Precise detection of low-level somatic mutation in resected epilepsy brain tissue

Sim, Nam Suk; Ko, Ara; Kim, Woo Kyeong; Kim, Se Hoon; Kim, Ju Seong; Shim, Kyu Won; Aronica, Eleonora; Mijnsbergen, Caroline; Spliet, Wim G.M.; Koh, Hyun Yong; Kim, Heung Dong; Lee, Joon Soo; Kim, Do Kyung; Kang, Hoon Chul; Lee, Jehee

doi:10.1007/s00401-019-02052-6

Cited by 108 publications

(186 citation statements)

References 38 publications

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“…All these changes, together with the enrichment of the mTORC2 downstream signalling pathway, suggest that abnormal expression of PARK7 and GAP-43 might be a result of the dysregulation of the mTOR pathway in the PPS model. Indeed, the mTOR pathway has been shown to be involved in many neurological disorders, such as autism spectrum disorders 47,48 , Alzheimer's disease, tuberous sclerosis complex 46,49,50 , focal cortical dysplasia 51,52 and, more recently, intractable epilepsy 49,[53][54][55][56][57][58] . The mTORC1 and mTORC2 complexes are also upregulated in tissue from patients with MTLE 59 .…”

Section: Discussionmentioning

confidence: 99%

Laser microdissection-based microproteomics of the hippocampus of a rat epilepsy model reveals regional differences in protein abundances

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Vieira

Matos

et al. 2020

Sci Rep

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cendes 8,9 & iscia Lopes-cendes 1,9* Mesial temporal lobe epilepsy (MTLE) is a chronic neurological disorder affecting almost 40% of adult patients with epilepsy. Hippocampal sclerosis (HS) is a common histopathological abnormality found in patients with MTLE. HS is characterised by extensive neuronal loss in different hippocampus subregions. In this study, we used laser microdissection-based microproteomics to determine the protein abundances in different regions and layers of the hippocampus dentate gyrus (DG) in an electric stimulation rodent model which displays classical HS damage similar to that found in patients with MTLE. Our results indicate that there are differences in the proteomic profiles of different layers (granule cell and molecular), as well as different regions, of the DG (ventral and dorsal). We have identified new signalling pathways and proteins present in specific layers and regions of the DG, such as PARK7, RACK1, and connexin 31/gap junction. We also found two major signalling pathways that are common to all layers and regions: inflammation and energy metabolism. Finally, our results highlight the utility of high-throughput microproteomics and spatial-limited isolation of tissues in the study of complex disorders to fully appreciate the large biological heterogeneity present in different cell populations within the central nervous system. Currently, it is well recognised that proteins and their biological roles are multifaceted and complex since all biological mechanisms rely on correct protein function. However, a major part of protein cellular machinery remains unknown, especially in disease-related processes. Therefore, studying proteins, specifically their presence and abundance, is relevant when addressing complex mechanisms leading to disease 1. Laser microdissection-based microproteomics allows for the study of the proteome of enriched specific cell types of interest obtained from a small amount of tissue (100 μg or less) 1-3. Epilepsy is a chronic neurological disorder affecting around 2% of the world population 27/02/2020 18:22:00. It presents a wide variety of clinic manifestations, aetiologies, severities, and prognoses. However, the occurrence of an epileptic seizure, caused by abnormal neuronal discharges, is the common feature of all types of epilepsy 4. Mesial temporal lobe epilepsy (MTLE) is the most frequent form in adults, present in 40% of patients with epilepsy, many of whom do not respond to clinical treatment 5-8 .

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Section: Discussionmentioning

confidence: 99%

Laser microdissection-based microproteomics of the hippocampus of a rat epilepsy model reveals regional differences in protein abundances

Canto

Vieira

Matos

et al. 2020

Sci Rep

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“…Further functional experiments are required. Second, due to the high cost of WES, in this study, we employed a mean read depth of 200× for each sample; thus, we might have missed some PDSVs located in the low coverage region . Third, the limitations in both WES and site‐specific amplicon sequencing techniques and the strict screening strategies employed might have resulted in missing some PDSVs.…”

