Lack of association of rare functional variants in TSC1/TSC2 genes with autism spectrum disorder / Samira BAHL in Molecular Autism, (March 2013)  

Public ISBD [article]  inMolecular Autism > (March 2013) . - 11 p. Titre : Lack of association of rare functional variants in TSC1/TSC2 genes with autism spectrum disorder Type de document : Texte imprimé et/ou numérique Auteurs : Samira BAHL, Auteur ; Colby CHIANG, Auteur ; Roberta L. BEAUCHAMP, Auteur ; Benjamin NEALE, Auteur ; Mark J. DALY, Auteur ; James GUSELLA, Auteur ; Michael E. TALKOWSKI, Auteur ; Vijaya RAMESH, Auteur Année de publication : 2013 Article en page(s) : 11 p. Langues : Anglais (eng) Mots-clés : Autism spectrum disorder  Tuberous sclerosis complex  Mammalian target of rapamycin  Next-generation sequencing  Rare variants Index. décimale : PER Périodiques Résumé : BACKGROUND:Autism spectrum disorder (ASD) is reported in 30 to 60% of patients with tuberous sclerosis complex (TSC) but shared genetic mechanisms that exist between TSC-associated ASD and idiopathic ASD have yet to be determined. Through the small G-protein Rheb, the TSC proteins, hamartin and tuberin, negatively regulate mammalian target of rapamycin complex 1 (mTORC1) signaling. It is well established that mTORC1 plays a pivotal role in neuronal translation and connectivity, so dysregulation of mTORC1 signaling could be a common feature in many ASDs. Pam, an E3 ubiquitin ligase, binds to TSC proteins and regulates mTORC1 signaling in the CNS, and the FBXO45-Pam ubiquitin ligase complex plays an essential role in neurodevelopment by regulating synapse formation and growth. Since mounting evidence has established autism as a disorder of the synapses, we tested whether rare genetic variants in TSC1, TSC2, MYCBP2, RHEB and FBXO45, genes that regulate mTORC1 signaling and/or play a role in synapse development and function, contribute to the pathogenesis of idiopathic ASD.METHODS:Exons and splice junctions of TSC1, TSC2, MYCBP2, RHEB and FBXO45 were resequenced for 300 ASD trios from the Simons Simplex Collection (SSC) using a pooled PCR amplification and next-generation sequencing strategy, targeted to the discovery of deleterious coding variation. These detected, potentially functional, variants were confirmed by Sanger sequencing of the individual samples comprising the pools in which they were identified.RESULTS:We identified a total of 23 missense variants in MYCBP2, TSC1 and TSC2. These variants exhibited a near equal distribution between the proband and parental pools, with no statistical excess in ASD cases (P 0.05). All proband variants were inherited. No putative deleterious variants were confirmed in RHEB and FBXO45. Three intronic variants, identified as potential splice defects in MYCBP2 did not show aberrant splicing upon RNA assay. Overall, we did not find an over-representation of ASD causal variants in the genes studied to support them as contributors to autism susceptibility.CONCLUSIONS:We did not observe an enrichment of rare functional variants in TSC1 and TSC2 genes in our sample set of 300 trios. En ligne : http://dx.doi.org/10.1186/2040-2392-4-5 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=202 [article] Lack of association of rare functional variants in TSC1/TSC2 genes with autism spectrum disorder [Texte imprimé et/ou numérique] / Samira BAHL, Auteur ; Colby CHIANG, Auteur ; Roberta L. BEAUCHAMP, Auteur ; Benjamin NEALE, Auteur ; Mark J. DALY, Auteur ; James GUSELLA, Auteur ; Michael E. TALKOWSKI, Auteur ; Vijaya RAMESH, Auteur . - 2013 . - 11 p. Langues : Anglais (eng) in Molecular Autism > (March 2013) . - 11 p. Mots-clés : Autism spectrum disorder  Tuberous sclerosis complex  Mammalian target of rapamycin  Next-generation sequencing  Rare variants Index. décimale : PER Périodiques Résumé : BACKGROUND:Autism spectrum disorder (ASD) is reported in 30 to 60% of patients with tuberous sclerosis complex (TSC) but shared genetic mechanisms that exist between TSC-associated ASD and idiopathic ASD have yet to be determined. Through the small G-protein Rheb, the TSC proteins, hamartin and tuberin, negatively regulate mammalian target of rapamycin complex 1 (mTORC1) signaling. It