Publications

@article{pmid41801223,

title = {An Open-Source Pipeline for Calcium Imaging and All-Optical Physiology in Human Stem Cell-Derived Neurons},

author = {Wardiya Afshar-Saber and Federico M Gasparoli and Ziqin Yang and Nicole A Teaney and Rachel Hobson and Lahin Lalani and Gayathri Srinivasan and Dosh Whye and Ranit Karmakar and Elizabeth D Buttermore and Kellen D Winden and Cidi Chen and Mustafa Sahin},

doi = {10.1002/advs.202515887},

issn = {2198-3844},

year  = {2026},

date = {2026-05-01},

journal = {Adv Sci (Weinh)},

volume = {13},

number = {26},

pages = {e15887},

abstract = {High-throughput, single-cell resolution profiling of neuronal activity is critical for understanding brain function and modeling neurological disorders, yet existing approaches are often limited by scalability and manual workflows. Here, we present an open-source, scalable imaging and analysis platform that integrates optogenetic stimulation, calcium imaging, automated acquisition, single-cell and network analyses. The platform enables robust quantification of spontaneous and evoked neuronal activity across hundreds of human stem cell-derived neurons over multiple timepoints, supporting functional phenotyping at both cellular and network levels. We demonstrate the versatility of the platform across multiple disease-relevant contexts, including models of CDKL5 Deficiency, SSADH Deficiency, and tuberous sclerosis complex (TSC). Additionally, we generate CRISPR-Cas9 knock-in hiPSC lines expressing GCaMP6s and demonstrate partial reversal through pharmacological intervention in TSC. By linking single-cell dynamics to network-level measures, this platform provides a generalizable framework for scalable functional phenotyping and high-throughput screening in human neuronal models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid41820375,

title = {Tuberous sclerosis complex},

author = {Kellen Winden and E Martina Bebin and Shafali Jeste and Darcy A Krueger and Elahna Paul and Mustafa Sahin},

doi = {10.1038/s41572-026-00688-9},

issn = {2056-676X},

year  = {2026},

date = {2026-03-01},

journal = {Nat Rev Dis Primers},

volume = {12},

number = {1},

abstract = {Tuberous sclerosis complex (TSC) is a rare genetic disease caused by heterozygous loss-of-function variants in TSC1 or TSC2. Patients present with benign tumours known as hamartomas in the brain, eyes, lungs, kidneys, heart and skin. Many hamartomas contain mosaic second hit variants in TSC1 or TSC2. The most disabling features of TSC include epilepsy and TSC-associated neuropsychiatric disorders (TAND) such as intellectual disability and autism spectrum disorder. Remarkable progress has been made both in understanding the pathogenesis of TSC and in its clinical management, largely due to the discovery of the link between TSC1 and TSC2 and the mechanistic target of rapamycin (mTOR) signalling pathway. TSC1 and TSC2 form a protein complex that inhibits mTOR. Naturally occurring inhibitors of mTOR (rapamycin) and its analogues, collectively known as rapalogues, have been used to test various hypotheses in preclinical models and are approved for the treatment of several manifestations of TSC. Approved drug treatments (rapalogues) exist for subependymal giant cell astrocytomas, renal angiomyolipomas, pulmonary lymphangioleiomyomatosis, facial angiofibromas and refractory seizures. However, there is still an unmet need for effective treatment of TAND and refractory epilepsy, despite the available medical and surgical options.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid41379617,

title = {Neuronal hyperactivity becomes mTORC1 independent due to transcriptional changes in tuberous sclerosis complex disease models},

author = {Wardiya Afshar-Saber and Juan F Ruiz and Isabel Gisser and Ziqin Yang and Leena Mehendale and Nicole A Teaney and Rachel Hobson and Madison R Glass and Truc T Pham and Elizabeth Bainbridge and Mustafa Sahin and Kellen D Winden},

