A combination of genetic and biochemical analyses for the diagnosis of PI3K-AKT-mTOR pathway-associated megalencephaly

Negishi, Yutaka; Miya, Fuyuki; Hattori, Ayako; Johmura, Yoshikazu; Nakagawa, Motoo; Ando, Nobutoshi; Hori, Ikumi; Togawa, Takao; Aoyama, Kohei; Ohashi, Kei; Fukumura, Shinobu; Mizuno, Seiji; Umemura, Atsushi; Kishimoto, Yoko; Okamoto, Nobuhiko; Kato, Mitsuhiro; Tsunoda, Tatsuhiko; Yamasaki, Mami; Kanemura, Yonehiro; Kosaki, Kenjiro; Nakanishi, Makoto; Saitoh, Shinji

doi:10.1186/s12881-016-0363-6

Cited by 21 publications

(16 citation statements)

References 30 publications

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“…For example, all five of the P/LP PTEN (MEM: 601728) variants found in this cohort were detected in peripheral blood, 30,31 as were four of the six PIK3R2 (MIM: 603157) variants. 27,32 Conversely, TEK (MEM: 600221) variants are often implicated in germline syndromes, 33 but all four P/LP TEK variants identified in this cohort were absent from peripheral blood. This included one case subject with two separate, confirmed somatic TEK variants (P337_S1 in Table S7).…”

Section: Tissue Distribution Suspected Dosm Variantsmentioning

confidence: 73%

Diagnostic Utility of Next-Generation Sequencing for Disorders of Somatic Mosaicism: A Five-Year Cumulative Cohort

McNulty

Evenson

Corliss

et al. 2019

The American Journal of Human Genetics

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Disorders of somatic mosaicism (DoSM) are a diverse group of syndromic and non-syndromic conditions caused by mosaic variants in genes that regulate cell survival and proliferation. Despite overlap in gene space and technical requirements, few clinical labs specialize in DoSM compared to oncology. We adapted a high-sensitivity next-generation sequencing cancer assay for DoSM in 2014. Some 343 individuals have been tested over the past 5 years, 58% of which had pathogenic and likely pathogenic (P/LP) findings, for a total of 206 P/LP variants in 22 genes. Parameters associated with the high diagnostic yield were: (1) deep sequencing (2,0003 coverage), (2) a broad gene set, and (3) testing affected tissues. Fresh and formalin-fixed paraffin embedded tissues performed equivalently for identification of P/LP variants (62% and 71% of individuals, respectively). Comparing cultured fibroblasts to skin biopsies suggested that culturing might boost the allelic fraction of variants that confer a growth advantage, specifically gain-of-function variants in PIK3CA. Buccal swabs showed high diagnostic sensitivity in case subjects where disease phenotypes manifested in the head or brain. Peripheral blood was useful as an unaffected comparator tissue to determine somatic versus constitutional origin but had poor diagnostic sensitivity. Descriptions of all tested individuals, specimens, and P/LP variants included in this cohort are available to further the study of the DoSM population.

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Section: Tissue Distribution Suspected Dosm Variantsmentioning

confidence: 73%

Diagnostic Utility of Next-Generation Sequencing for Disorders of Somatic Mosaicism: A Five-Year Cumulative Cohort

McNulty

Evenson

Corliss

et al. 2019

The American Journal of Human Genetics

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“…Increased expression of phospho‐S6 protein was demonstrated in mutation‐positive and mutation‐negative patients in whom western blotting was performed. This approach could be useful to identify patients who are suitable for the diagnosis of mTORopathies and the design of future clinical trials using an mTOR inhibitor .…”

Section: Genetics Of Fcds (See Also Review Article Of Marsan and Baulmentioning

confidence: 99%

Review: The international consensus classification of Focal Cortical Dysplasia – a critical update 2018

Najm

Sarnat

Blümcke

2018

Neuropathology Appl Neurobio

161

150

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The Diagnostic Methods commission of the International League against Epilepsy (ILAE) released a first international consensus classification of Focal Cortical Dysplasia (FCD) in 2011. Since that time, this FCD classification has been widely used in clinical diagnosis and research (more than 740 papers cited in Pubmed between 1/1/2012 and 7/1/2017). Herein, we review the new data that will inform and revise the FCD classification. Many recent papers described moleculargenetic characteristics in FCD type II including multiple mutations in the mTOR pathway. In addition, the electro-clinico-imaging phenotype and surgical outcomes of FCD type II (in particular type IIb) were further defined and validated. These results pave the way for the design of an integrated clinico-pathological and genetic classification system, as recently recommended by the WHO for the classification of malignant brain tumours.On the other hand, little new information was acquired on FCD types I and III. Focal cortical dysplasia type I subtypes are still lacking a comprehensive description of clinical phenotypes, reproducible imaging characteristics, and specific molecular/genetic biomarkers. Associated FCD III subtypes also became rare in published literature. Despite temporal lobe epilepsy being the most common focal epilepsy in adults, we have not identified neurophysiological, imaging, histopathological and/or genetic biomarkers to reliably classify FCD III with or without hippocampal sclerosis. In respect of pathogenesis, FCD adjacent to a non-developmental, postnatally acquired lesion is difficult to explain and perhaps does not exist. This update may help foster shared efforts towards a better understanding of FCD, potential future updates of classification and novel targeted treatments.

