bims-tubesc Biomed News
on Molecular mechanisms in tuberous sclerosis
Issue of 2022‒04‒03
sixteen papers selected by
Marti Cadena Sandoval

  1. J Clin Invest. 2022 Mar 31. pii: e155858. [Epub ahead of print]
      BACKGROUND: Tuberous Sclerosis Complex (TSC) is a neurogenetic syndrome due to loss-of-function mutations in TSC2 or TSC1, characterized by tumors at multiple body sites, including facial angiofibroma (FAF). Here, an ultrasensitive assessment of the extent and range of UV-induced mutations in TSC facial skin was performed.METHODS: A Multiplex High-sensitivity PCR Assay (MHPA) was developed, enabling mutation detection at extremely low (<0.1%) variant allele frequencies (VAF).
    RESULTS: MHPA assays were developed for both TSC2 and TP53, and applied to 81 samples, including 66 skin biopsies. UV-induced second hit mutation causing inactivation of TSC2 was pervasive in TSC facial skin with an average of 4.8 mutations per 2 mm biopsy at median VAF 0.08%, generating >150,000 incipient facial tumors (subclinical 'micro-FAFs') in the average TSC subject. The MHPA analysis also led to the identification of a refined UV-related indel signature and a recurrent complex mutation pattern, consisting of both a single or dinucleotide variant, and a 1-9 nt deletion, in cis.
    CONCLUSION: TSC facial skin can be viewed as harboring a patchwork of clonal fibroblast proliferations (micro-FAF) with indolent growth, a small proportion of which develop into clinically observable FAF. Our observations also expand the spectrum of UV-related mutation signatures.
    FUNDING: This work was supported by the TSC Alliance, Engles Family Fund for Research in TSC and LAM, and National Institutes of Health, National Heart, Lung, and Blood Institute [U01HL131022-04; Intramural Research Program].
    Keywords:  Dermatology; Genetics; Molecular genetics; Skin cancer; Tumor suppressors
  2. Front Neurol. 2022 ;13 782479
      Objective: Tuberous sclerosis complex (TSC) is a genetic disease that arises from TSC1 or TSC2 abnormalities and induces the overactivation of the mammalian/mechanistic target of rapamycin pathways. The neurological symptoms of TSC include epilepsy and tuberous sclerosis complex-associated neuropsychiatric disorders (TAND). Although TAND affects TSC patients' quality of life, the specific region in the brain associated with TAND remains unknown. We examined the association between white matter microstructural abnormalities and TAND, using diffusion tensor imaging (DTI).Methods: A total of 19 subjects with TSC and 24 age-matched control subjects were enrolled. Tract-based spatial statistics (TBSS) were performed to assess group differences in fractional anisotropy (FA) between the TSC and control groups. Atlas-based association analysis was performed to reveal TAND-related white matter in subjects with TSC. Multiple linear regression was performed to evaluate the association between TAND and the DTI parameters; FA and mean diffusivity in seven target regions and projection fibers.
    Results: The TBSS showed significantly reduced FA in the right hemisphere and particularly in the inferior frontal occipital fasciculus (IFOF), inferior longitudinal fasciculus (ILF), superior longitudinal fasciculus (SLF), uncinate fasciculus (UF), and genu of corpus callosum (CC) in the TSC group relative to the control group. In the association analysis, intellectual disability was widely associated with all target regions. In contrast, behavioral problems and autistic features were associated with the limbic system white matter and anterior limb of the internal capsule (ALIC) and CC.
    Conclusion: The disruption of white matter integrity may induce underconnectivity between cortical and subcortical regions. These findings suggest that TANDs are not the result of an abnormality in a specific brain region, but rather caused by connectivity dysfunction as a network disorder. This study indicates that abnormal white matter connectivity including the limbic system is relevant to TAND. The analysis of brain and behavior relationship is a feasible approach to reveal TAND related white matter and neural networks. TAND should be carefully assessed and treated at an early stage.
