Identification of de novo EP300 and PLAU variants in a patient with Rubinstein–Taybi syndrome-related arterial vasculopathy and skeletal anomaly

AbstractRubinstein–Taybi syndrome (RSTS) is a human genetic disorder characterized by distinctive craniofacial features, broad thumbs and halluces, and intellectual disability. Mutations in the CREB binding protein (CREBBP) and E1A binding protein p300 (EP300) are the known causes of RSTS disease. EP300 regulates transcription via chromatin remodeling and plays an important role in cell proliferation and differentiation. Plasminogen activator, urokinase (PLAU) encodes a serine protease that converts plasminogen to plasmin and is involved in several biological processes such as the proteolysis of extracellular matrix-remodeling proteins and the promotion of vascular permeability and angiogenesis. Recently, we discovered a patient who presented with RSTS-related skeletal anomaly and peripheral arterial vasculopathy. To investigate the genetic cause of the disease, we performed trio whole genome sequencing of the genomic DNA from the proband and the proband’s parents. We identified two de novo variants coined c.1760T>G (p.Leu587Arg) and c.664G>A (p.Ala222Thr) in EP300 and PLAU, respectively. Furthermore, functional loss of EP300a and PLAUb in zebrafish synergistically affected the intersegmental vessel formation and resulted in the vascular occlusion phenotype. Therefore, we hypothesize that the de novo EP300 variant may have caused RSTS, while both the identified EP300 and PLAU variants may have contributed to the patient’s vascular phenotype.

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O-GlcNAc: Regulator of Signaling and Epigenetics Linked to X-linked Intellectual Disability

Frontiers in Genetics ◽

10.3389/fgene.2020.605263 ◽

2020 ◽

Vol 11 ◽

Author(s):

Daniel Konzman ◽

Lara K. Abramowitz ◽

Agata Steenackers ◽

Mana Mohan Mukherjee ◽

Hyun-Jin Na ◽

...

Keyword(s):

Intellectual Disability ◽

Parental Stress ◽

De Novo ◽

Genetic Disorder ◽

Nutrient Sensing ◽

Model Organisms ◽

Transcriptional Networks ◽

Hexosamine Biosynthetic Pathway ◽

Human Genetic Disorder ◽

Glcnac Transferase

Cellular identity in multicellular organisms is maintained by characteristic transcriptional networks, nutrient consumption, energy production and metabolite utilization. Integrating these cell-specific programs are epigenetic modifiers, whose activity is often dependent on nutrients and their metabolites to function as substrates and co-factors. Emerging data has highlighted the role of the nutrient-sensing enzyme O-GlcNAc transferase (OGT) as an epigenetic modifier essential in coordinating cellular transcriptional programs and metabolic homeostasis. OGT utilizes the end-product of the hexosamine biosynthetic pathway to modify proteins with O-linked β-D-N-acetylglucosamine (O-GlcNAc). The levels of the modification are held in check by the O-GlcNAcase (OGA). Studies from model organisms and human disease underscore the conserved function these two enzymes of O-GlcNAc cycling play in transcriptional regulation, cellular plasticity and mitochondrial reprogramming. Here, we review these findings and present an integrated view of how O-GlcNAc cycling may contribute to cellular memory and transgenerational inheritance of responses to parental stress. We focus on a rare human genetic disorder where mutant forms of OGT are inherited or acquired de novo. Ongoing analysis of this disorder, OGT- X-linked intellectual disability (OGT-XLID), provides a window into how epigenetic factors linked to O-GlcNAc cycling may influence neurodevelopment.

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Introduction of a de novo Creb-binding protein gene mutation in sperm to produce a Rubinstein-Taybi syndrome model using inbred C57BL/6 mice

Brain Research ◽

10.1016/j.brainres.2020.147140 ◽

2020 ◽

Vol 1749 ◽

pp. 147140

Author(s):

Tsuyoshi Takagi ◽

Yujiro Higashi ◽

Masato Asai ◽

Shunsuke Ishii

Keyword(s):

Gene Mutation ◽

Protein Gene ◽

De Novo ◽

Binding Protein ◽

Creb Binding Protein ◽

Binding Protein Gene

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A complex of distal appendage–associated kinases linked to human disease regulates ciliary trafficking and stability

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2018740118 ◽

2021 ◽

Vol 118 (16) ◽

pp. e2018740118

Author(s):

Abdelhalim Loukil ◽

Chloe Barrington ◽

Sarah C. Goetz

Keyword(s):

Human Disease ◽

Cellular Response ◽

De Novo ◽

Genetic Disorder ◽

Structural Defects ◽

De Novo Mutations ◽

Superresolution Microscopy ◽

Mother Centriole ◽

Multistep Process ◽

Human Genetic Disorder

Cilia biogenesis is a complex, multistep process involving the coordination of multiple cellular trafficking pathways. Despite the importance of ciliogenesis in mediating the cellular response to cues from the microenvironment, we have only a limited understanding of the regulation of cilium assembly. We previously identified Tau tubulin kinase 2 (TTBK2) as a key regulator of ciliogenesis. Here, using CRISPR kinome and biotin identification screening, we identify the CK2 catalytic subunit CSNK2A1 as an important modulator of TTBK2 function in cilia trafficking. Superresolution microscopy reveals that CSNK2A1 is a centrosomal protein concentrated at the mother centriole and associated with the distal appendages. Csnk2a1 mutant cilia are longer than those of control cells, showing instability at the tip associated with ciliary actin cytoskeleton changes. These cilia also abnormally accumulate key cilia assembly and SHH-related proteins. De novo mutations of Csnk2a1 were recently linked to the human genetic disorder Okur-Chung neurodevelopmental syndrome (OCNDS). Consistent with the role of CSNK2A1 in cilium stability, we find that expression of OCNDS-associated Csnk2a1 variants in wild-type cells causes ciliary structural defects. Our findings provide insights into mechanisms involved in ciliary length regulation, trafficking, and stability that in turn shed light on the significance of cilia instability in human disease.

