 nucleotide variants. We identify 3432 functionally abnormal variants, in three distinct classes. We train a machine learning classifier to identify functionally abnormal variants of NDD-relevance. This classifier has at least 97% sensitivity and 99% specificity to detect variants pathogenic for NDD, substantially out-performing in silico predictors, and resolving up to 93% of variants of uncertain significance. Moreover, functionally-abnormal variants can account for almost all of the excess nonsynonymous DDX3X somatic mutations seen in DDX3X-driven cancers. Systematic maps of variant effects generated in experimentally tractable cell types have the potential to transform clinical interpretation of both germline and somatic disease-associated variation.
Introduction:
We report on a 4-year-old female patient who presented with severe intellectual disability, autistic features, hyperlaxity of joints, and progressive scoliosis. Whole-exome sequencing identified a de novo missense variant (c.976C>T; p.Arg326Cys) in DDX3X.
Case presentation:
The girl was born with congenital diaphragmatic hernia a finding which had not previously been associated with variants in DDX3X. Her brain MRI showed hypogenesis of corpus callosum, ventriculomegaly, frontal and perisylvian polymicrogyria, and hypoplastic pons in addition to Dandy-Walker malformation.
Conclusion:
Our results confirmed the phenotype and genotype correlation of missense variants and the polymicrogyria. Moreover, it further expands the knowledge of the phenotypic and molecular features of DDX3X-related intellectual disability.
Cortical development depends on neuronal migration of both excitatory and inhibitory interneurons. Neuronal migration disorders (NMDs) are conditions characterised by anatomical cortical defects leading to varying degrees of neurocognitive impairment, developmental delay and seizures. Refractory epilepsy affects 15 million people worldwide, and it is thought that cortical developmental disorders are responsible for 25% of childhood cases. However, little is known about the epidemiology of these disorders, nor are their aetiologies fully understood, though many are associated with sporadic genetic mutations.
In this review, we aim to highlight X‐linked NMDs including lissencephaly, periventricular nodular heterotopia and polymicrogyria because of their mostly familial inheritance pattern. We focus on the most prominent genes responsible: including DCX , ARX , FLNA , FMR1 , L1CAM , SRPX2 , DDX3X , NSHDL , CUL4B and OFD1 , outlining what is known about their prevalence among NMDs, and the underlying pathophysiology. X‐linked disorders are important to recognise clinically, as females often have milder phenotypes. Consequently, there is a greater chance they survive to reproductive age and risk passing the mutations down. Effective genetic screening is important to prevent and treat these conditions, and for this, we need to know gene mutations and have a clear understanding of the function of the genes involved. This review summarises the knowledge base and provides clear direction for future work by both scientists and clinicians alike.
RNA molecules rely on proteins across their life cycle. DDX3X encodes an X-linked DEAD-box RNA helicase with a Y-linked paralog, DDX3Y. DDX3X is central to the RNA life cycle and is implicated in many conditions, including cancer and the neurodevelopmental disorder DDX3X syndrome. DDX3X-linked conditions often exhibit sex differences, possibly due to differences between expression or function of the X- and Y-linked paralogs DDX3X and DDX3Y. DDX3X-related diseases have different mutational landscapes, indicating different roles of DDX3X. Understanding the role of DDX3X in normal and disease states will inform the understanding of DDX3X in disease. We review the function of DDX3X and DDX3Y, discuss how mutation type and sex bias contribute to human diseases involving DDX3X, and review possible DDX3X-targeting treatments.
Background: One shortcoming of employing the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP)-recommended five-category variant classification scheme (″pathogenic″, ″likely pathogenic″, ″uncertain significance″, ″likely benign″ and ″benign″) in medical genetics lies in the schemeprime or minutes inherent inability to deal properly with variants that fall midway between ″pathogenic″ and ″benign″. Employing chronic pancreatitis as a disease model, and focusing on the four most studied chronic pancreatitis-related genes, we recently expanded the five-category ACMG/AMP scheme into a seven-category variant classification system. With the addition of two new classificatory categories, ″predisposing″ and ″likely predisposing″, our seven-category system promises to provide improved classification for the entire spectrum of variants in any disease-causing gene. The applicability and practical utility of our seven-category variant classification system however remains to be demonstrated in other disease/gene contexts, and this has been the aim of the current analysis.