doi = {10.1016/j.celrep.2025.116664},

issn = {2211-1247},

year  = {2025},

date = {2025-12-01},

journal = {Cell Rep},

volume = {44},

number = {12},

pages = {116664},

abstract = {Tuberous sclerosis complex (TSC) is caused by variants in either TSC1 or TSC2, which cooperate to inhibit the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with neurological disorders that are attributed to disinhibition of mTORC1, but the mechanisms connecting dysregulation of mTORC1 to molecular and physiological changes in neurons remain unclear. In this study, we aim to understand transcriptional changes in TSC and identify downregulation of the immediate-early gene EGR1 in TSC2-deficient excitatory neurons. Furthermore, we find that activity-dependent transcription is impaired in TSC due to abnormalities in maturation-dependent DNA demethylation. Finally, we determine that mTORC1 inhibition started late in neuronal maturation of human neurons is only partially effective in reversing gene expression changes and ineffective in reducing spontaneous neuronal hyperactivity in TSC. These data demonstrate a critical window in early brain development where mTORC1 dysregulation leads to transcriptional changes that contribute to persistent neuronal abnormalities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39953287,

title = {Phenotypic rescue via mTOR inhibition in neuron-specific Pten knockout mice reveals AKT and mTORC1-site specific changes},

author = {Angelica D'Amore and Maria Sundberg and Rui Lin and Ella T Lubbers and Kellen D Winden and Lucy Yu and Kinga Gawlinska and Dawid Gawlinski and Sam G Lopez and Yongho Choe and Emma V Wightman and Yini Liang and Meera Modi and Christopher J Yuskaitis and Henry Hing Cheong Lee and Alexander Rotenberg and Mustafa Sahin},

doi = {10.1038/s41380-025-02916-2},

issn = {1476-5578},

year  = {2025},

date = {2025-07-01},

journal = {Mol Psychiatry},

volume = {30},

number = {7},

pages = {3077--3089},

abstract = {Phosphatase and Tensin Homolog (PTEN) is a dual-specific protein and lipid phosphatase that regulates AKT and downstream signaling of the mechanistic target of rapamycin (mTOR). PTEN functions as a tumor suppressor gene whose mutations result in PTEN Hamartoma Tumor Syndrome (PHTS) characterized by increased cancer risk and neurodevelopmental comorbidity. Here, we generated a novel neuron-specific Pten knock-out mouse model (Syn-Cre/Pten HOM) to test the ability of pharmacologic mTOR inhibition to rescue Pten mutation-associated disease phenotypes in vivo and in vitro. We found that treatment with the mTOR inhibitor, everolimus, increased the survival of Syn-Cre/Pten HOM mice while some neurologic phenotypes persisted. Transcriptomic analyses revealed that in contrast to mice harboring a neuron-specific deletion of the Tuberous Sclerosis Complex 2 gene (Syn-Cre/Tsc2 KO), genes that are under AKT regulation were significantly increased in the Syn-Cre/Pten HOM mice. In addition, genes associated with synapse, extracellular matrix, and myelination were broadly increased in Syn-Cre/Pten HOM mouse neocortex. These findings were confirmed by immunostaining of cortical sections in vivo, which revealed excessive immunoreactivity of myelin basic protein and perineuronal nets (PNN), the specialized extracellular matrix surrounding fast-spiking parvalbumin (PV) interneurons. We also detected increased expression of Synapsin I/PSD95 positive synapses and network hyperactivity phenotypes in Syn-Cre/Pten HOM mice neurons compared to wild-type (WT) neurons in vitro. Strikingly, everolimus treatment rescued the number of synapses and network hyperactivity in the Syn-Cre/Pten HOM mice cortical neuron cultures. Taken together, our results revealed in vivo and in vitro molecular and neuronal network mechanisms underlying neurological phenotypes of PHTS. Notably, pharmacologic mTOR inhibition by everolimus led to successful downstream signaling rescue, including mTOR complex 1 (mTORC1) site-specific suppression of S6 phosphorylation, correlating with phenotypic rescue found in our novel neuron-specific Syn-Cre/Pten HOM mice.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39994410,

