Brain Tissue Low-Level Mosaicism for MTOR Mutation Causes Smith–Kingsmore Phenotype with Recurrent Hypoglycemia—A Novel Phenotype and a Further Proof for Testing of an Affected Tissue

De novo somatic variants in genes encoding components of the PI3K–AKT3–mTOR pathway, including MTOR, have been linked to hemimegalencephaly or focal cortical dysplasia. Similarly to other malformations of cortical development, this condition presents with developmental delay and intractable epilepsy, often necessitating surgical treatment. We describe a first patient with the Smith–Kingsmore syndrome phenotype with recurrent hypoglycemia caused by low-level mosaic MTOR mutation restricted to the brain. We provide discussion on different aspects of somatic mosaicism. Deep exome sequencing combined with a variant search in multiple tissues and careful phenotyping may constitute a key to the diagnosis of the causes of rare brain anomalies.

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Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset

Human Genomics ◽

10.1186/s40246-021-00369-6 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Daniel D. Domogala ◽

Tomasz Gambin ◽

Roni Zemet ◽

Chung Wah Wu ◽

Katharina V. Schulze ◽

...

Keyword(s):

Exome Sequencing ◽

Peripheral Blood ◽

De Novo ◽

Somatic Mosaicism ◽

Hair Follicles ◽

Clinical Diagnostics ◽

Diagnostic Methods ◽

Single Nucleotide Variants ◽

Bioinformatics Pipeline ◽

Low Level

Abstract Background Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) < 10% is often undetected in clinical settings. To date, only a few studies have attempted to analyze tissue distribution of low-level parental mosaicism in a large clinical exome sequencing (ES) cohort. Methods Using a customized bioinformatics pipeline, we analyzed apparent de novo single-nucleotide variants or indels identified in the affected probands in ES trio data at Baylor Genetics clinical laboratories. Clinically relevant variants with VAFs between 30 and 70% in probands and lower than 10% in one parent were studied. DNA samples extracted from saliva, buccal cells, redrawn peripheral blood, urine, hair follicles, and nail, representing all three germ layers, were tested using PCR amplicon next-generation sequencing (amplicon NGS) and droplet digital PCR (ddPCR). Results In a cohort of 592 clinical ES trios, we found 61 trios, each with one parent suspected of low-level mosaicism. In 21 parents, the variants were validated using amplicon NGS and seven of them by ddPCR in peripheral blood DNA samples. The parental VAFs in blood samples varied between 0.08 and 9%. The distribution of VAFs in additional tissues ranged from 0.03% in hair follicles to 9% in re-drawn peripheral blood. Conclusions Our study illustrates the importance of analyzing ES data using sensitive computational and molecular methods for low-level parental somatic mosaicism for clinically relevant variants previously diagnosed in routine clinical diagnostics as apparent de novo.

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Detection of Low-Level Parental Somatic Mosaicism for Clinically Relevant Snvs and Indels Identified in a Large Exome Sequencing Dataset

10.21203/rs.3.rs-1020672/v1 ◽

2021 ◽

Author(s):

Daniel David Domogala ◽

Tomasz Gambin ◽

Roni Zemet ◽

Chung Wah Wu ◽

Katharina Schulze ◽

...

Keyword(s):

Exome Sequencing ◽

Peripheral Blood ◽

De Novo ◽

Somatic Mosaicism ◽

Hair Follicles ◽

Clinical Diagnostics ◽

Diagnostic Methods ◽

Single Nucleotide Variants ◽

Bioinformatics Pipeline ◽

Low Level

Abstract Background Due to the limitations of the current routine diagnostic methods, low-level somatic mosaicism with variant allele fraction (VAF) <10% is often undetected in clinical settings. To date, only a few studies have attempted to analyze tissue distribution of low-level parental mosaicism in a large clinical exome sequencing (ES) cohort. Methods Using a customized bioinformatics pipeline, we have analyzed apparent de novo single nucleotide variants or indels identified in the affected probands in ES trio data at Baylor Genetics clinical laboratories. Clinically relevant variants with VAFs between 30-70% in probands and lower than 10% in one parent were studied. DNA samples extracted from saliva, buccal cells, redrawn peripheral blood, urine, hair follicles, and nail, representing all three germ layers, were tested using PCR amplicon next generation sequencing (amplicon NGS) and droplet digital PCR (ddPCR). Results In a cohort of 592 clinical ES trios, we have found 61 trios, each with one parent suspected of low-level mosaicism. In 21 parents, the variants were validated using amplicon NGS and seven of them by ddPCR in peripheral blood DNA samples. The parental VAFs in blood samples varied between 0.08–9%. The distribution of VAFs in additional tissues ranged from 0.03% in hair follicles to 9% in re-drawn peripheral blood. Conclusions Our study illustrates the importance of analyzing ES data using sensitive computational and molecular methods for low-level parental somatic mosaicism for clinically relevant variants previously diagnosed in routine clinical diagnostics as apparent de novo.