is well established that mTORC1 plays a pivotal role in neuronal translation and connectivity, so dysregulation of mTORC1 signaling could be a common feature in many ASDs. Pam, an E3 ubiquitin ligase, binds to TSC proteins and regulates mTORC1 signaling in the CNS, and the FBXO45-Pam ubiquitin ligase complex plays an essential role in neurodevelopment by regulating synapse formation and growth. Since mounting evidence has established autism as a disorder of the synapses, we tested whether rare genetic variants in TSC1, TSC2, MYCBP2, RHEB and FBXO45, genes that regulate mTORC1 signaling and/or play a role in synapse development and function, contribute to the pathogenesis of idiopathic ASD.METHODS:Exons and splice junctions of TSC1, TSC2, MYCBP2, RHEB and FBXO45 were resequenced for 300 ASD trios from the Simons Simplex Collection (SSC) using a pooled PCR amplification and next-generation sequencing strategy, targeted to the discovery of deleterious coding variation. These detected, potentially functional, variants were confirmed by Sanger sequencing of the individual samples comprising the pools in which they were identified.RESULTS:We identified a total of 23 missense variants in MYCBP2, TSC1 and TSC2. These variants exhibited a near equal distribution between the proband and parental pools, with no statistical excess in ASD cases (P 0.05). All proband variants were inherited. No putative deleterious variants were confirmed in RHEB and FBXO45. Three intronic variants, identified as potential splice defects in MYCBP2 did not show aberrant splicing upon RNA assay. Overall, we did not find an over-representation of ASD causal variants in the genes studied to support them as contributors to autism susceptibility.CONCLUSIONS:We did not observe an enrichment of rare functional variants in TSC1 and TSC2 genes in our sample set of 300 trios. En ligne : http://dx.doi.org/10.1186/2040-2392-4-5 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=202

Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations / Pauline MARTIN ; Francis ROBERT ; Krzysztof J. SZKOP ; Nicholas E. REDMOND ; Srirupa BHATTACHARYYA ; Jennifer WANG ; Shan CHEN ; Roberta L. BEAUCHAMP ; Irene NOBELI ; Jerry PELLETIER ; Ola LARSSON ; Vijaya RAMESH in Molecular Autism, 14 (2023)  

Public ISBD [article]  inMolecular Autism > 14 (2023) . - 39 p. Titre : Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations Type de document : Texte imprimé et/ou numérique Auteurs : Pauline MARTIN, Auteur ; Francis ROBERT, Auteur ; Krzysztof J. SZKOP, Auteur ; Nicholas E. REDMOND, Auteur ; Srirupa BHATTACHARYYA, Auteur ; Jennifer WANG, Auteur ; Shan CHEN, Auteur ; Roberta L. BEAUCHAMP, Auteur ; Irene NOBELI, Auteur ; Jerry PELLETIER, Auteur ; Ola LARSSON, Auteur ; Vijaya RAMESH, Auteur Article en page(s) : 39 p. Langues : Anglais (eng) Mots-clés : Humans  *Tuberous Sclerosis/genetics/metabolism  Tumor Suppressor Proteins/genetics  Sirolimus/pharmacology  *Autism Spectrum Disorder  Mechanistic Target of Rapamycin Complex 1  Stem Cells/metabolism  Autism spectrum disorder  Early neurodevelopment  Neural progenitor cells  Polysome profiling  Rmc-6272  Tsc1  Translatome  Tuberous sclerosis complex  mTORC1 Index. décimale : PER Périodiques Résumé : BACKGROUND: Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in the TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD) and intellectual disability. Hamartin (TSC1) and tuberin (TSC2) proteins form a complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. Loss of TSC1 or TSC2 activates mTORC1 that, among several targets, controls protein synthesis by inhibiting translational repressor eIF4E-binding proteins. Using TSC1 patient-derived neural progenitor cells (NPCs), we recently reported early ND phenotypic changes, including increased cell proliferation and altered neurite outgrowth in TSC1-null NPCs, which were unaffected by the mTORC1 inhibitor rapamycin. METHODS: Here, we used polysome profiling, which quantifies changes in mRNA abundance and translational efficiencies at a transcriptome-wide level, to compare CRISPR-edited TSC1-null with CRISPR-corrected TSC1-WT NPCs generated from one TSC donor (one