title = {PTEN mutations impair CSF dynamics and cortical networks by dysregulating periventricular neural progenitors},

author = {Tyrone DeSpenza and Emre Kiziltug and Garrett Allington and Daniel G Barson and Stephen McGee and David O'Connor and Stephanie M Robert and Kedous Y Mekbib and Pranav Nanda and Ana B W Greenberg and Amrita Singh and Phan Q Duy and Francesca Mandino and Shujuan Zhao and Anna Lynn and Benjamin C Reeves and Arnaud Marlier and Stephanie A Getz and Carol Nelson-Williams and Hermela Shimelis and Lauren K Walsh and Junhui Zhang and Wei Wang and Mackenzi L Prina and Annaliese OuYang and Asan F Abdulkareem and Hannah Smith and John Shohfi and Neel H Mehta and Evan Dennis and Laetitia R Reduron and Jennifer Hong and William Butler and Bob S Carter and Engin Deniz and Evelyn M R Lake and R Todd Constable and Mustafa Sahin and Siddharth Srivastava and Kellen Winden and Ellen J Hoffman and Marina Carlson and Murat Gunel and Richard P Lifton and Seth L Alper and Sheng Chih Jin and Michael C Crair and Andres Moreno-De-Luca and Bryan W Luikart and Kristopher T Kahle},

doi = {10.1038/s41593-024-01865-3},

issn = {1546-1726},

year  = {2025},

date = {2025-03-01},

journal = {Nat Neurosci},

volume = {28},

number = {3},

pages = {536--557},

abstract = {Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (ventriculomegaly) is a defining feature of congenital hydrocephalus (CH) and an under-recognized concomitant of autism. Here, we show that de novo mutations in the autism risk gene PTEN are among the most frequent monogenic causes of CH and primary ventriculomegaly. Mouse Pten-mutant ventriculomegaly results from aqueductal stenosis due to hyperproliferation of periventricular Nkx2.1 neural progenitor cells (NPCs) and increased CSF production from hyperplastic choroid plexus. Pten-mutant ventriculomegalic cortices exhibit network dysfunction from increased activity of Nkx2.1 NPC-derived inhibitory interneurons. Raptor deletion or postnatal everolimus treatment corrects ventriculomegaly, rescues cortical deficits and increases survival by antagonizing mTORC1-dependent Nkx2.1 NPC pathology. Thus, PTEN mutations concurrently alter CSF dynamics and cortical networks by dysregulating Nkx2.1 NPCs. These results implicate a nonsurgical treatment for CH, demonstrate a genetic association of ventriculomegaly and ASD, and help explain neurodevelopmental phenotypes refractory to CSF shunting in select individuals with CH.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39612590,

title = {Construction destruction: Contribution of dyregulated proteostasis to neurodevelopmental disorders},

author = {Kellen D Winden and Juan F Ruiz and Mustafa Sahin},

doi = {10.1016/j.conb.2024.102934},

issn = {1873-6882},

year  = {2025},

date = {2025-02-01},

journal = {Curr Opin Neurobiol},

volume = {90},

pages = {102934},

abstract = {Genetic causes of neurodevelopmental disorders (NDDs) such as epilepsy and autism spectrum disorder are rapidly being uncovered. The genetic risk factors that are responsible for various NDDs fall into many categories, and while some genes such as those involved in synaptic transmission are expected, there are several other classes of genes whose involvement in these disorders is not intuitive. One such group of genes is involved in protein synthesis and degradation, and the balance between these opposing pathways is termed proteostasis. Here, we review these pathways, the genetics of the related neurological disorders, and some potential disease mechanisms. Improved understanding of this collection of genetic disorders will be informative for the pathogenesis of these disorders and imply novel therapeutic strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38110041,

title = {ALDH5A1-deficient iPSC-derived excitatory and inhibitory neurons display cell type specific alterations},