Section: Discussionmentioning

confidence: 99%

Somatic variants in new candidate genes identified in focal cortical dysplasia type II

et al. 2020

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Objective: Focal cortical dysplasia type II (FCDII) is a malformation of cortex development commonly found in children with drug-resistant epilepsy. FCDII has been associated with somatic mutations in mammalian target of rapamycin (mTOR)-related pathway genes and an upregulation of mTOR. Somatic mutations were found in 10%-63% of FCDII samples; the frequency of the mutant allele was 0.93%-33.5%. This study aimed to find new candidate genes involved in FCDII. Methods: We collected resected FCD lesions, perilesional brain tissues, and peripheral blood from 17 children with pathologically confirmed FCDII. We performed whole exome sequencing and followed a set of screening and analysis strategies to identify potentially deleterious somatic variants (PDSVs) in brain-expressed genes.We performed site-specific amplicon sequencing to validate the results. We also performed an in vitro functional study on an IRS1 variant. Results: In six of 17 samples, we identified seven PDSVs in seven genes, including two frameshift variants and five missense variants. The frequencies of the variant allele were 1.29%-5.50%. The genes were MTOR, TSC2, IRS1, RAB6B, RALA, HTR6, and ZNF337. PDSVs in IRS1, RAB6B, ZNF337, RALA, and HTR6 had not been previously associated with FCD. In one lesion, two PDSVs were found in two genes. In a transfected cell line, we demonstrated that the c.1791dupG (identified in FCDII from Patient 1) led to a truncated IRS1 and significant mTOR hyperactivation compared to cells that carried wild-type IRS1. mTOR was also activated in FCDII tissue from

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“…Another study analyzed 446 tissue samples from 232 patients with intractable epilepsy with various brain pathologies, using deep sequencing of known epilepsy‐related genes (up to 28 genes), followed by confirmatory site‐specific amplicon sequencing . Pathogenic mutations of mTOR‐related genes were discovered in 31.9% (74/232).…”

Section: Discussionmentioning

confidence: 99%

“…4,6,7 Another study analyzed 446 tissue samples from 232 patients with intractable epilepsy with various brain pathologies, using deep sequencing of known epilepsy-related genes (up to 28 genes), followed by confirmatory site-specific amplicon sequencing. 18 Pathogenic mutations of mTOR-related genes were discovered in 31.9% (74/232). Baldassari et al enrolled 80 cases in a single-center study and found pathogenic mutations in several mTOR pathway genes, providing a framework for efficient FCD and HME genetic testing, linking neuropathology to recent genetic discoveries, and emphasizing the usefulness of molecular assessment in the children with refractory epilepsy who are thus surgical candidates.…”

Section: Clinical Characteristicsmentioning

confidence: 99%

mTOR pathway somatic variants and the molecular pathogenesis of hemimegalencephaly

et al. 2020

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Objectives Recently, defects in the protein kinase mTOR (mammalian target of rapamycin) and its associated pathway have been correlated with hemimegalencephaly (HME). mTOR acts as a central regulator of important physiological cellular functions such as growth and proliferation, metabolism, autophagy, death, and survival. This study was aimed at identifying specific variants in mTOR signaling pathway genes in patients diagnosed with HME. Methods Using amplicon and whole exome sequencing (WES) of resected brain and paired blood samples from five HME patients, we were able to identify pathogenic mosaic variants in the mTOR pathway genes MTOR, PIK3CA, and DEPDC5. Results These results strengthen the hypothesis that somatic variants in PI3K‐Akt‐mTOR pathway genes contribute to HME. We also describe one patient presenting with a pathogenic variant on DEPDC5 gene, which reinforces the role of DEPDC5 on cortical structural changes due to mTORC1 hyperactivation. These findings also provide insights into when in brain development these variants occurred. An early developmental variant is expected to affect a larger number of cells and to result in a larger malformation, whereas the same variant occurring later in development would cause a minor malformation. Significance In the future, numerous somatic variants in known or new genes will undoubtedly be revealed in resected brain samples, making it possible to draw correlations between genotypes and phenotypes and allow for a genetic clinical diagnosis that may help to predict a given patient's outcome.

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Precise detection of low-level somatic mutation in resected epilepsy brain tissue

Cited by 108 publications

References 38 publications

Laser microdissection-based microproteomics of the hippocampus of a rat epilepsy model reveals regional differences in protein abundances

Laser microdissection-based microproteomics of the hippocampus of a rat epilepsy model reveals regional differences in protein abundances

Somatic variants in new candidate genes identified in focal cortical dysplasia type II

mTOR pathway somatic variants and the molecular pathogenesis of hemimegalencephaly

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