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Somatic double-hit in MTOR and RPS6 in hemimegalencephaly with intractable epilepsy

Human Molecular Genetics ◽

10.1093/hmg/ddz194 ◽

2019 ◽

Vol 28 (22) ◽

pp. 3755-3765 ◽

Cited By ~ 8

Author(s):

Cristiana Pelorosso ◽

Françoise Watrin ◽

Valerio Conti ◽

Emmanuelle Buhler ◽

Antoinette Gelot ◽

...

Keyword(s):

Brain Tissue ◽

Focal Cortical Dysplasia ◽

Mammalian Target Of Rapamycin ◽

Somatic Mosaicism ◽

Intractable Epilepsy ◽

Cortical Dysplasia ◽

Mtor Pathway ◽

Activating Mutations ◽

Severe Intellectual Disability ◽

Double Hit

Abstract Single germline or somatic activating mutations of mammalian target of rapamycin (mTOR) pathway genes are emerging as a major cause of type II focal cortical dysplasia (FCD), hemimegalencephaly (HME) and tuberous sclerosis complex (TSC). A double-hit mechanism, based on a primary germline mutation in one allele and a secondary somatic hit affecting the other allele of the same gene in a small number of cells, has been documented in some patients with TSC or FCD. In a patient with HME, severe intellectual disability, intractable seizures and hypochromic skin patches, we identified the ribosomal protein S6 (RPS6) p.R232H variant, present as somatic mosaicism at ~15.1% in dysplastic brain tissue and ~11% in blood, and the MTOR p.S2215F variant, detected as ~8.8% mosaicism in brain tissue, but not in blood. Overexpressing the two variants independently in animal models, we demonstrated that MTOR p.S2215F caused neuronal migration delay and cytomegaly, while RPS6 p.R232H prompted increased cell proliferation. Double mutants exhibited a more severe phenotype, with increased proliferation and migration defects at embryonic stage and, at postnatal stage, cytomegalic cells exhibiting eccentric nuclei and binucleation, which are typical features of balloon cells. These findings suggest a synergistic effect of the two variants. This study indicates that, in addition to single activating mutations and double-hit inactivating mutations in mTOR pathway genes, severe forms of cortical dysplasia can also result from activating mutations affecting different genes in this pathway. RPS6 is a potential novel disease-related gene.

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Utility of depth electrode placement in the neurosurgical management of bottom-of-sulcus lesions: technical note

Journal of Neurosurgery Pediatrics ◽

10.3171/2019.4.peds18639 ◽

2019 ◽

Vol 24 (3) ◽

pp. 284-292

Author(s):

Eisha A. Christian ◽

Elysa Widjaja ◽

Ayako Ochi ◽

Hiroshi Otsubo ◽

Stephanie Holowka ◽

...

Keyword(s):

Pediatric Patients ◽

Focal Cortical Dysplasia ◽

Target Identification ◽

Cortical Dysplasia ◽

Technical Note ◽

Electrode Placement ◽

Electrode Implantation ◽

Depth Electrodes ◽

Intracranial Electrode ◽

The Brain

OBJECTIVESmall lesions at the depth of the sulcus, such as with bottom-of-sulcus focal cortical dysplasia, are not visible from the surface of the brain and can therefore be technically challenging to resect. In this technical note, the authors describe their method of using depth electrodes as landmarks for the subsequent resection of these exacting lesions.METHODSA retrospective review was performed on pediatric patients who had undergone invasive electroencephalography with depth electrodes that were subsequently used as guides for resection in the period between July 2015 and June 2017.RESULTSTen patients (3–15 years old) met the criteria for this study. At the same time as invasive subdural grid and/or strip insertion, between 2 and 4 depth electrodes were placed using a hand-held frameless neuronavigation technique. Of the total 28 depth electrodes inserted, all were found within the targeted locations on postoperative imaging. There was 1 patient in whom an asymptomatic subarachnoid hemorrhage was demonstrated on postprocedural imaging. Depth electrodes aided in target identification in all 10 cases.CONCLUSIONSDepth electrodes placed at the time of invasive intracranial electrode implantation can be used to help localize, target, and resect primary zones of epileptogenesis caused by bottom-of-sulcus lesions.