author = {Wardiya Afshar-Saber and Nicole A Teaney and Kellen D Winden and Hellen Jumo and Xutong Shi and Gabrielle McGinty and Jed Hubbs and Cidi Chen and Itay Tokatly Latzer and Federico Gasparoli and Darius Ebrahimi-Fakhari and Elizabeth D Buttermore and Jean-Baptiste Roullet and Phillip L Pearl and Mustafa Sahin},

doi = {10.1016/j.nbd.2023.106386},

issn = {1095-953X},

year  = {2024},

date = {2024-01-01},

journal = {Neurobiol Dis},

volume = {190},

pages = {106386},

abstract = {Succinic semialdehyde dehydrogenase deficiency (SSADHD) is a neurometabolic disorder caused by ALDH5A1 mutations presenting with autism and epilepsy. SSADHD leads to impaired GABA metabolism and results in accumulation of GABA and γ-hydroxybutyrate (GHB), which alter neurotransmission and are thought to lead to neurobehavioral symptoms. However, why increased inhibitory neurotransmitters lead to seizures remains unclear. We used induced pluripotent stem cells from SSADHD patients (one female and two male) and differentiated them into GABAergic and glutamatergic neurons. SSADHD iGABA neurons show altered GABA metabolism and concomitant changes in expression of genes associated with inhibitory neurotransmission. In contrast, glutamatergic neurons display increased spontaneous activity and upregulation of mitochondrial genes. CRISPR correction of the pathogenic variants or SSADHD mRNA expression rescue various metabolic and functional abnormalities in human neurons. Our findings uncover a previously unknown role for SSADHD in excitatory human neurons and provide unique insights into the cellular and molecular basis of SSADHD and potential therapeutic interventions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38233389,

title = {High-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia},

author = {Afshin Saffari and Barbara Brechmann and Cedric Böger and Wardiya Afshar Saber and Hellen Jumo and Dosh Whye and Delaney Wood and Lara Wahlster and Julian E Alecu and Marvin Ziegler and Marlene Scheffold and Kellen Winden and Jed Hubbs and Elizabeth D Buttermore and Lee Barrett and Georg H H Borner and Alexandra K Davies and Darius Ebrahimi-Fakhari and Mustafa Sahin},

doi = {10.1038/s41467-023-44264-1},

issn = {2041-1723},

year  = {2024},

date = {2024-01-01},

journal = {Nat Commun},

volume = {15},

number = {1},

pages = {584},

abstract = {Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adapter protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, BCH-HSP-C01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate potential mechanisms of action of BCH-HSP-C01. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39881808,

title = {Using cortical organoids to understand the pathogenesis of malformations of cortical development},

author = {Kellen D Winden and Isabel Gisser and Mustafa Sahin},

doi = {10.3389/fnins.2024.1522652},

issn = {1662-4548},

year  = {2024},

date = {2024-01-01},

journal = {Front Neurosci},

volume = {18},

pages = {1522652},

abstract = {Malformations of cortical development encompass a broad range of disorders associated with abnormalities in corticogenesis. Widespread abnormalities in neuronal formation or migration can lead to small head size or microcephaly with disorganized placement of cell types. Specific, localized malformations are termed focal cortical dysplasias (FCD). Neurodevelopmental disorders are common in all types of malformations of cortical development with the most prominent being refractory epilepsy, behavioral disorders such as autism spectrum disorder (ASD), and learning disorders. Several genetic pathways have been associated with these disorders from control of cell cycle and cytoskeletal dynamics in global malformations to variants in growth factor signaling pathways, especially those interacting with the mechanistic target of rapamycin (mTOR), in FCDs. Despite advances in understanding these disorders, the underlying developmental pathways that lead to lesion formation and mechanisms through which defects in cortical development cause specific neurological symptoms often remains unclear. One limitation is the difficulty in modeling these disorders, as animal models frequently do not faithfully mirror the human phenotype. To circumvent this obstacle, many investigators have turned to three-dimensional human stem cell models of the brain, known as organoids, because they recapitulate early neurodevelopmental processes. High throughput analysis of these organoids presents a promising opportunity to model pathophysiological processes across the breadth of malformations of cortical development. In this review, we highlight advances in understanding the pathophysiology of brain malformations using organoid models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37494191,