    Keywords:  DTI; MRI; TAND; TSC; limbic system; white matter
  3. Sleep Med. 2022 Mar 14. pii: S1389-9457(22)00078-8. [Epub ahead of print]92 81-87
      BACKGROUND AND OBJECTIVE: Tuberous Sclerosis Complex (TSC) is a rare systemic disease with a high prevalence of sleep disorders (SD), although they are still largely under-recognized. The objective of this study was to assess the prevalence of SD in adult patients with TSC, and to evaluate the relationship between sleep, epilepsy, and TSC associated neuropsychiatric disorders (TAND).MATERIALS AND METHODS: We administered Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI) and Epworth Sleepiness Scale (ESS) to 114 adult patients referring to different Italian centers. We also collected information on epilepsy and TAND.
    RESULTS: PSQI, ISI, and ESS revealed a positive score, respectively, in 52 (46.0%), 30 (26.5%), and 16 (14.1%) patients. PSQI was positive in 26.7% of seizure free patients versus 61.9% with active epilepsy (p = 0.003), and the association remained significative applying a multivariate logistic model considering age, antiseizure medications, TAND and nocturnal epileptic seizures (p = 0.02). ISI was positive in 3.3% of seizure free patients versus 41.3% with active epilepsy (p = 0.0004). Applying a multivariate logistic model with the independent variables listed above, the association remained significant (p = 0.007). On the other hand, multivariate logistic model considering active epilepsy as an independent variable, revealed that TAND didn't appear a significant risk factor for positive PSQI (p = 0.43) nor ISI (p = 0.09).
    CONCLUSIONS: Our results confirmed that SD are highly prevalent in adults with TSC, with active epilepsy acting as a significant risk factor. A careful assessment of sleep, above all in epileptic patients, is of crucial importance.
    Keywords:  Adults; Epilepsy; Neuropsychiatric disorders; Sleep; Sleep disorders; Tuberous sclerosis
  4. Medicine (Baltimore). 2022 Mar 18. pii: e29024. [Epub ahead of print]101(11):
      ABSTRACT: Tuberous sclerosis complex (TSC) is a rare genetic disorder with multisystem involvement. TSC is characterized by benign hamartomas in multiple organs, including the brain, and its clinical phenotypes may be associated with abnormal functional connections. We aimed to use resting-state functional connectivity to provide findings of disrupted functional brain networks in TSC patients using graph theoretical analysis (GTA) and network-based statistic (NBS) analysis.Forty TSC patients (age = 24.11+/-11.44 years old) and 18 age-matched (25.13+/- 10.01 years old) healthy controls were recruited; they underwent resting-state functional magnetic resonance imaging using a 3T magnetic resonance imaging scanner. After image preprocessing and removing physiological noises, GTA was used to calculate the topological parameters of the brain network. NBS analysis was then used to determine the differences in cerebrum functional connectivity between the 2 groups.In GTA, several topological parameters, including the clustering coefficient, local efficiency, transitivity, and modularity, were better in controls than in TSC patients (P < .05). In NBS analysis, the edges of the brain networks between the groups were compared. One subnetwork showed more edges in controls than in TSC patients (P < .05), including the connections from the frontal lobe to the temporal and parietal lobe.The study results provide the findings on disrupted functional connectivity and organization in TSC patients compared with controls. The findings may help better understand the underlying physiological mechanisms of brain connection in TSC.
  5. Front Oncol. 2022 ;12 852859
      The tuberous sclerosis complex (TSC) is a rare genetic syndrome and multisystem disease resulting in tumor formation in major organs. A molecular hallmark of TSC is a dysregulation of the mammalian target of rapamycin (mTOR) through loss-of-function mutations in either tumor suppressor TSC1 or TSC2. Here, we sought to identify drug vulnerabilities conferred by TSC2 tumor-suppressor loss through cell-based chemical biology screening. Our small-molecule chemical screens reveal a sensitivity to inhibitors of checkpoint kinase 1/2 (CHK1/2), regulators of cell cycle, and DNA damage response, in both in vitro and in vivo models of TSC2-deficient renal angiomyolipoma (RA) tumors. Further, we performed transcriptional profiling on TSC2-deficient RA cell models and discovered that these recapitulate some of the features from TSC patient kidney tumors compared to normal kidneys. Taken together, our study provides a connection between mTOR-dependent tumor growth and CHK1/2, highlighting the importance of CHK1/2 inhibition as a potential antitumor strategy in TSC2-deficient tumors.