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Aquaporin-1 and aquaporin-9 gene variations in sudden infant death syndrome

International Journal of Legal Medicine ◽

10.1007/s00414-020-02493-9 ◽

2021 ◽

Author(s):

Siri Hauge Opdal ◽

Linda Ferrante ◽

Torleiv Ole Rognum ◽

Arne Stray-Pedersen

Keyword(s):

Sudden Infant Death Syndrome ◽

Infant Death ◽

Brain Function ◽

Sudden Infant Death ◽

Sudden Infant ◽

Unexpected Death ◽

Aquaporin 9 ◽

Genes Encoding ◽

External Risk ◽

The Brain

AbstractSeveral studies have indicated that a vulnerability in the development and regulation of brain function is involved in sudden infant death syndrome (SIDS). The aim of this study was to investigate the genes encoding the brain aquaporins (AQPs) AQP1 and AQP9 in SIDS. The hypothesis was that specific variants of these genes are part of the genetic vulnerability predisposing infants to sudden unexpected death. The study included 168 SIDS cases with a median age of 15.5 (range 2–52) weeks and 372 adolescent/adult deceased controls with a median age of 44 (range 11–91) years. In the AQP1 gene, the rs17159702 CC/CT genotypes were found to be associated with SIDS (p = 0.02). In the AQP9 gene, the combination of a TT genotype of rs8042354, rs2292711 and rs13329178 was more frequent in SIDS cases than in controls (p = 0.03). In the SIDS group, an association was found between genetic variations in the AQP1 gene and maternal smoking and between the 3xTT combination in the AQP9 gene and being found lifeless in a prone position. In conclusion, this study adds further evidence to the involvement of brain aquaporins in SIDS, suggesting that specific variants of AQP genes constitute a genetic predisposition, making the infant vulnerable to sudden death together with external risk factors and probably other genetic factors.

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De novo TRPV4 Leu619Pro variant causes a new channelopathy characterised by giant cell lesions of the jaws and skull, skeletal abnormalities and polyneuropathy

Journal of Medical Genetics ◽

10.1136/jmedgenet-2020-107427 ◽

2021 ◽

pp. jmedgenet-2020-107427

Author(s):

Aviel Ragamin ◽

Carolina C Gomes ◽

Karen Bindels-de Heus ◽

Renata Sandoval ◽

Angelia V Bassenden ◽

...

Keyword(s):

Giant Cell ◽

De Novo ◽

Neuromuscular Disorders ◽

Somatic Mosaicism ◽

Ion Leakage ◽

Gain Of Function ◽

Therapeutic Modalities ◽

Organ Systems ◽

Heterozygous Variant ◽

Systemic Disorder

BackgroundPathogenic germline variants in Transient Receptor Potential Vanilloid 4 Cation Channel (TRPV4) lead to channelopathies, which are phenotypically diverse and heterogeneous disorders grossly divided in neuromuscular disorders and skeletal dysplasia. We recently reported in sporadic giant cell lesions of the jaws (GCLJs) novel, somatic, heterozygous, gain-of-function mutations in TRPV4, at Met713.MethodsHere we report two unrelated women with a de novo germline p.Leu619Pro TRPV4 variant and an overlapping systemic disorder affecting all organs individually described in TRPV4 channelopathies.ResultsFrom an early age, both patients had several lesions of the nervous system including progressive polyneuropathy, and multiple aggressive giant cell-rich lesions of the jaws and craniofacial/skull bones, and other skeletal lesions. One patient had a relatively milder disease phenotype possibly due to postzygotic somatic mosaicism. Indeed, the TRPV4 p.Leu619Pro variant was present at a lower frequency (variant allele frequency (VAF)=21.6%) than expected for a heterozygous variant as seen in the other proband, and showed variable regional frequency in the GCLJ (VAF ranging from 42% to 10%). In silico structural analysis suggests that the gain-of-function p.Leu619Pro alters the ion channel activity leading to constitutive ion leakage.ConclusionOur findings define a novel polysystemic syndrome due to germline TRPV4 p.Leu619Pro and further extend the spectrum of TRPV4 channelopathies. They further highlight the convergence of TRPV4 mutations on different organ systems leading to complex phenotypes which are further mitigated by possible post-zygotic mosaicism. Treatment of this disorder is challenging, and surgical intervention of the GCLJ worsens the lesions, suggesting the future use of MEK inhibitors and TRPV4 antagonists as therapeutic modalities for unmet clinical needs.