title = {Increased degradation of FMRP contributes to neuronal hyperexcitability in tuberous sclerosis complex},

author = {Kellen D Winden and Truc T Pham and Nicole A Teaney and Juan Ruiz and Ryan Chen and Cidi Chen and Mustafa Sahin},

doi = {10.1016/j.celrep.2023.112838},

issn = {2211-1247},

year  = {2023},

date = {2023-08-01},

journal = {Cell Rep},

volume = {42},

number = {8},

pages = {112838},

abstract = {Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental disorder, but new therapies have been impeded by a lack of understanding of the pathological mechanisms. Tuberous sclerosis complex (TSC) and fragile X syndrome are associated with alterations in the mechanistic target of rapamycin (mTOR) and fragile X messenger ribonucleoprotein 1 (FMRP), which have been implicated in the development of ASD. Previously, we observed that transcripts associated with FMRP were down-regulated in TSC2-deficient neurons. In this study, we find that FMRP turnover is dysregulated in TSC2-deficient rodent primary neurons and human induced pluripotent stem cell (iPSC)-derived neurons and is dependent on the E3 ubiquitin ligase anaphase-promoting complex. We also demonstrate that overexpression of FMRP can partially rescue hyperexcitability in TSC2-deficient iPSC-derived neurons. These data indicate that FMRP dysregulation represents an important pathological mechanism in the development of abnormal neuronal activity in TSC and illustrate a molecular convergence between these two neurogenetic disorders.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35800463,

title = {Translating Ribosome Affinity Purification (TRAP) of Cell Type-specific mRNA from Mouse Brain Lysates},

author = {Catherine L Salussolia and Kellen D Winden and Mustafa Sahin},

doi = {10.21769/BioProtoc.4407},

issn = {2331-8325},

year  = {2022},

date = {2022-05-01},

journal = {Bio Protoc},

volume = {12},

number = {9},

pages = {e4407},

abstract = {Mammalian tissues are highly heterogenous and complex, posing a challenge in understanding the molecular mechanisms regulating protein expression within various tissues. Recent studies have shown that translation at the level of the ribosome is highly regulated, and can vary independently of gene expression observed at a transcriptome level, as well as between cell populations, contributing to the diversity of mammalian tissues. Earlier methods that analyzed gene expression at the level of translation, such as polysomal- or ribosomal-profiling, required large amounts of starting material to isolate enough RNA for analysis by microarray or RNA-sequencing. Thus, rare or less abundant cell types within tissues were not able to be properly studied with these methods. Translating ribosome affinity purification (TRAP) utilizes the incorporation of an eGFP-affinity tag on the large ribosome subunit, driven by expression of cell-type specific Cre-lox promoters, to allow for identification and capture of transcripts from actively translating ribosomes in a cell-specific manner. As a result, TRAP offers a unique opportunity to evaluate the entire mRNA translation profile within a specific cell type, and increase our understanding regarding the cellular complexity of mammalian tissues.  Schematic demonstrating TRAP protocol for identifying ribosome-bound transcripts specifically within cerebellar Purkinje cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36405918,

title = {16p13.11 deletion variants associated with neuropsychiatric disorders cause morphological and synaptic changes in induced pluripotent stem cell-derived neurons},

author = {Elizabeth D Buttermore and Nickesha C Anderson and Pin-Fang Chen and Nina R Makhortova and Kristina H Kim and Syed M A Wafa and Sean Dwyer and John M Micozzi and Kellen D Winden and Bo Zhang and Min-Joon Han and Robin J Kleiman and Catherine A Brownstein and Mustafa Sahin and Joseph Gonzalez-Heydrich},