    Keywords:  AZD7762; CHEK1/2; Chk1/2; TSC2; checkpoint kinase inhibitors; mTOR; tuberous sclerosis complex; tumor xenografts
  6. PLoS Biol. 2022 Mar 31. 20(3): e3001594
      Mechanistic target of rapamycin complex I (mTORC1) is central to cellular metabolic regulation. mTORC1 phosphorylates a myriad of substrates, but how different substrate specificity is conferred on mTORC1 by different conditions remains poorly defined. Here, we show how loss of the mTORC1 regulator folliculin (FLCN) renders mTORC1 specifically incompetent to phosphorylate TFE3, a master regulator of lysosome biogenesis, without affecting phosphorylation of other canonical mTORC1 substrates, such as S6 kinase. FLCN is a GTPase-activating protein (GAP) for RagC, a component of the mTORC1 amino acid (AA) sensing pathway, and we show that active RagC is necessary and sufficient to recruit TFE3 onto the lysosomal surface, allowing subsequent phosphorylation of TFE3 by mTORC1. Active mutants of RagC, but not of RagA, rescue both phosphorylation and lysosomal recruitment of TFE3 in the absence of FLCN. These data thus advance the paradigm that mTORC1 substrate specificity is in part conferred by direct recruitment of substrates to the subcellular compartments where mTORC1 resides and identify potential targets for specific modulation of specific branches of the mTOR pathway.
  7. Nat Commun. 2022 Apr 01. 13(1): 1760
      The evolutionarily conserved serine/threonine kinase mTORC1 is a central regulator of cell growth and proliferation. mTORC1 is activated on the lysosome surface. However, once mTORC1 is activated, it is unclear whether mTORC1 phosphorylates local lysosomal proteins to regulate specific aspects of lysosomal biology. Through cross-reference analyses of the lysosome proteome with the mTORC1-regulated phosphoproteome, we identify STK11IP as a lysosome-specific substrate of mTORC1. mTORC1 phosphorylates STK11IP at Ser404. Knockout of STK11IP leads to a robust increase of autophagy flux. Dephosphorylation of STK11IP at Ser404 represses the role of STK11IP as an autophagy inhibitor. Mechanistically, STK11IP binds to V-ATPase, and regulates the activity of V-ATPase. Knockout of STK11IP protects mice from fasting or Methionine/Choline-Deficient Diet (MCD)-induced fatty liver. Thus, our study demonstrates that STK11IP phosphorylation represents a mechanism for mTORC1 to regulate lysosomal acidification and autophagy, and points to STK11IP as a promising therapeutic target for the amelioration of diseases with aberrant autophagy signaling.
  8. Expert Opin Pharmacother. 2022 Mar 28. 1-11
      INTRODUCTION: Autism, like other neurodevelopmental disorders (NDDs), has a strong association with epilepsy. There are known common genetic pathways in both autism and epilepsy. There are also specific genetic syndromes associated with both complex epilepsy and the autism phenotype.AREAS COVERED: This review explores the evidence for common genetic etiologies and pathophysiological pathways in relation to both epilepsy and autism. Autism with comorbid epilepsy are associated with a high prevalence of medical and psychiatric comorbidities. This paper discusses how this influences assessment, treatment, and outcomes. The evidence for the treatment of specific seizure types in the context of NDDs is also examined alongside clinical commentary.
    EXPERT OPINION: Despite the strong association, there is a limited evidence base to support the efficacy and tolerability of anti-seizure medications specifically in autism, with no Level 1 evidence or National Guidance available. Autism and epilepsy should be approached under a NDD model with cautious introduction and titration of anti-seizure medication. Alongside this, there is evidence to support a move toward precision medicine in specific genetic syndromes such as Tuberous Sclerosis Complex and other genetic seizure disorders. The first-line treatments that should be considered for focal seizures include carbamazepine, lamotrigine, and levetiracetam.