clone/genotype). To assess the relevance of identified gene expression alterations, we performed polysome profiling in postmortem brains from ASD donors and age-matched controls. We further compared effects on translation of a subset of transcripts and rescue of early ND phenotypes in NPCs following inhibition of mTORC1 using the allosteric inhibitor rapamycin versus a third-generation bi-steric, mTORC1-selective inhibitor RMC-6272. RESULTS: Polysome profiling of NPCs revealed numerous TSC1-associated alterations in mRNA translation that were largely recapitulated in human ASD brains. Moreover, although rapamycin treatment partially reversed the TSC1-associated alterations in mRNA translation, most genes related to neural activity/synaptic regulation or ASD were rapamycin-insensitive. In contrast, treatment with RMC-6272 inhibited rapamycin-insensitive translation and reversed TSC1-associated early ND phenotypes including proliferation and neurite outgrowth that were unaffected by rapamycin. CONCLUSIONS: Our work reveals ample mRNA translation alterations in TSC1 patient-derived NPCs that recapitulate mRNA translation in ASD brain samples. Further, suppression of TSC1-associated but rapamycin-insensitive translation and ND phenotypes by RMC-6272 unveils potential implications for more efficient targeting of mTORC1 as a superior treatment strategy for TAND. En ligne : https://dx.doi.org/10.1186/s13229-023-00572-3 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=518 [article] Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations [Texte imprimé et/ou numérique] / Pauline MARTIN, Auteur ; Francis ROBERT, Auteur ; Krzysztof J. SZKOP, Auteur ; Nicholas E. REDMOND, Auteur ; Srirupa BHATTACHARYYA, Auteur ; Jennifer WANG, Auteur ; Shan CHEN, Auteur ; Roberta L. BEAUCHAMP, Auteur ; Irene NOBELI, Auteur ; Jerry PELLETIER, Auteur ; Ola LARSSON, Auteur ; Vijaya RAMESH, Auteur . - 39 p. Langues : Anglais (eng) in Molecular Autism > 14 (2023) . - 39 p. Mots-clés : Humans  *Tuberous Sclerosis/genetics/metabolism  Tumor Suppressor Proteins/genetics  Sirolimus/pharmacology  *Autism Spectrum Disorder  Mechanistic Target of Rapamycin Complex 1  Stem Cells/metabolism  Autism spectrum disorder  Early neurodevelopment  Neural progenitor cells  Polysome profiling  Rmc-6272  Tsc1  Translatome  Tuberous sclerosis complex  mTORC1 Index. décimale : PER Périodiques Résumé : BACKGROUND: Tuberous sclerosis complex (TSC) is an inherited neurocutaneous disorder caused by mutations in the TSC1 or TSC2 genes, with patients often exhibiting neurodevelopmental (ND) manifestations termed TSC-associated neuropsychiatric disorders (TAND) including autism spectrum disorder (ASD) and intellectual disability. Hamartin (TSC1) and tuberin (TSC2) proteins form a complex inhibiting mechanistic target of rapamycin complex 1 (mTORC1) signaling. Loss of TSC1 or TSC2 activates mTORC1 that, among several targets, controls protein synthesis by inhibiting translational repressor eIF4E-binding proteins. Using TSC1 patient-derived neural progenitor cells (NPCs), we recently reported early ND phenotypic changes, including increased cell proliferation and altered neurite outgrowth in TSC1-null NPCs, which were unaffected by the mTORC1 inhibitor rapamycin. METHODS: Here, we used polysome profiling, which quantifies changes in mRNA abundance and translational efficiencies at a transcriptome-wide level, to compare CRISPR-edited TSC1-null with CRISPR-corrected TSC1-WT NPCs generated from one TSC donor (one clone/genotype). To assess the relevance of identified gene expression alterations, we performed polysome profiling in postmortem brains from ASD donors and age-matched controls. We further compared effects on translation of a subset of transcripts and rescue of early ND phenotypes in NPCs following inhibition of mTORC1 using the allosteric inhibitor rapamycin versus a third-generation bi-steric, mTORC1-selective inhibitor RMC-6272. RESULTS: Polysome profiling of NPCs revealed numerous TSC1-associated alterations in mRNA translation that were largely recapitulated in human ASD brains. Moreover, although rapamycin treatment partially reversed the TSC1-associated alterations in