doi = {10.3389/fpsyt.2022.924956},

issn = {1664-0640},

year  = {2022},

date = {2022-01-01},

journal = {Front Psychiatry},

volume = {13},

pages = {924956},

abstract = {16p13.11 copy number variants (CNVs) have been associated with autism, schizophrenia, psychosis, intellectual disability, and epilepsy. The majority of 16p13.11 deletions or duplications occur within three well-defined intervals, and despite growing knowledge of the functions of individual genes within these intervals, the molecular mechanisms that underlie commonly observed clinical phenotypes remain largely unknown. Patient-derived, induced pluripotent stem cells (iPSCs) provide a platform for investigating the morphological, electrophysiological, and gene-expression changes that result from 16p13.11 CNVs in human-derived neurons. Patient derived iPSCs with varying sizes of 16p13.11 deletions and familial controls were differentiated into cortical neurons for phenotypic analysis. High-content imaging and morphological analysis of patient-derived neurons demonstrated an increase in neurite branching in patients compared with controls. Whole-transcriptome sequencing revealed expression level changes in neuron development and synaptic-related gene families, suggesting a defect in synapse formation. Subsequent quantification of synapse number demonstrated increased numbers of synapses on neurons derived from early-onset patients compared to controls. The identification of common phenotypes among neurons derived from patients with overlapping 16p13.11 deletions will further assist in ascertaining common pathways and targets that could be utilized for screening drug candidates. These studies can help to improve future treatment options and clinical outcomes for 16p13.11 deletion patients.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34706228,

title = {Arthritis flares mediated by tissue-resident memory T cells in the joint},

author = {Margaret H Chang and Anaïs Levescot and Nathan Nelson-Maney and Rachel B Blaustein and Kellen D Winden and Allyn Morris and Alexandra Wactor and Spoorthi Balu and Ricardo Grieshaber-Bouyer and Kevin Wei and Lauren A Henderson and Yoichiro Iwakura and Rachael A Clark and Deepak A Rao and Robert C Fuhlbrigge and Peter A Nigrovic},

doi = {10.1016/j.celrep.2021.109902},

issn = {2211-1247},

year  = {2021},

date = {2021-10-01},

journal = {Cell Rep},

volume = {37},

number = {4},

pages = {109902},

abstract = {Rheumatoid arthritis is a systemic autoimmune disease, but disease flares typically affect only a subset of joints, distributed in a distinctive pattern for each patient. Pursuing this intriguing pattern, we show that arthritis recurrence is mediated by long-lived synovial resident memory T cells (T). In three murine models, CD8+ cells bearing T markers remain in previously inflamed joints during remission. These cells are bona fide T, exhibiting a failure to migrate between joints, preferential uptake of fatty acids, and long-term residency. Disease flares result from T activation by antigen, leading to CCL5-mediated recruitment of circulating effector cells. Correspondingly, T depletion ameliorates recurrence in a site-specific manner. Human rheumatoid arthritis joint tissues contain a comparable CD8+-predominant T population, which is most evident in late-stage leukocyte-poor synovium, exhibiting limited T cell receptor diversity and a pro-inflammatory transcriptomic signature. Together, these findings establish synovial T as a targetable mediator of disease chronicity in autoimmune arthritis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34259631,

title = {Loss of Tsc1 in cerebellar Purkinje cells induces transcriptional and translation changes in FMRP target transcripts},

author = {Jasbir Singh Dalal and Kellen Diamond Winden and Catherine Lourdes Salussolia and Maria Sundberg and Achint Singh and Truc Thanh Pham and Pingzhu Zhou and William T Pu and Meghan T Miller and Mustafa Sahin},

doi = {10.7554/eLife.67399},

issn = {2050-084X},

year  = {2021},

date = {2021-07-01},

journal = {Elife},

volume = {10},

abstract = {Tuberous sclerosis complex (TSC) is a genetic disorder that is associated with multiple neurological manifestations. Previously, we demonstrated that  loss in cerebellar Purkinje cells (PCs) can cause altered social behavior in mice. Here, we performed detailed transcriptional and translational analyses of -deficient PCs to understand the molecular alterations in these cells. We found that target transcripts of the Fragile X Mental Retardation Protein (FMRP) are reduced in mutant PCs with evidence of increased degradation. Surprisingly, we observed unchanged ribosomal binding for many of these genes using translating ribosome affinity purification. Finally, we found that multiple FMRP targets, including SHANK2, were reduced, suggesting that compensatory increases in ribosomal binding efficiency may be unable to overcome reduced transcript levels. These data further implicate dysfunction of FMRP and its targets in TSC and suggest that treatments aimed at restoring the function of these pathways may be beneficial.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid34006844,