    Keywords:  Comorbidities; focal seizures; genomic variants; neurodevelopment; pervasive development
  9. Mol Cell. 2022 Mar 21. pii: S1097-2765(22)00211-8. [Epub ahead of print]
      mTORC1 controls cellular metabolic processes in response to nutrient availability. Amino acid signals are transmitted to mTORC1 through the Rag GTPases, which are localized on the lysosomal surface by the Ragulator complex. The Rag GTPases receive amino acid signals from multiple upstream regulators. One negative regulator, GATOR1, is a GTPase activating protein (GAP) for RagA. GATOR1 binds to the Rag GTPases via two modes: an inhibitory mode and a GAP mode. How these two binding interactions coordinate to process amino acid signals is unknown. Here, we resolved three cryo-EM structural models of the GATOR1-Rag-Ragulator complex, with the Rag-Ragulator subcomplex occupying the inhibitory site, the GAP site, and both binding sites simultaneously. When the Rag GTPases bind to GATOR1 at the GAP site, both Rag subunits contact GATOR1 to coordinate their nucleotide loading states. These results reveal a potential GAP mechanism of GATOR1 during the mTORC1 inactivation process.
    Keywords:  GAP; GATOR1; Rag GTPase; enzyme mechanism; mTOR complex 1; mTORC1; nutrient sensing
  10. Expert Opin Emerg Drugs. 2022 Apr 01. 1-16
      INTRODUCTION: Despite the existence of over 30 anti-seizure medications (ASM), including 20 over the last 30 years, a third of patients with epilepsy remain refractory to treatment, with no disease-modifying or preventive therapies until very recently. The development of new ASMs with new mechanisms of action is therefore critical. Recent clinical trials of new treatments have shifted focus from traditional common epilepsies to rare, genetic epilepsies with known mechanistic targets for treatment and disease-specific animal models.AREAS COVERED: ASMs in phase 2a/b-3 clinical trials target cholesterol, serotonin, sigma-1 receptors, potassium channels and metabotropic glutamate receptors. Neuroinflammation, protein misfolding, abnormal thalamocortical firing, and molecular deficiencies are among the targeted pathways. Clinically, the current phase 2a/b-3 agents hold promise for variety of epilepsy conditions, from developmental epileptic encephalopathies (Dravet Syndrome, Lennox-Gastaut syndrome, CDKL5 and PCDH19, Rett's Syndrome), infantile spasms, tuberous sclerosis as well as focal and idiopathic generalized epilepsies and acute rescue therapy for cluster seizures.
    EXPERT OPINION: New delivery mechanisms increase potency and site-specificity of existing drugs. Novel mechanisms of action involve cholesterol degradation, mitochondrial pathways, anti-inflammation, and neuro-regeneration. Earlier identification of genetic conditions through genetic testing will allow for earlier use of disease specific and disease-modifying therapies.
    Keywords:  ADX-71149; BIS-001; CVL-865; CX-8998; JNJ-40411813; NBI-827104; NRP-2945; RWJ-333369; SPN-817; STAP-001; STK-001; Soticlestat; TAK-935; XEN-1101; YKP3098; ZX-008; anavex 2-73; blarcarmesine; carisbamate; cenobamate; darigabat; fenfluramine; ganaxolone; genetic epilepsy; huperzine; intracerebroventricular valproate; lorcaserin; staccato alprazolam
  11. Front Mol Neurosci. 2022 ;15 810081
      Epilepsy is a neurological disorder that affects over 65 million people globally. It is characterized by periods of seizure activity of the brain as a result of excitation and inhibition (E/I) imbalance, which is regarded as the core underpinning of epileptic activity. Both gain- and loss-of-function (GOF and LOF) mutations of ion channels, synaptic proteins and signaling molecules along the mechanistic target of rapamycin (mTOR) pathway have been linked to this imbalance. The pathogenesis of epilepsy often has its roots in the early stage of brain development. It remains a major challenge to extrapolate the findings from many animal models carrying these GOF or LOF mutations to the understanding of disease mechanisms in the developing human brain. Recent advent of the human pluripotent stem cells (hPSCs) technology opens up a new avenue to recapitulate patient conditions and to identify druggable molecular targets. In the following review, we discuss the progress, challenges and prospects of employing hPSCs-derived neural cultures to study epilepsy. We propose a tentative working model to conceptualize the possible impact of these GOF and LOF mutations in ion channels and mTOR signaling molecules on the morphological and functional remodeling of intrinsic excitability, synaptic transmission and circuits, ultimately E/I imbalance and behavioral phenotypes in epilepsy.