Results: We have sought to demonstrate the potential universality of pathological variants that could be ascribed the new variant terminology (′predisposing′) by trialing it across three Mendelian disease contexts (i.e., autosomal dominant, autosomal recessive and X-linked). To this end, we firstly employed illustrative genes/variants characteristic of these three contexts. On the basis of our own knowledge and expertise, we identified a series of variants that fitted well with our ″predisposing″ category, including ″hypomorphic″ variants in the PKD1 gene and ″variants of varying clinical consequence″ in the CFTR gene. These examples, followed by reasonable extrapolations, enabled us to infer the widespread occurrence of ″predisposing″ variants in disease-causing genes. Such ″predisposing″ variants are likely to contribute significantly to the complexity of human genetic disease and may account not only for a considerable proportion of the unexplained cases of monogenic and oligogenic disease but also for much of the ″missing heritability″ characteristic of complex disease.
Conclusion: Employing an evidence-based approach together with reasonable extrapolations, we demonstrate both the applicability and utility of our seven-category variant classification system for disease-causing genes. The recognition of the new ″predisposing″ category not only has immediate implications for variant detection and interpretation but should also have important consequences for reproductive genetic counseling.
DEAD/H-box helicases are implicated in virtually every aspect of RNA metabolism, including transcription, pre-mRNA splicing, ribosomes biogenesis, nuclear export, translation initiation, RNA degradation, and mRNA editing. Most of these helicases are upregulated in various cancers and mutations in some of them are associated with several malignancies. Lately, synthetic lethality (SL) and synthetic dosage lethality (SDL) approaches, where genetic interactions of cancer-related genes are exploited as therapeutic targets, are emerging as a leading area of cancer research. Several DEAD/H-box helicases, including DDX3, DDX9 (Dbp9), DDX10 (Dbp4), DDX11 (ChlR1), and DDX41 (Sacy-1), have been subjected to SL analyses in humans and different model organisms. It remains to be explored whether SDL can be utilized to identity druggable targets in DEAD/H-box helicase overexpressing cancers. In this review, we analyze gene expression data of a subset of DEAD/H-box helicases in multiple cancer types and discuss how their SL/SDL interactions can be used for therapeutic purposes. We also summarize the latest developments in clinical applications, apart from discussing some of the challenges in drug discovery in the context of targeting DEAD/H-box helicases.
Background. Heterozygous pathogenic variants in the DDX3X gene account for 1–3% of females with intellectual and developmental disabilities (IDD). The clinical presentation is variable, including a wide range of neurological and behavioral deficits and structural defects of the brain. Approximately 52% of affected females remain nonverbal after five years of age. Case presentation: We report a 7 year old nonverbal female with a likely novel de novo pathogenic heterozygous variant in the DDX3X gene affecting the non-canonical splice-site in the intron 1 (NM_001356:c.45+12G>A). The patient presents with features typical for the DDX3X phenotype, such as: movement disorders, behavioral problems, a diagnosis of autism spectrum disorder (ASD), and some other features uncommon for DDX3X such as: muscle hypertonia and spinal asymmetry evaluated through the scoliometer. Conclusions. Due to its rare occurrence, the clinical picture of DDX3X syndrome is yet to be fully determined. So far, behavioral disorders, including those from ASD, and neurological abnormalities seem to be the dominant features of this disorder.
Only a few patients with deletions or duplications at Xp11.4, bridging USP9X, DDX3X, and CASK genes, have been described so far. Here, we report on a female harboring a de novo Xp11.4p11.3 deletion and a male with an overlapping duplication inherited from an unaffected mother, presenting with syndromic intellectual disability. We discuss the role of USP9X, DDX3X, and CASK genes in human development and describe the effects of Xp11.4 deletion and duplications in female and male patients, respectively.
Current studies estimate that 1-3% of females with unexplained Intellectual Disability (ID) present de novo splice site, nonsense, frameshift, or missense mutations in the DDX3X protein (DEAD-Box Helicase 3 X-Linked). However, the cellular and molecular mechanisms by which DDX3X mutations impair brain development are not fully comprehended. Here, we show that the ID-linked missense mutation L556S renders DDX3X prone to aggregation. By using a combination of biophysical assays, and imaging approaches, we demonstrate that this mutant assembles solid-like condensates and amyloid-like fibrils. Although we observed greatly reduced expression of the mutant allele in the patient who exhibits skewed X inactivation, this appears to be enough to sequestrate healthy protein into solid-like ectopic granules, compromising cell function. Therefore, our data suggests ID-linked DDX3X L556S mutation as a disorder arising from protein misfolding and aggregation.