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The L1-dependant and Pol III transcribed Alu retrotransposon, from its discovery to innate immunity

Molecular Biology Reports ◽

10.1007/s11033-021-06258-4 ◽

2021 ◽

Vol 48 (3) ◽

pp. 2775-2789

Author(s):

Ludwig Stenz

Keyword(s):

Human Genome ◽

Viral Infections ◽

De Novo ◽

Current Knowledge ◽

Innate Immune ◽

De Novo Mutation ◽

Neuronal Diversity ◽

Alu Sequences ◽

Pol Iii ◽

The Brain

AbstractThe 300 bp dimeric repeats digestible by AluI were discovered in 1979. Since then, Alu were involved in the most fundamental epigenetic mechanisms, namely reprogramming, pluripotency, imprinting and mosaicism. These Alu encode a family of retrotransposons transcribed by the RNA Pol III machinery, notably when the cytosines that constitute their sequences are de-methylated. Then, Alu hijack the functions of ORF2 encoded by another transposons named L1 during reverse transcription and integration into new sites. That mechanism functions as a complex genetic parasite able to copy-paste Alu sequences. Doing that, Alu have modified even the size of the human genome, as well as of other primate genomes, during 65 million years of co-evolution. Actually, one germline retro-transposition still occurs each 20 births. Thus, Alu continue to modify our human genome nowadays and were implicated in de novo mutation causing diseases including deletions, duplications and rearrangements. Most recently, retrotransposons were found to trigger neuronal diversity by inducing mosaicism in the brain. Finally, boosted during viral infections, Alu clearly interact with the innate immune system. The purpose of that review is to give a condensed overview of all these major findings that concern the fascinating physiology of Alu from their discovery up to the current knowledge.

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De Novo Development of a Cavernous Malformation of the Brain: Significance of Factors with Paracrine and Endocrine Activity: Case Report

Neurosurgery ◽

10.1227/00006123-200203000-00042 ◽

2002 ◽

Vol 50 (3) ◽

pp. 646-650 ◽

Cited By ~ 6

Author(s):

Wolf Lüdemann ◽

Verena Ellerkamp ◽

Alexandru C. Stan ◽

Sami Hussein

Keyword(s):

Case Report ◽

De Novo ◽

Cavernous Malformation ◽

Endocrine Activity ◽

The Brain

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Limbic Expression of mRNA Coding for Chemoreceptors in Human Brain—Lessons from Brain Atlases

International Journal of Molecular Sciences ◽

10.3390/ijms22136858 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6858

Author(s):

Fanny Gaudel ◽

Gaëlle Guiraudie-Capraz ◽

François Féron

Keyword(s):

G Proteins ◽

The Body ◽

Trace Amines ◽

Chemical Senses ◽

Brain Areas ◽

Genes Encoding ◽

The Central Nervous System ◽

Human Brains ◽

The Brain ◽

Brain Atlases

Animals strongly rely on chemical senses to uncover the outside world and adjust their behaviour. Chemical signals are perceived by facial sensitive chemosensors that can be clustered into three families, namely the gustatory (TASR), olfactory (OR, TAAR) and pheromonal (VNR, FPR) receptors. Over recent decades, chemoreceptors were identified in non-facial parts of the body, including the brain. In order to map chemoreceptors within the encephalon, we performed a study based on four brain atlases. The transcript expression of selected members of the three chemoreceptor families and their canonical partners was analysed in major areas of healthy and demented human brains. Genes encoding all studied chemoreceptors are transcribed in the central nervous system, particularly in the limbic system. RNA of their canonical transduction partners (G proteins, ion channels) are also observed in all studied brain areas, reinforcing the suggestion that cerebral chemoreceptors are functional. In addition, we noticed that: (i) bitterness-associated receptors display an enriched expression, (ii) the brain is equipped to sense trace amines and pheromonal cues and (iii) chemoreceptor RNA expression varies with age, but not dementia or brain trauma. Extensive studies are now required to further understand how the brain makes sense of endogenous chemicals.

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The brain transcriptome of the wolf spider, Schizocosa ocreata

BMC Research Notes ◽

10.1186/s13104-021-05648-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Daniel Stribling ◽

Peter L. Chang ◽

Justin E. Dalton ◽

Christopher A. Conow ◽

Malcolm Rosenthal ◽

...

Keyword(s):

Gene Expression ◽

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

De Novo Transcriptome Assembly ◽

De Novo Transcriptome ◽

Wolf Spiders ◽

Schizocosa Ocreata ◽

Genomic Studies ◽

The Brain

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders (Schizocosa ocreata). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases.

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