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Tuberous sclerosis complex (TSC) is an autosomal dominant disorder that affects several organs in the human body including the brain, heart, kidneys, eyes, skin, spleen, liver and lungs [Roach, et al., 1999]. TSC is characterized by hamartomas that rarely progress to malignancy in the affected organs. Clinical symptoms of TSC include cortical tubers and subependymal nodules in the brain, seizures, mental retardation, ungual and periungual fibromas, angiofibromas of the face, and angiomyolipomas in the kidneys [Roach, et al., 1999]. TSC displays genetic heterogeneity with two known loci: TSC1 on chromosome 9q34 [Fryer, et al., 1987a] and TSC2 on chromosome 16p13.3 [Kandt, et al., 1992]. The genes for both loci have been isolated and characterized [ The European Chromosome 16 Tuberous Sclerosis Consortium, 1993; van Slegtenhorst, et al., 1997]. The TSC1 gene contains 21 coding and two non-coding exons and encodes for an 8.6 kb mRNA. It spans 45 kb of genomic DNA and codes for hamartin, a 1,164 amino acid protein of 130 kDa. The TSC2 encodes for a 200 kDa protein, tuberin, and spans 43 kb of genomic DNA. The TSC2 gene consists of 41 coding exons and one non-coding exon and encodes for a 5.4 kb mRNA. Both genes are known to function as tumor suppressors [Carbonara, et al., 1994; Green, et al., 1994a; Green, et al., 1994b]. Several groups have performed mutation analysis of both the genes in patients mainly from the western and Japanese populations. A total of 133 mutations in the TSC1 gene and 350 mutations in the TSC2 gene have been reported so far (Human Gene Mutation Database; http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html). However, there is no report on the mutation analysis of the TSC genes from the Indian population. In this study, a total of 24 TSC cases were ascertained from the Indian population and a comprehensive mutation analysis of both the TSC genes was carried out in them to understand the function of both the genes, to locate important domains and also to find the mutational hotspots for molecular diagnosis of TSC. A total of 12 mutations, including seven novel mutations were identified. It was also shown that the most recurrent mutations (c.1831C>T and c.1832G>A) are, in part, due to methylation of the CpG dinucleotide. There are still 15-25% TSC cases in western populations with undetected mutations [Cheadle, et al., 2000a]. Further, there are familial TSC cases linked either to the TSC1 on 9q34 or TSC2 on 16p13.3 which fail to show any mutations in the coding sequences of both genes [Cheadle, et al., 2000a]. The failure to detect mutations in these cases could be due to several reasons. First, it could be that the mutations lie in the regulatory regions (promoters and enhancers) of both the genes, presently unidentified for the TSC1 gene [Cheadle, et al., 2000a]. Second, it is possible that the mutations lie outside of the coding sequences, within intronic sequences, or in the 5’ or 3’ UTRs [Cheadle, et al., 2000a]. Third, it may be due to the limitation of the techniques used to identify mutations [Cheadle, et al., 2000a]. In order to look for mutations in the promoter, the TSC1 gene promoter was characterized using luciferase reporter gene transfection assay. The promoter for the TSC2 gene is known [Kobayashi, et al., 1997]. The promoters of both TSC1 and TSC2 genes were sequenced in all the 24 cases to look for mutations. During the characterization of the TSC1 gene promoter, a novel isoform involving the non-coding exon 1 of the TSC1 gene was discovered serendipitously.