    Keywords:  epilepsy; homeostasis; iPSC; ion channel; mTOR signaling
  12. Front Immunol. 2022 ;13 771732
      Cellular metabolism plays an important role in regulating both human and murine NK cell functions. However, it remains unclear whether cellular metabolic process impacts on the function of decidual NK cells (dNK), essential tissue-resident immune cells maintaining the homeostasis of maternal-fetal interface. Remarkably, we found that glycolysis blockage enhances dNK VEGF-A production but restrains its proliferation. Furthermore, levels of IFN-γ and TNF-α secreted by dNK get decreased when glycolysis or oxidative phosphorylation (OXPHOS) is inhibited. Additionally, glycolysis, OXPHOS, and fatty acid oxidation disruption has little effects on the secretion and the CD107a-dependent degranulation of dNK. Mechanistically, we discovered that the mammalian target of rapamycin complex 1 (mTORC1) signaling inhibition leads to decreased glycolysis and OXPHOS in dNK. These limited metabolic processes are associated with attenuated dNK functions, which include restricted production of cytokines including IFN-γ and TNF-α, diminished CD107a-dependent degranulation, and restrained dNK proliferation. Finally, we reported that the protein levels of several glycolysis-associated enzymes are altered and the mTORC1 activity is significantly lower in the decidua of women with recurrent pregnancy loss (RPL) compared with normal pregnancy, which might give new insights about the pathogenesis of RPL. Collectively, our data demonstrate that glucose metabolism and mTORC1 signaling support dNK functions in early pregnancy.
    Keywords:  RPL; cytokines; cytotoxicity; decidual NK cells; mTORC1; metabolism
  13. Life Sci Alliance. 2022 Jul;pii: e202101239. [Epub ahead of print]5(7):
      Within the endolysosomal pathway in mammalian cells, ESCRT complexes facilitate degradation of proteins residing in endosomal membranes. Here, we show that mammalian ESCRT-I restricts the size of lysosomes and promotes degradation of proteins from lysosomal membranes, including MCOLN1, a Ca2+ channel protein. The altered lysosome morphology upon ESCRT-I depletion coincided with elevated expression of genes annotated to biogenesis of lysosomes due to prolonged activation of TFEB/TFE3 transcription factors. Lack of ESCRT-I also induced transcription of cholesterol biosynthesis genes, in response to inefficient delivery of cholesterol from endolysosomal compartments. Among factors that could possibly activate TFEB/TFE3 signaling upon ESCRT-I deficiency, we excluded lysosomal cholesterol accumulation and Ca2+-mediated dephosphorylation of TFEB/TFE3. However, we discovered that this activation occurs due to the inhibition of Rag GTPase-dependent mTORC1 pathway that specifically reduced phosphorylation of TFEB at S112. Constitutive activation of the Rag GTPase complex in cells lacking ESCRT-I restored S112 phosphorylation and prevented TFEB/TFE3 activation. Our results indicate that ESCRT-I deficiency evokes a homeostatic response to counteract lysosomal nutrient starvation, that is, improper supply of nutrients derived from lysosomal degradation.