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A complex of distal appendage-associated kinases linked to human disease regulates ciliary trafficking and stability

10.1101/2020.08.21.261560 ◽

2020 ◽

Author(s):

Abdelhalim Loukil ◽

Chloe Barrington ◽

Sarah C. Goetz

Keyword(s):

Human Disease ◽

Cellular Response ◽

Primary Cilia ◽

De Novo ◽

Genetic Disorder ◽

Neurodevelopmental Disorder ◽

Super Resolution ◽

Structural Defects ◽

Mother Centriole ◽

Human Genetic Disorder

ABSTRACTCilia biogenesis is a complex, multi-step process involving the coordination of multiple cellular trafficking pathways. Despite the importance of ciliogenesis in mediating the cellular response to cues from the microenvironment, we have only a limited understanding of the regulation of cilium assembly. We previously identified a kinase that acts as a key regulator of ciliogenesis, TTBK2. Here, using CRISPR kinome screening, we identify the CK2 subunit CSNK2A1 as an important modulator of TTBK2 function in cilia trafficking. Super-resolution microscopy reveals that CSNK2A1 is a centrosomal protein concentrated at the mother centriole and associated with the distal appendages where it physically interacts with TTBK2. Further, Csnk2a1 knockout partially corrects defects in cilia formation and length in Ttbk2 hypomorphic cells. Csnk2a1 mutant cilia are longer than those of control cells and exhibit instability, particularly at the tip. Csnk2a1 mutant cilia also abnormally accumulate key cilia assembly and SHH-related proteins including IFT, GLI2, KIF7, and Smoothened (SMO). De novo mutations of Csnk2a1 were recently linked to the human genetic disorder Okur-Chung neurodevelopmental syndrome (OCNDS). Consistent with the role of CSNK2A1 in cilium stability, we find that expression of OCNDS-associated Csnk2a1 variants in wild-type cells cause ciliary structural defects. Our findings provide new insights into mechanisms involved in ciliary length regulation, trafficking, and stability that in turn shed light on the significance and implications of cilia instability in human disease.SIGNIFICANCE STATEMENTPrimary cilia (PC) are sensory organelles that play essential roles during development and adulthood. Abnormal functioning of PC causes human disorders called ciliopathies. Hence, a thorough understanding of the molecular regulation of PC is critical. Our findings highlight CSNK2A1 as a novel modulator of cilia trafficking and stability, tightly related to TTBK2 function. Enriched at the centrosome, CSNK2A1 prevents abnormal accumulation of key ciliary proteins, instability at the tip, and aberrant activation of the Sonic Hedgehog pathway. Further, we establish that Csnk2a1 mutations associated with Okur-Chung neurodevelopmental disorder (OCNDS) alter cilia morphology. Thus, we report a potential linkage between CSNK2A1 ciliary function and OCNDS.

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Regulation of the Mutually Exclusive Exons 8a and 8 in the CaV1.2 Calcium Channel Transcript by Polypyrimidine Tract-binding Protein

Journal of Biological Chemistry ◽

10.1074/jbc.m110.208116 ◽

2011 ◽

Vol 286 (12) ◽

pp. 10007-10016 ◽

Cited By ~ 49

Author(s):

Zhen Zhi Tang ◽

Shalini Sharma ◽

Sika Zheng ◽

Geetanjali Chawla ◽

Julia Nikolic ◽

...

Keyword(s):

Neuronal Development ◽

Binding Protein ◽

Genetic Disorder ◽

Specific Pattern ◽

Polypyrimidine Tract ◽

Embryonic Mouse ◽

Polypyrimidine Tract Binding ◽

Splicing Regulators ◽

Polypyrimidine Tract Binding Protein ◽

Human Genetic Disorder

CaV1.2 calcium channels play roles in diverse cellular processes such as gene regulation, muscle contraction, and membrane excitation and are diversified in their activity through extensive alternative splicing of the CaV1.2 mRNA. The mutually exclusive exons 8a and 8 encode alternate forms of transmembrane segment 6 (IS6) in channel domain 1. The human genetic disorder Timothy syndrome is caused by mutations in either of these two CaV1.2 exons, resulting in disrupted Ca2+ homeostasis and severe pleiotropic disease phenotypes. The tissue-specific pattern of exon 8/8a splicing leads to differences in symptoms between patients with exon 8 or 8a mutations. Elucidating the mechanisms controlling the exon 8/8a splicing choice will be important in understanding the spectrum of defects associated with the disease. We found that the polypyrimidine tract-binding protein (PTB) mediates a switch from exon 8 to 8a splicing. PTB and its neuronal homolog, nPTB, are widely studied splicing regulators controlling large sets of alternative exons. During neuronal development, PTB expression is down-regulated with a concurrent increase in nPTB expression. Exon 8a is largely repressed in embryonic mouse brain but is progressively induced during neuronal differentiation as PTB is depleted. This splicing repression is mediated by the direct binding of PTB to sequence elements upstream of exon 8a. The nPTB protein is a weaker repressor of exon 8a, resulting in a shift in exon choice when nPTB replaces PTB in cells. These results provide mechanistic understanding of how these two exons, important for human disease, are controlled.

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