Tuberous sclerosis complex (TSC) is an autosomal-dominant neurocutaneous disease caused by loss of the TSC1 (encoding hamartin) or TSC2 (encoding tuberin) genes. Neurologic symptoms are common and varied in TSC and include epilepsy and behavioral conditions like autism spectrum disorders (ASD). Between 17 and 61% of children with TSC exhibit symptoms of ASD. The purpose of this study was to investigate a potential correlate of poor neurological outcome in TSC by assessing the integrity of brain language pathways and the relationship to ASD. 42 patients with TSC and 42 age-matched control subjects were scanned with advanced diffusion-weighted MRI. White matter language pathways were identified with a validated automatic method and analyzed for microstructural characteristics, including fractional anisotropy (FA) and mean diffusivity (MD). Well-defined white matter pathways in the brain are characterized by high FA and low MD. During normal development, brain white matter pathways increase in FA and decrease in MD. Out of 42 patients with TSC, 12 had ASD (29%). After controlling for age, TSC patients without ASD showed a small decrease in FA of the arcuate fasciculus compared to control subjects, and TSC patients with ASD had much lower FA than both control subjects and TSC patients without ASD. Similarly, while TSC patients without ASD had only a small increase in MD compared to control subjects in the arcuate fasciculus, TSC patients with ASD had much higher MD than control subjects and TSC patients without ASD. A new method for assessing the microstructure of young patients showed similar results with decreased compactness in language pathways of TSC patients with ASD. Another new method designed to better analyze regions with crossing pathways showed modifications in language pathway microstructure that correlated with ASD diagnosis in the TSC patients. Preliminary analysis of neuropsychiatric data also showed a trend toward an association of arcuate fasciculus MD with verbal IQ, although the result was not significant after multiple comparisons correction. It remains unclear why some patients with TSC develop ASD, while others have better language outcomes. Our results suggest that aberrant development of language pathways may act as a marker for poor neurological outcome in TSC patients. The impaired microstructure in language pathways of TSC patients may be responsible for the development of ASD, although prospective studies examining the development of language pathways and subsequent ASD diagnosis in this patient population remain essential. It is also possible that a primary problem with language leads to decreased use and subsequent poor development of language pathways. Early diagnosis of ASD is crucial for improving the outcomes of affected children.

BACKGROUND: Lymphangioleiomyomatosis (LAM) is a rare disease characterized by cystic destruction of the lung. It occurs in 80% of people with Tuberous Sclerosis Complex disorder (TSC), a multisystem, autosomal dominant disorder caused by mutations in tumor suppressor genes TSC1 and TSC2. Spontaneous biallelic mutations in these genes can give rise to sporadic LAM. Mammalian target of rapamycin complex I (mTORC1), a master regulator of cellular anabolic metabolism is hyperactivated in LAM cells. Upregulation of protein synthesis and downregulation of autophagy creates a state of starvation stress that upregulates pathways of extracellular nutrient acquisition. Macropinocytosis, a form of clathrin-independent endocytosis, is upregulated in TSC2-deficient cells. We performed a high-throughput compound screen utilizing a repurposing drug library. We identified that ritanserin, a diacylglycerol kinase alpha (DGKA) inhibitor, synergizes with Chloroquine (CQ) to selectively inhibit proliferation of TSC2-deficient mouse embryonic fibroblasts (MEFs) compared to TSC2+/+ MEFs. OBJECTIVE: We hypothesized that TSC2-deficient cells rely on macropinocytosis to support their growth during the periods of stress and starvation and that ritanserin synergizes with CQ to inhibit proliferation in TSC2-deficient cells by inhibiting macropinocytosis. METHODS: Crystal violet-based proliferation assays were used to monitor the effect of pharmacological and genetic inhibition of DGKA on cell proliferation. Immunoblotting was used to measure the expression levels of TSC2, tS6R, pS6R, Cleaved PARP, Cleaved Caspase 3 and Actin. siRNA induced Htr2a knockdown and shRNA induced DGKA knockdown cell culture models were used to define the dual functions of ritanserin and observe their effects on macropinocytosis and cell proliferation. LC/MS was used to measure cell lipid content and how it changes in