  14. Brain. 2022 Mar 31. pii: awab376. [Epub ahead of print]
      Focal malformations of cortical development including focal cortical dysplasia, hemimegalencephaly and megalencephaly, are a spectrum of neurodevelopmental disorders associated with brain overgrowth, cellular and architectural dysplasia, intractable epilepsy, autism and intellectual disability. Importantly, focal cortical dysplasia is the most common cause of focal intractable paediatric epilepsy. Gain and loss of function variants in the PI3K-AKT-MTOR pathway have been identified in this spectrum, with variable levels of mosaicism and tissue distribution. In this study, we performed deep molecular profiling of common PI3K-AKT-MTOR pathway variants in surgically resected tissues using droplet digital polymerase chain reaction (ddPCR), combined with analysis of key phenotype data. A total of 159 samples, including 124 brain tissue samples, were collected from 58 children with focal malformations of cortical development. We designed an ultra-sensitive and highly targeted molecular diagnostic panel using ddPCR for six mutational hotspots in three PI3K-AKT-MTOR pathway genes, namely PIK3CA (p.E542K, p.E545K, p.H1047R), AKT3 (p.E17K) and MTOR (p.S2215F, p.S2215Y). We quantified the level of mosaicism across all samples and correlated genotypes with key clinical, neuroimaging and histopathological data. Pathogenic variants were identified in 17 individuals, with an overall molecular solve rate of 29.31%. Variant allele fractions ranged from 0.14 to 22.67% across all mutation-positive samples. Our data show that pathogenic MTOR variants are mostly associated with focal cortical dysplasia, whereas pathogenic PIK3CA variants are more frequent in hemimegalencephaly. Further, the presence of one of these hotspot mutations correlated with earlier onset of epilepsy. However, levels of mosaicism did not correlate with the severity of the cortical malformation by neuroimaging or histopathology. Importantly, we could not identify these mutational hotspots in other types of surgically resected epileptic lesions (e.g. polymicrogyria or mesial temporal sclerosis) suggesting that PI3K-AKT-MTOR mutations are specifically causal in the focal cortical dysplasia-hemimegalencephaly spectrum. Finally, our data suggest that ultra-sensitive molecular profiling of the most common PI3K-AKT-MTOR mutations by targeted sequencing droplet digital polymerase chain reaction is an effective molecular approach for these disorders with a good diagnostic yield when paired with neuroimaging and histopathology.
    Keywords:  ddPCR; epilepsy; focal cortical dysplasia; hemimegalencephaly; mosaicism
  15. Mol Cancer Res. 2022 Mar 29. pii: molcanres.0545.2021. [Epub ahead of print]
      In patients with trastuzumab-resistant HER2-positive breast cancer, the combination of everolimus (mTORC1 inhibitor) with trastuzumab failed to show a clinically significant benefit. However, the combination of mTOR inhibition and the antibody-drug conjugate (ADC) trastuzumab-emtansine (T-DM1) remains unexplored. We tested T-DM1 plus everolimus in a broad panel of HER2-positive breast cancer cell lines. The combination was superior to T-DM1 alone in four cell lines (HCC1954, SKBR3, EFM192A, and MDA-MB-36) and in two cultures from primary tumor cells derived from HER2-positive patient-derived xenografts (PDX), but not in BT474 cells. In the trastuzumab-resistant HCC1954 cell line, we characterized the effects of the combination using TAK-228 (mTORC1 and 2 inhibitor) and knockdown of the different mTOR complex components. T-DM1 did not affect mTOR downstream signaling nor induct autophagy. Importantly, mTOR inhibition increased intracellular T-DM1 levels, leading to increased lysosomal accumulation of the compound. The increased efficacy of mTOR inhibition plus T-DM1 was abrogated by lysosome inhibitors (chloroquine and bafilomycin A1). Our experiments suggest that BT474 are less sensitive to T-DM1 due to lack of optimal lysosomal processing and intrinsic resistance to the DM1 moiety. Finally, we performed several in vivo experiments that corroborated the superior activity of T-DM1 and everolimus in HCC1954 and PDX-derived mouse models. In summary, everolimus in combination with T-DM1 showed strong antitumor effects in HER2-positive breast cancer, both in vitro and in vivo. This effect might be related, at least partially, to mTOR-dependent lysosomal processing of T-DM1, a finding that might apply to other ADCs that require lysosomal processing. Implications: Inhibition of mTOR increases the anti-tumor activity of T-DM1, supporting that the combination of mTOR inhibitors and antibody-drug conjugates warrants clinical evaluation in patients with HER2-positive breast cancer.