ARHGEF9 defects lead to an X‐linked intellectual disability (XLID) disorder related to inhibitory synaptic dysfunction. This condition is more frequent in males with a few affected females reported. Up‐to now, sequence variants and gross deletions have been identified in males, while only chromosomal aberrations have been reported in affected females who showed a skewed pattern of X‐chromosome inactivation (XCI), suggesting an X‐linked recessive (XLR) disorder.
We report three novel loss‐of‐function (LoF) variants in ARHGEF9: a de novo synonymous variant affecting splicing (NM_015185.2: c.1056G>A, p.(Lys352=)) in one female; a nonsense variant in another female (c.865C>T, p.(Arg289*)) that is also present as a somatically mosaic variant in her father, and a de novo nonsense variant in a boy (c.899G>A; p.(Trp300*)). Both females showed a random XCI. Thus, we suggest that missense variants are responsible for an XLR disorder affecting males and that LoF variants, mainly occuring de novo, may be responsible for an X‐Linked dominant (XLD) disorder affecting males and females.
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Background
DDX3X syndrome is a recently identified genetic disorder that accounts for 1-3% of cases of unexplained developmental delay (DD) and/or intellectual disability (ID) in females and is associated with motor and language delays, and autism spectrum disorder (ASD). To date, the published phenotypic characterization of this syndrome has primarily relied on medical record review; in addition, the behavioral dimensions of the syndrome have not been fully explored.
Methods
We carried out multi-day, prospective, detailed phenotyping of DDX3X syndrome in 14 females and 1 male, focusing on behavioral, psychological, and neurological measures; three participants in this cohort have been previously reported. We compared results against population norms and contrasted phenotypes between individuals harboring either (i) protein-truncating variants or (ii) missense variants and in-frame deletions.
Results
Eighty percent of individuals met criteria for ID, 60% for ASD and 53% for attention- deficit/hyperactivity disorder (ADHD). Motor and language delays were common as were sensory processing abnormalities. The cohort included 5 missense, 3 intronic/splice-site, 2 nonsense, 2 frameshift, 2 in-frame deletions, and one initiation codon variant. Genotype-phenotype correlations indicated that missense variants/in-frame deletions were associated with more severe language, motor, and adaptive deficits in comparison to protein-truncating variants.
Limitations
Sample size is modest, however, DDX3X is a rare and underdiagnosed disorder.
Conclusion
This study, representing a first, prospective, detailed characterization of DDX3X syndrome, extends our understanding of the neurobehavioral phenotype. Gold-standard diagnostic approaches demonstrated high rates of ID, ASD, and ADHD. In addition, sensory deficits were observed to be a key part of the syndrome. Even with a modest sample, we observe evidence for genotype-phenotype correlations with missense variants/in-frame deletions yielding a more severe phenotype.
Key Words: autism, developmental delay, genotype-phenotype correlation, intellectual disability, DDX3X syndrome
Cerebral palsy (CP) is a non-progressive disorder of movement and posture due to a static insult to the brain. Some conditions of other disorders can mimic CP, and thus CP needs to be pursued for its underlying cause. In this paper, we reported a novel DDX3X mutation in a girl afflicted with MRX102 which had been confused with CP in her early life. The application of whole exome sequencing may be the best method to distinguish between actual CP and other disorders with similar characteristics. A thorough and conscientious review is suggested during the diagnostic progress.
De novo variants in DDX3X account for 1–3% of unexplained intellectual disability (ID) cases and are amongst the most common causes of ID especially in females. Forty‐seven patients (44 females, 3 males) have been described. We identified 31 additional individuals carrying 29 unique DDX3X variants, including 30 postnatal individuals with complex clinical presentations of developmental delay or ID, and one fetus with abnormal ultrasound findings. Rare or novel phenotypes observed include respiratory problems, congenital heart disease, skeletal muscle mitochondrial DNA depletion, and late‐onset neurologic decline. Our findings expand the spectrum of DNA variants and phenotypes associated with DDX3X disorders.
Background:
Intellectual disability (ID) is a common condition with a population prevalence frequency of 1-3% and an enrichment for males, driven in part by the contribution of mutant alleles on the X-chromosome. Among the more than 500 genes associated with ID, DDX3X represents an outlier in sex specificity. Nearly all reported pathogenic variants of DDX3X are de novo, affect mostly females, and appear to be loss of function variants, consistent with the hypothesis that haploinsufficiency at this locus on the X-chromosome is likely to be lethal in males.