mRNA translation, most genes related to neural activity/synaptic regulation or ASD were rapamycin-insensitive. In contrast, treatment with RMC-6272 inhibited rapamycin-insensitive translation and reversed TSC1-associated early ND phenotypes including proliferation and neurite outgrowth that were unaffected by rapamycin. CONCLUSIONS: Our work reveals ample mRNA translation alterations in TSC1 patient-derived NPCs that recapitulate mRNA translation in ASD brain samples. Further, suppression of TSC1-associated but rapamycin-insensitive translation and ND phenotypes by RMC-6272 unveils potential implications for more efficient targeting of mTORC1 as a superior treatment strategy for TAND. En ligne : https://dx.doi.org/10.1186/s13229-023-00572-3 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=518

TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling / Pauline MARTIN in Molecular Autism, 11 (2020)  

Public ISBD [article]  inMolecular Autism > 11 (2020) . - 2 p. Titre : TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling Type de document : Texte imprimé et/ou numérique Auteurs : Pauline MARTIN, Auteur ; Vilas WAGH, Auteur ; Surya A. REIS, Auteur ; Serkan ERDIN, Auteur ; Roberta L. BEAUCHAMP, Auteur ; Ghalib SHAIKH, Auteur ; Michael E. TALKOWSKI, Auteur ; Elizabeth THIELE, Auteur ; Steven D. SHERIDAN, Auteur ; Stephen J. HAGGARTY, Auteur ; Vijaya RAMESH, Auteur Article en page(s) : 2 p. Langues : Anglais (eng) Mots-clés : CRISPR/Cas9  Disease modeling  Early neurodevelopment  Induced pluripotent stem cells  mek-erk1/2  MNK1/2-eIF4E  Neural progenitor cells  tsc1  Tuberous sclerosis complex  mTORC1  Therapeutics, Psy Therapeutics, and Souvien Therapeutics, none of who were involved  in this study. SDS is a scientific advisor for Outermost Therapeutics, Inc., which  played no part in the present study. The other authors declare no competing  interests. Index. décimale : PER Périodiques Résumé : BACKGROUND: Tuberous sclerosis complex (TSC) is a neurodevelopmental disorder with frequent occurrence of epilepsy, autism spectrum disorder (ASD), intellectual disability (ID), and tumors in multiple organs. The aberrant activation of mTORC1 in TSC has led to treatment with mTORC1 inhibitor rapamycin as a lifelong therapy for tumors, but TSC-associated neurocognitive manifestations remain unaffected by rapamycin. METHODS: Here, we generated patient-specific, induced pluripotent stem cells (iPSCs) from a TSC patient with a heterozygous, germline, nonsense mutation in exon 15 of TSC1 and established an isogenic set of heterozygous (Het), null and corrected wildtype (Corr-WT) iPSCs using CRISPR/Cas9-mediated gene editing. We differentiated these iPSCs into neural progenitor cells (NPCs) and examined neurodevelopmental phenotypes, signaling and changes in gene expression by RNA-seq. RESULTS: Differentiated NPCs revealed enlarged cell size in TSC1-Het and Null NPCs, consistent with mTORC1 activation. TSC1-Het and Null NPCs also revealed enhanced proliferation and altered neurite outgrowth in a genotype-dependent manner, which was not reversed by rapamycin. Transcriptome analyses of TSC1-NPCs revealed differentially expressed genes that display a genotype-dependent linear response, i.e., genes upregulated/downregulated in Het were further increased/decreased in Null. In particular, genes linked to ASD, epilepsy, and ID were significantly upregulated or downregulated warranting further investigation. In TSC1-Het and Null NPCs, we also observed basal activation of ERK1/2, which was further activated upon rapamycin treatment. Rapamycin also increased MNK1/2-eIF4E signaling in TSC1-deficient NPCs. CONCLUSION: MEK-ERK and MNK-eIF4E pathways regulate protein translation, and our results suggest that aberrant translation distinct in TSC1/2-deficient NPCs could play a role in neurodevelopmental defects. Our data showing upregulation of these signaling pathways by rapamycin support a strategy to combine a MEK or a MNK inhibitor with rapamycin that may be superior for TSC-associated CNS defects. Importantly, our generation of isogenic sets of NPCs from TSC patients provides a valuable platform for translatome and large-scale drug