response to ritanserin. Fluorophore-labeled BSA and 70-kDa Dextran were used to measure macropinocytosis. Lysotracker was used to measure the number of lysosomes, while DQ-BSA was used to measure lysosomal functionality. RESULTS: TSC2-deficient cells express higher levels and show upregulated activity of DGKA. Genetic and pharmacologic inhibition of DGKA prevents TSC2-deficient cells from acquiring nutrients via macropinocytosis. Phospholipid metabolism is altered in TSC2-deficient cells, marked by the accumulation of phosphatidic acid and ceramides. Treatment with ritanserin leads to the accumulation of diacylglycerol and phospholipids, as well as a reduction in phosphatidic acid. CONCLUSIONS: TSC2-deficient cells rely on macropinocytosis to meet their metabolic needs. Diacylglycerol kinase alpha (DGKA) is required for macropinocytic nutrient uptake. Pharmacologic or genetic inhibition of DGKA creates metabolic stress in TSC2-deficient cells, which ultimately leads to increased apoptotic response to treatment with CQ. This project identifies a novel connection between mTOR signaling, lysosome metabolism and macropinocytosis, and a vulnerability that allows the selective targeting of LAM cells. / 2021-06-07T00:00:00Z

Through mutations in the genes TSC1 and TSC2, the genetic disorder Tuberous Sclerosis Complex (TSC) causes begin tumors to develop in different organs across the body. Of the many ways that this disorder can manifest, the brain is one of the most commonly affected organs in TSC. Mutations in TSC1 or TSC2 result in mTORC1 hyperactivation and can impact how the brain forms early in development. Most patients with TSC exhibit seizures and over half display some level of intellectual disability, highlighting the impact that mTORC1 hyperactivation can have on brain function and cognition. However, despite our understanding of the genetic cause of TSC, the mechanisms downstream of TSC1/TSC2 and mTORC1 that mediate TSC neuropathology are not well understood. Therefore, additional study of the cellular and molecular underlying the aberrant neurodevelopment found in TSC and other mTOR-overactivation disorders (collectively known as mTORopathies) is necessary for further understanding of these disorders. Of the pathways that have been identified to interact with mTORC1, there has been great interest in understanding the relationship between mTORC1 and Hippo-YAP/TAZ signaling. The Hippo pathway is an evolutionarily considered pathway that is crucial for regulating organ size through its control of the transcriptional co-activators YAP/TAZ. As exhibited through study of the murine brain, hyperactivation of YAP/TAZ causes changes in how the cortex develops, with several features overlapping with mTORC1 hyperactivation (including aberrant neuronal migration, changes in neuron structure, and increased progenitor proliferation). While the relationship between mTORC1 and YAP/TAZ has been explored in other systems, its connection in the brain has yet to be explored. In Chapter 1 of this dissertation, I first review how TSC affects cortical development as a whole by addressing what is known about the specific cell types and signaling pathways that are affected this disorder. Of the signaling pathways described, the Hippo- YAP/TAZ pathway is discussed in particular detail, addressing its role not only in the context of TSC and in terms of its interaction with mTORC1 signaling, but also in terms of its general role in cortical development. In discussing these studies, I describe the phenotypes seen in different mouse models and in the human brain, allowing for the identification of pathological features that are common between species and between different Cre lines. Following this initial review, I present our experimental aims, hypotheses, and experimental overview for this project in Chapter 2. In Chapter 3, I describe our investigation into the role of YAP/TAZ in the abnormal neurodevelopment that occurs in TSC. Through our analysis of human cortical tuber samples, I demonstrate that YAP/TAZ are elevated at the protein level and that two of their established target genes, CYR61 and CCN2, are elevated at the mRNA and protein levels. Having demonstrated that YAP/TAZ levels and activity are elevated in cortical tuber samples, I next went on to establish whether YAP/TAZ are similarly changed in our TSC animal model. Examination of Emx1-Cre driven Tsc2 cKO mice showed that the level of Yap/Taz were significantly elevated at E16.5. Having established that both YAP/TAZ levels are elevated in our animal model, I next sought to determine whether concurrent genetic manipulation of Yap/Taz in our Tsc2 cKO animals would reduce the severity