title = {16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro},

author = {Maria Sundberg and Hannah Pinson and Richard S Smith and Kellen D Winden and Pooja Venugopal and Derek J C Tai and James F Gusella and Michael E Talkowski and Christopher A Walsh and Max Tegmark and Mustafa Sahin},

doi = {10.1038/s41467-021-23113-z},

issn = {2041-1723},

year  = {2021},

date = {2021-05-01},

journal = {Nat Commun},

volume = {12},

number = {1},

pages = {2897},

abstract = {Reciprocal copy number variations (CNVs) of 16p11.2 are associated with a wide spectrum of neuropsychiatric and neurodevelopmental disorders. Here, we use human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neurons carrying CNVs of 16p11.2 duplication (16pdup) and 16p11.2 deletion (16pdel), engineered using CRISPR-Cas9. We show that 16pdel iPSC-derived DA neurons have increased soma size and synaptic marker expression compared to isogenic control lines, while 16pdup iPSC-derived DA neurons show deficits in neuronal differentiation and reduced synaptic marker expression. The 16pdel iPSC-derived DA neurons have impaired neurophysiological properties. The 16pdel iPSC-derived DA neuronal networks are hyperactive and have increased bursting in culture compared to controls. We also show that the expression of RHOA is increased in the 16pdel iPSC-derived DA neurons and that treatment with a specific RHOA-inhibitor, Rhosin, rescues the network activity of the 16pdel iPSC-derived DA neurons. Our data suggest that 16p11.2 deletion-associated iPSC-derived DA neuron hyperactivation can be rescued by RHOA inhibition.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid33051600,

title = {Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile},

author = {Krinio Giannikou and Zachary Zhu and Jaegil Kim and Kellen D Winden and Magdalena E Tyburczy and David Marron and Joel S Parker and Zachary Hebert and Anika Bongaarts and Len Taing and Henry W Long and William V Pisano and Sanda Alexandrescu and Brianna Godlewski and Mark Nellist and Katarzyna Kotulska and Sergiusz Jozwiak and Marcin Roszkowski and Marek Mandera and Elizabeth A Thiele and Hart Lidov and Gad Getz and Orrin Devinsky and Michael S Lawrence and Keith L Ligon and David W Ellison and Mustafa Sahin and Eleonora Aronica and David M Meredith and David J Kwiatkowski},