Results:
We evaluated two male siblings with syndromic features characterized by mild-to-moderate ID and progressive spasticity. Quad-based whole-exome sequencing revealed a maternally inherited missense variant encoding p.R79K in DDX3X in both siblings and no other apparent pathogenic variants. We assessed its possible relevance to their phenotype using an established functional assay for DDX3X activity in zebrafish embryos and found that this allele causes a partial loss of DDX3X function and thus represents a hypomorphic variant.
Conclusions:
Our genetic and functional data suggest that partial loss of function of DDX3X can cause syndromic ID. The p.R79K allele affects a region of the protein outside the critical RNA helicase domain, offering a credible explanation for the observed retention of partial function, viability in hemizygous males, and lack of pathology in females. These findings expand the gender spectrum of pathology of this locus and suggest that analysis for DDX3X variants should be considered relevant for both males and females.
Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.
An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools’ predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. To enable comprehensive evaluation of variants, the predictions are complemented with annotations from eight databases. The web server is freely available to the community at http://loschmidt.chemi.muni.cz/predictsnp2.
DDX3X is a DEAD-box RNA helicase that has been implicated in multiple aspects of RNA metabolism including translation initiation and the assembly of stress granules (SGs). Recent genomic studies have reported recurrent DDX3X mutations in numerous tumors including medulloblastoma (MB), but the physiological impact of these mutations is poorly understood. Here we show that a consistent feature of MB-associated mutations is SG hyper-assembly and concomitant translation impairment. We used CLIP-seq to obtain a comprehensive assessment of DDX3X binding targets and ribosome profiling for high-resolution assessment of global translation. Surprisingly, mutant DDX3X expression caused broad inhibition of translation that impacted DDX3X targeted and non-targeted mRNAs alike. Assessment of translation efficiency with single-cell resolution revealed that SG hyper-assembly correlated precisely with impaired global translation. SG hyper-assembly and translation impairment driven by mutant DDX3X were rescued by a genetic approach that limited SG assembly and by deletion of the N-terminal low complexity domain within DDX3X. Thus, in addition to a primary defect at the level of translation initiation caused by DDX3X mutation, SG assembly itself contributes to global translation inhibition. This work provides mechanistic insights into the consequences of cancer-related DDX3X mutations, suggesting that globally reduced translation may provide a context-dependent survival advantage that must be considered as a possible contributor to tumorigenesis.
Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders.
Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational
spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile
consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition
to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations
in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability
of large-scale sequencing to reveal fundamental tumorigenic mechanisms.
Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.
Medulloblastomas are the most common malignant brain tumours in children. Identifying and understanding the genetic events that drive these tumours is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma on the basis of transcriptional and copy number profiles. Here we use whole-exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas have low mutation rates consistent with other paediatric tumours, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were newly identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR and LDB1. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant, but not wild-type, β-catenin. Together, our study reveals the alteration of WNT, hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic β-catenin signalling in medulloblastoma.
Medulloblastoma is a malignant childhood brain tumour comprising four discrete subgroups. Here, to identify mutations that drive medulloblastoma, we sequenced the entire genomes of 37 tumours and matched normal blood. One-hundred and thirty-six genes harbouring somatic mutations in this discovery set were sequenced in an additional 56 medulloblastomas. Recurrent mutations were detected in 41 genes not yet implicated in medulloblastoma; several target distinct components of the epigenetic machinery in different disease subgroups, such as regulators of H3K27 and H3K4 trimethylation in subgroups 3 and 4 (for example, KDM6A and ZMYM3), and CTNNB1-associated chromatin re-modellers in WNT-subgroup tumours (for example, SMARCA4 and CREBBP). Modelling of mutations in mouse lower rhombic lip progenitors that generate WNT-subgroup tumours identified genes that maintain this cell lineage (DDX3X), as well as mutated genes that initiate (CDH1) or cooperate (PIK3CA) in tumorigenesis. These data provide important new insights into the pathogenesis of medulloblastoma subgroups and highlight targets for therapeutic development.
Recently, de novo heterozygous variants in DDX3X have been reported in about 1.5% of 2659 females with previously unexplained intellectual disability (ID). We report on the identification of DDX3X variants in two unrelated girls with clinical features of Toriello-Carey Syndrome (T-CS). In patient 1, the recurrent variant c.1703C>T; p.(P568L) was identified when reconsidering X-linked de novo heterozygous variants in exome sequencing data. In patient 2, the DDX3X variant c.1600C>G; p.(R534G) was also detected by exome sequencing. Based on these data, de novo heterozygous DDX3X variants should be considered not only in females with unexplained ID, but also in individuals with a clinical diagnosis of T-CS.