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“…The AKT complex is one of the most central molecules of this pathway that mediates many of its functions by regulating several downstream pathways. Mutations of the AKT3 gene have been reported in several patients to date, including seven with constitutional mutations causing megalencephaly with polymicrogyria (Riviere et al, 2012;Jamuar et al, 2014;Nakamura et al, 2014;Harada et al, 2015;Nellist et al, 2015;Negishi et al, 2017), and four with the mosaic p.E17K mutation causing hemimegalencephaly (Lee et al, 2012;Poduri et al, 2012;Riviere et al, 2012;Jansen et al, 2015). However, our understanding regarding the clinical and molecular spectrum associated with mutations of this critical gene is limited, with no clear genotype-phenotype correlations.…”

Section: Introductionmentioning

confidence: 99%

Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly

Alcantara

Timms

Gripp

et al. 2017

Brain

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Mutations of genes within the phosphatidylinositol-3-kinase (PI3K)-AKT-MTOR pathway are well known causes of brain overgrowth (megalencephaly) as well as segmental cortical dysplasia (such as hemimegalencephaly, focal cortical dysplasia and polymicrogyria). Mutations of the AKT3 gene have been reported in a few individuals with brain malformations, to date. Therefore, our understanding regarding the clinical and molecular spectrum associated with mutations of this critical gene is limited, with no clear genotype-phenotype correlations. We sought to further delineate this spectrum, study levels of mosaicism and identify genotype-phenotype correlations of AKT3-related disorders. We performed targeted sequencing of AKT3 on individuals with these phenotypes by molecular inversion probes and/or Sanger sequencing to determine the type and level of mosaicism of mutations. We analysed all clinical and brain imaging data of mutation-positive individuals including neuropathological analysis in one instance. We performed ex vivo kinase assays on AKT3 engineered with the patient mutations and examined the phospholipid binding profile of pleckstrin homology domain localizing mutations. We identified 14 new individuals with AKT3 mutations with several phenotypes dependent on the type of mutation and level of mosaicism. Our comprehensive clinical characterization, and review of all previously published patients, broadly segregates individuals with AKT3 mutations into two groups: patients with highly asymmetric cortical dysplasia caused by the common p.E17K mutation, and patients with constitutional AKT3 mutations exhibiting more variable phenotypes including bilateral cortical malformations, polymicrogyria, periventricular nodular heterotopia and diffuse megalencephaly without cortical dysplasia. All mutations increased kinase activity, and pleckstrin homology domain mutants exhibited enhanced phospholipid binding. Overall, our study shows that activating mutations of the critical AKT3 gene are associated with a wide spectrum of brain involvement ranging from focal or segmental brain malformations (such as hemimegalencephaly and polymicrogyria) predominantly due to mosaic AKT3 mutations, to diffuse bilateral cortical malformations, megalencephaly and heterotopia due to constitutional AKT3 mutations. We also provide the first detailed neuropathological examination of a child with extreme megalencephaly due to a constitutional AKT3 mutation. This child has one of the largest documented paediatric brain sizes, to our knowledge. Finally, our data show that constitutional AKT3 mutations are associated with megalencephaly, with or without autism, similar to PTEN-related disorders. Recognition of this broad clinical and molecular spectrum of AKT3 mutations is important for providing early diagnosis and appropriate management of affected individuals, and will facilitate targeted design of future human clinical trials using PI3K-AKT pathway inhibitors.

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A combination of genetic and biochemical analyses for the diagnosis of PI3K-AKT-mTOR pathway-associated megalencephaly

Cited by 21 publications

References 30 publications

Diagnostic Utility of Next-Generation Sequencing for Disorders of Somatic Mosaicism: A Five-Year Cumulative Cohort

Diagnostic Utility of Next-Generation Sequencing for Disorders of Somatic Mosaicism: A Five-Year Cumulative Cohort

Review: The international consensus classification of Focal Cortical Dysplasia – a critical update 2018

Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly

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