screening studies. Overall, our studies further support the notion that early developmental events such as NPC proliferation and initial process formation, such as neurite number and length that occur prior to neuronal differentiation, represent primary events in neurogenesis critical to disease pathogenesis of neurodevelopmental disorders such as ASD. En ligne : http://dx.doi.org/10.1186/s13229-019-0311-3 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=427 [article] TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling [Texte imprimé et/ou numérique] / Pauline MARTIN, Auteur ; Vilas WAGH, Auteur ; Surya A. REIS, Auteur ; Serkan ERDIN, Auteur ; Roberta L. BEAUCHAMP, Auteur ; Ghalib SHAIKH, Auteur ; Michael E. TALKOWSKI, Auteur ; Elizabeth THIELE, Auteur ; Steven D. SHERIDAN, Auteur ; Stephen J. HAGGARTY, Auteur ; Vijaya RAMESH, Auteur . - 2 p. Langues : Anglais (eng) in Molecular Autism > 11 (2020) . - 2 p. Mots-clés : CRISPR/Cas9  Disease modeling  Early neurodevelopment  Induced pluripotent stem cells  mek-erk1/2  MNK1/2-eIF4E  Neural progenitor cells  tsc1  Tuberous sclerosis complex  mTORC1  Therapeutics, Psy Therapeutics, and Souvien Therapeutics, none of who were involved  in this study. SDS is a scientific advisor for Outermost Therapeutics, Inc., which  played no part in the present study. The other authors declare no competing  interests. Index. décimale : PER Périodiques Résumé : BACKGROUND: Tuberous sclerosis complex (TSC) is a neurodevelopmental disorder with frequent occurrence of epilepsy, autism spectrum disorder (ASD), intellectual disability (ID), and tumors in multiple organs. The aberrant activation of mTORC1 in TSC has led to treatment with mTORC1 inhibitor rapamycin as a lifelong therapy for tumors, but TSC-associated neurocognitive manifestations remain unaffected by rapamycin. METHODS: Here, we generated patient-specific, induced pluripotent stem cells (iPSCs) from a TSC patient with a heterozygous, germline, nonsense mutation in exon 15 of TSC1 and established an isogenic set of heterozygous (Het), null and corrected wildtype (Corr-WT) iPSCs using CRISPR/Cas9-mediated gene editing. We differentiated these iPSCs into neural progenitor cells (NPCs) and examined neurodevelopmental phenotypes, signaling and changes in gene expression by RNA-seq. RESULTS: Differentiated NPCs revealed enlarged cell size in TSC1-Het and Null NPCs, consistent with mTORC1 activation. TSC1-Het and Null NPCs also revealed enhanced proliferation and altered neurite outgrowth in a genotype-dependent manner, which was not reversed by rapamycin. Transcriptome analyses of TSC1-NPCs revealed differentially expressed genes that display a genotype-dependent linear response, i.e., genes upregulated/downregulated in Het were further increased/decreased in Null. In particular, genes linked to ASD, epilepsy, and ID were significantly upregulated or downregulated warranting further investigation. In TSC1-Het and Null NPCs, we also observed basal activation of ERK1/2, which was further activated upon rapamycin treatment. Rapamycin also increased MNK1/2-eIF4E signaling in TSC1-deficient NPCs. CONCLUSION: MEK-ERK and MNK-eIF4E pathways regulate protein translation, and our results suggest that aberrant translation distinct in TSC1/2-deficient NPCs could play a role in neurodevelopmental defects. Our data showing upregulation of these signaling pathways by rapamycin support a strategy to combine a MEK or a MNK inhibitor with rapamycin that may be superior for TSC-associated CNS defects. Importantly, our generation of isogenic sets of NPCs from TSC patients provides a valuable platform for translatome and large-scale drug screening studies. Overall, our studies further support the notion that early developmental events such as NPC proliferation and initial process formation, such as neurite number and length that occur prior to neuronal differentiation, represent primary events in neurogenesis critical to disease pathogenesis of neurodevelopmental disorders such as ASD. En ligne : http://dx.doi.org/10.1186/s13229-019-0311-3 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=427

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