of neuropathology seen in these mice. Triple conditional knockout (tcKO) of Yap/Taz/Tsc2 was sufficient to mitigate several features seen with mTORC1 hyperactivation in the brain, including the cortical thickness increases, abnormal neuronal migration in the cortex, hippocampal lamination defects, and hypomyelination found in their single Tsc2 cKO counterparts. Overall, these findings provide additional evidence that mTORC1 hyperactivation positively regulates YAP/TAZ. For the first time, this study describes elevation of YAP/TAZ in the brains of individuals with TSC and in the brains of a TSC mouse model. Furthermore, I provide evidence that reduction of Yap/Taz may have a beneficial effect on neuropathology in TSC, highlighting an area for future research in the development of novel therapeutics for this disorder. / Biomedical Sciences

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Tuberous sclerosis complex (TSC) is an autosomal dominant disorder caused by pathogenic variants in either TSC1 or TSC2 tumor suppressor genes. It affects more often the brain, skin, kidneys, heart, lungs, and retina. The protein products of both genes, TSC1 (hamartin) and TSC2 (tuberin), interact, assembling a complex that inhibits mTORC1. Cells with bi-allelic inactivation of either TSC1 or TSC2 genes present hyperactivation of mTORC1, which phosphorylates downstream targets, up-regulating cell proliferation and growth. Moreover, a functional role as heat-shock protein (HSP) co-chaperone has been assigned to TSC1 protein. The first aim of the thesis was to analyze the nature, distribution and functional effects of TSC1 and TSC2 DNA variants from 100 patients with definite clinical diagnosis of TSC. We analyzed leukocyte DNA of 115 TSC patients from three Brazilian tertiary referral hospitals. Pathogenic DNA variants were detected in 99 (86,09%) unrelated individuals; 17 (17,17%) in TSC1 and 82 (82,82%) in TSC2. Clear loss-of-function mutations were detected in 87 patients, of which frameshift (29.29%) and nonsense (29.29%) variants were the most common types. In- frame deletions, missense and putative splicing DNA variants with uncertain clinical significance (VUS) have been functionally assessed. Five variants significantly increased phosphorylation of the reporter residue S6K Thr 389 . Forty-one novel pathogenic DNA variants and 19 novel single nucleotide variants have been detected. Among the 11 individuals with no mutation identified, seven presented rare putative missense, splicing or in- frame deletion DNA VUS. To understand the regulatory relationship of TSC1/2 gene expression, we aimed to evaluate TSC1 and TSC2 mRNA and protein levels in human cell lines with bi-allelic inactivation of each gene. We employed high throughput transcriptome analysis (RNA-Seq) and Western blotting of HEK293T and other six HEK293T-derived cell lines that had the genomic sequence of the TSC1 and or TSC2 genes edited by the CRISPR (clustered regularly interspaced short palindromic repeats)-CAS9 system. In lack of either TSC1 or TSC2 protein, a significant reduction of the respective mRNA was observed, inferring no positive transcriptional feedback. Serum-deprived cell lines without TSC1 decreased TSC2 mRNA levels. Under these conditions, TSC1 mRNA levels were not negatively affected by the lack of TSC2. In one cell line with loss of TSC1 (1C2) TSC1/2 mRNA and TSC2 protein levels were consistently decreased independently on serum. RNA-Seq gene ontology analyses comparing 1C2 to HEK293T reference cell line disclosed down-regulation of translational pathways independently on serum; and up-regulation of protein folding and stability pathways upon serum withdrawal. Our data are consistent with the role of TSC1 as HSP co-chaperone, and suggest that TSC1 mRNA may be regulated at both transcriptional and decay levels / O complexo de esclerose tuberosa (TSC) é um distúrbio autossômico dominante causado por variantes patogênicas em um de dois genes supressores de tumor TSC1 ou TSC2. Afeta mais frequentemente o cérebro, a pele, os rins, o coração, os pulmões e a retina. Os produtos proteicos de ambos os genes, TSC1 (hamartina) e TSC2 (tuberina), interagem formando um complexo que inibe o mTORC1. As células com inactivação bi- alélica dos genes TSC1 ou TSC2 apresentam hiperactivação de mTORC1, que fosforila alvos a jusante, regulando positivamente a proliferação e o crescimento celular. Além disso, o papel funcional da co-chaperona da proteína de choque térmico (HSP) foi atribuído à proteína TSC1. O primeiro objetivo dessa tese foi analisar a natureza, distribuição e os efeitos funcionais das variantes de DNA de TSC1 e TSC2 de 100 pacientes com diagnóstico clínico