The X-linked DEAD-box RNA helicase DDX3 (DDX3X) is a multifunctional protein that has been implicated in gene regulation,
cell cycle control, apoptosis, and tumorigenesis. However, the precise physiological function of Ddx3x during development remains unknown. Here, we show that loss of Ddx3x results in an early post-implantation lethality in male mice. The size of the epiblast marked by Oct3/4 is dramatically reduced
in embryonic day 6.5 (E6.5) Ddx3x−/Y embryos. Preferential paternal X chromosome inactivation (XCI) in extraembryonic tissues of Ddx3x heterozygous (Ddx3x−/+) female mice with a maternally inherited null allele leads to placental abnormalities and embryonic lethality during development.
In the embryonic tissues, Ddx3x exhibits developmental- and tissue-specific differences in escape from XCI. Targeted Ddx3x ablation in the epiblast leads to widespread apoptosis and abnormal growth, which causes embryonic lethality in the Sox2-cre/+;Ddx3xflox/Y mutant around E11.5. The observation of significant increases in γH2AX and p-p53Ser15 indicates DNA damage, which suggests that loss of Ddx3x leads to higher levels of genome damage. Significant upregulation of p21WAF1/Cip1 and p15Ink4b results in cell cycle arrest and apoptosis in Ddx3x-deficient cells. These results have uncovered that mouse Ddx3x is essential for both embryo and extraembryonic development.
Intellectual disability (ID) affects approximately 1%–3% of humans with a gender bias toward males. Previous studies have identified mutations in more than 100 genes on the X chromosome in males with ID, but there is less evidence for de novo mutations on the X chromosome causing ID in females. In this study we present 35 unique deleterious de novo mutations in DDX3X identified by whole exome sequencing in 38 females with ID and various other features including hypotonia, movement disorders, behavior problems, corpus callosum hypoplasia, and epilepsy. Based on our findings, mutations in DDX3X are one of the more common causes of ID, accounting for 1%–3% of unexplained ID in females. Although no de novo DDX3X mutations were identified in males, we present three families with segregating missense mutations in DDX3X, suggestive of an X-linked recessive inheritance pattern. In these families, all males with the DDX3X variant had ID, whereas carrier females were unaffected. To explore the pathogenic mechanisms accounting for the differences in disease transmission and phenotype between affected females and affected males with DDX3X missense variants, we used canonical Wnt defects in zebrafish as a surrogate measure of DDX3X function in vivo. We demonstrate a consistent loss-of-function effect of all tested de novo mutations on the Wnt pathway, and we further show a differential effect by gender. The differential activity possibly reflects a dose-dependent effect of DDX3X expression in the context of functional mosaic females versus one-copy males, which reflects the complex biological nature of DDX3X mutations.
Natural killer/T-cell lymphoma (NKTCL) is a malignant proliferation of CD56(+) and cytoCD3(+) lymphocytes with aggressive clinical course, which is prevalent in Asian and South American populations. The molecular pathogenesis of NKTCL has largely remained elusive. We identified somatic gene mutations in 25 people with NKTCL by whole-exome sequencing and confirmed them in an extended validation group of 80 people by targeted sequencing. Recurrent mutations were most frequently located in the RNA helicase gene DDX3X (21/105 subjects, 20.0%), tumor suppressors (TP53 and MGA), JAK-STAT-pathway molecules (STAT3 and STAT5B) and epigenetic modifiers (MLL2, ARID1A, EP300 and ASXL3). As compared to wild-type protein, DDX3X mutants exhibited decreased RNA-unwinding activity, loss of suppressive effects on cell-cycle progression in NK cells and transcriptional activation of NF-κB and MAPK pathways. Clinically, patients with DDX3X mutations presented a poor prognosis. Our work thus contributes to the understanding of the disease mechanism of NKTCL.
Intellectual disability is an extremely stigmatizing condition and involves utilization of large public health resources, but most data about its burden is based on studies conducted in developed countries. The aim of this meta-analysis was to collate data from published literature and estimate the prevalence of intellectual disability across all such studies. The review includes studies published between 1980 and 2009, and includes data from populations that provided an overall estimate of the prevalence of intellectual disability. Meta-analysis was done using random effects to account for heterogeneity. Sub-group analyses were also done. The prevalence of intellectual disability across all 52 studies included in the meta-analysis was 10.37/1000 population. The estimates varied according to income group of the country of origin, the age-group of the study population, and study design. The highest rates were seen in countries from low- and middle income countries. Studies based on identification of cases by using psychological assessments or scales showed higher prevalence compared to those using standard diagnostic systems and disability instruments. Prevalence was higher among studies based on children/adolescents, compared to those on adults. Higher prevalence in low and middle income group countries is of concern given the limitations in available resources in such countries to manage intellectual disability. The importance of using standardized diagnostic systems to correctly estimate the burden is underlined. The public health and research implications of this meta-analysis have been discussed.
Many patients suffering from developmental disorders harbor submicroscopic deletions or duplications that, by affecting the copy number of dosage-sensitive genes or disrupting normal gene expression, lead to disease. However, many aberrations are novel or extremely rare, making clinical interpretation problematic and genotype-phenotype correlations uncertain. Identification of patients sharing a genomic rearrangement and having phenotypic features in common leads to greater certainty in the pathogenic nature of the rearrangement and enables new syndromes to be defined. To facilitate the analysis of these rare events, we have developed an interactive web-based database called DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. DECIPHER catalogs common copy-number changes in normal populations and thus, by exclusion, enables changes that are novel and potentially pathogenic to be identified. DECIPHER enhances genetic counseling by retrieving relevant information from a variety of bioinformatics resources. Known and predicted genes within an aberration are listed in the DECIPHER patient report, and genes of recognized clinical importance are highlighted and prioritized. DECIPHER enables clinical scientists worldwide to maintain records of phenotype and chromosome rearrangement for their patients and, with informed consent, share this information with the wider clinical research community through display in the genome browser Ensembl. By sharing cases worldwide, clusters of rare cases having phenotype and structural rearrangement in common can be identified, leading to the delineation of new syndromes and furthering understanding of gene function.
RNA helicases are highly conserved enzymes that utilize the energy derived from NTP hydrolysis to modulate the structure of RNA. RNA helicases participate in all biological processes that involve RNA, including transcription, splicing and translation. Based on the sequence of the helicase domain, they are classified into families, such as DDX and DHX families of human RNA helicases. The specificity of RNA helicases to their targets is likely due to several factors, such as the sequence, interacting molecules, subcellular localization and the expression pattern of the helicases. There are several examples of the involvement of RNA helicases in differentiation. Human DDX3 has two closely related genes designated DDX3Y and DDX3X, which are localized to the Y and X chromosomes, respectively. DDX3Y protein is specifically expressed in germ cells and is essential for spermatogenesis. DDX25 is another RNA helicase which has been shown to be required for spermatogenesis. DDX4 shows specific expression in germ cells. The Drosophila ortholog of DDX4, known as vasa, is required for the formation of germ cells and oogenesis by a mechanism that involves regulating the translation of mRNAs essential for differentiation. Abstrakt is the Drosphila ortholog of DDX41, which has been shown to be involved in visual and CNS system development. DDX5 (p68) and its related DDX17 (p72) have also been implicated in organ/tissue differentiation. The ability of RNA helicases to modulate the structure and thus availability of critical RNA molecules for processing leading to protein expression is the likely mechanism by which RNA helicases contribute to differentiation.
) are not shown here. These include c.284 + 1G > A and c.865-1G > A (both in females), and the hemizygous c.443 + 3A > T variant in a male [Color figure can be viewed at wileyonlinelibrary.com] natural killer/T-cell lymphoma
- Firth
The DDX3X protein, adapted from DECIPHER (Firth et al., 2009), with the location of the unique amino acid substitutions from
published cohorts (Dikow et al., 2017; Kellaris et al., 2018; Snijders Blok et al., 2015; Wang et al., 2018). The three male patients described here
are underlined in red while mutations affecting the same amino acid are shown in blue. The three splice site variants identified by Wang et al.
(2018) are not shown here. These include c.284 + 1G > A and c.865-1G > A (both in females), and the hemizygous c.443 + 3A > T variant in
a male [Color figure can be viewed at wileyonlinelibrary.com]
natural killer/T-cell lymphoma. Nature Genetics, 47(9), 1061-1066.
https://doi.org/10.1038/ng.3358
Large-scale discovery of novel genetic causes of developmental disorders
- Deciphering Developmental Disorders Study