definitivo de TSC. Analisamos o DNA de leucócitos de 115 pacientes com TSC de três hospitais brasileiros de referência. Variantes de DNA patogênico foram detectadas em 99 (86,09%) indivíduos não relacionados; 17 (17,17%) em TSC1 e 82 (82,82%) em TSC2. Mutações de perda de função foram detectadas em 87 pacientes, dos quais as variantes frameshift (29,29%) e nonsense (29,29%) foram os tipos mais comuns. Deleções in-frame, variantes missense e variantes de splicing com significância clínica incerta (VUS) foram avaliadas funcionalmente. Cinco variantes aumentaram significativamente a fosforilação do resíduo repórter S6K Thr 389 . Quarenta e uma novas variantes de DNA patogênico e 19 novas variantes de nucleotídeo único foram detectadas. Entre os 11 indivíduos sem mutação identificada, sete apresentaram variantes raras missense, splicing ou deleções in-frame do tipo VUS. Para entender a relação regulatória da expressão do gene TSC1/2, tivemos com segundo objetivo avaliar os níveis de mRNA e proteína de TSC1 e TSC2 em linhagens de células humanas com inativação bi-alélica de cada gene. Empregamos uma análise de transcriptoma de alto rendimento (RNA-Seq) e Western blotting de HEK293T e outras seis linhagens celulares derivadas de HEK293T que possuíam a sequência genomica dos genes TSC1 e/ou TSC2 editados por CRISPR- CAS9. Na falta da proteína TSC1 ou TSC2, foi observada uma redução significativa do respectivo mRNA, inferindo ausência de feedback transcricional positivo. Linhagens celulares privadas de soro TSC1 -/- diminuíram os níveis de mRNA de TSC2. Sob estas condições, os níveis de mRNA de TSC1 não foram afetados negativamente pela falta de TSC2. Numa linhagem celular com a perda de TSC1 (1C2), os RNAm de TSC1/2 e os níveis de proteína de TSC2 foram consistentemente diminuídos independentemente no soro. Análise de RNA-Seq comparando a linhagens celular de 1C2 com a referência HEK293T revelou uma regulação negativa de vias de tradução independentemente no soro; e supra-regulação das vias de enrolamento e estabilidade das proteínas após a retirada do soro. Nossos dados são consistentes com o papel do TSC1 como co-chaperona de HSP, e sugerem que o mRNA de TSC1 pode ser regulador nos níveis de transcrição

The mammary gland is a dynamic organ that undergoes the majority of its development in the postnatal period in four stages; mature virgin, pregnancy, lactation, and involution. Every stage relies on tightly regulated cellular proliferation, programmed cell death, and tissue remodeling mechanisms. Misregulation of autophagy, an intracellular catabolic process to maintain energy stores, has long been associated with mammary tumorigenesis and other pathologies. We hypothesize that appropriate regulation and execution of autophagy are necessary for proper development of the mammary ductal tree and maintenance of the secretory epithelia during late pregnancy and lactation. To test this hypothesis we examined the role of two genes during development of the mammary gland. Beclin1 (Becn1) is an essential autophagy gene. Since the Becn1 knockout model is embryonic lethal, we have generated a Becn1 conditional knockout (cKO). We used two discrete mammary gland-specific Cre transgenic lines to interrogate the role of BECN1 during development. We report that MMTV-CreD; Becn1fl/fl mice have a hyper-branching phenotype and WAP-Cre; Becn1fl/- mice are unable to sustain a lactation phase. Becn1 mutants exhibit abnormal glandular morphology during pregnancy and after parturition. Moreover, when autophagy is chemically inhibited in vitro, mammary epithelial cells have an increased mean number of lipid droplets per cell. MTOR inhibits autophagy upstream of BECN1; we looked higher in the regulatory pathway for regulatory candidates. It has been well characterized that Tuberous sclerosis complex 1 (TSC1), in a heterodimer with its primary binding partner TSC2, inhibits MTOR signaling via inhibition of RHEB. Using the Tsc1 floxed model we generated a mammary gland specific Tsc1 cKO and found that these mice phenocopy the Becn1 cKO mice, including a gross lactation failure. Tsc1 cKO glands have altered morphology, retained lipid droplets in secretory epithelia, and an overall increase in MTOR signaling. We show that TSC1 and BECN1 are interacting partners, and that the interaction is nutrient responsive. These results suggest that Becn1 and Tsc1 are necessary for proper mammary gland development and differentiation. Furthermore, we have demonstrated a novel murine protein-protein interaction and an important link between regulation of MTOR pathway and regulation of autophagy in a developmental context.

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