doi = {10.1038/s41379-020-00659-9},

issn = {1530-0285},

year  = {2021},

date = {2021-02-01},

journal = {Mod Pathol},

volume = {34},

number = {2},

pages = {264--279},

abstract = {Subependymal giant-cell astrocytomas (SEGAs) are slow-growing brain tumors that are a hallmark feature seen in 5-10% of patients with Tuberous Sclerosis Complex (TSC). Though histologically benign, they can cause serious neurologic symptoms, leading to death if untreated. SEGAs consistently show biallelic loss of TSC1 or TSC2. Herein, we aimed to define other somatic events beyond TSC1/TSC2 loss and identify potential transcriptional drivers that contribute to SEGA formation. Paired tumor-normal whole-exome sequencing was performed on 21 resected SEGAs from 20 TSC patients. Pathogenic variants in TSC1/TSC2 were identified in 19/21 (90%) SEGAs. Copy neutral loss of heterozygosity (size range: 2.2-46 Mb) was seen in 76% (16/21) of SEGAs (44% chr9q and 56% chr16p). An average of 1.4 other somatic variants (range 0-7) per tumor were identified, unlikely of pathogenic significance. Whole transcriptome RNA-sequencing analyses revealed 190 common differentially expressed genes in SEGA (n = 16, 13 from a prior study) in pairwise comparison to each of: low grade diffuse gliomas (n = 530) and glioblastoma (n = 171) from The Cancer Genome Atlas (TCGA) consortium, ganglioglioma (n = 10), TSC cortical tubers (n = 15), and multiple normal tissues. Among these, homeobox transcription factors (TFs) HMX3, HMX2, VAX1, SIX3; and TFs IRF6 and EOMES were all expressed >12-fold higher in SEGAs (FDR/q-value < 0.05). Immunohistochemistry supported the specificity of IRF6, VAX1, SIX3 for SEGAs in comparison to other tumor entities and normal brain. We conclude that SEGAs have an extremely low somatic mutation rate, suggesting that TSC1/TSC2 loss is sufficient to drive tumor growth. The unique and highly expressed SEGA-specific TFs likely reflect the neuroepithelial cell of origin, and may also contribute to the transcriptional and epigenetic state that enables SEGA growth following two-hit loss of TSC1 or TSC2 and mTORC1 activation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32579942,

title = {Phenotypic Screen with TSC-Deficient Neurons Reveals Heat-Shock Machinery as a Druggable Pathway for mTORC1 and Reduced Cilia},

author = {Alessia Di Nardo and Isadora Lenoël and Kellen D Winden and Alina Rühmkorf and Meera E Modi and Lee Barrett and Ebru Ercan-Herbst and Pooja Venugopal and Robert Behne and Carla A M Lopes and Robin J Kleiman and Mónica Bettencourt-Dias and Mustafa Sahin},

doi = {10.1016/j.celrep.2020.107780},

issn = {2211-1247},

year  = {2020},

date = {2020-06-01},

journal = {Cell Rep},

volume = {31},

number = {12},

pages = {107780},

abstract = {Tuberous sclerosis complex (TSC) is a neurogenetic disorder that leads to elevated mechanistic targeting of rapamycin complex 1 (mTORC1) activity. Cilia can be affected by mTORC1 signaling, and ciliary deficits are associated with neurodevelopmental disorders. Here, we examine whether neuronal cilia are affected in TSC. We show that cortical tubers from TSC patients and mutant mouse brains have fewer cilia. Using high-content image-based assays, we demonstrate that mTORC1 activity inversely correlates with ciliation in TSC1/2-deficient neurons. To investigate the mechanistic relationship between mTORC1 and cilia, we perform a phenotypic screen for mTORC1 inhibitors with TSC1/2-deficient neurons. We identify inhibitors of the heat shock protein 90 (Hsp90) that suppress mTORC1 through regulation of phosphatidylinositol 3-kinase (PI3K)/Akt signaling. Pharmacological inhibition of Hsp90 rescues ciliation through downregulation of Hsp27. Our study uncovers the heat-shock machinery as a druggable signaling node to restore mTORC1 activity and cilia due to loss of TSC1/2, and it provides broadly applicable platforms for studying TSC-related neuronal dysfunction.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31591157,

title = {Biallelic Mutations in  Lead to Abnormalities Associated with Cortical Tubers in Human iPSC-Derived Neurons},

author = {Kellen D Winden and Maria Sundberg and Cindy Yang and Syed M A Wafa and Sean Dwyer and Pin-Fang Chen and Elizabeth D Buttermore and Mustafa Sahin},

doi = {10.1523/JNEUROSCI.0642-19.2019},

issn = {1529-2401},

year  = {2019},

date = {2019-11-01},

journal = {J Neurosci},

volume = {39},

number = {47},

pages = {9294--9305},

abstract = {Tuberous sclerosis complex (TSC) is a genetic disorder caused by mutations in  or  Patients frequently have epilepsy, autism spectrum disorder, and/or intellectual disability, as well as other systemic manifestations. In this study, we differentiated human induced pluripotent stem cells (iPSCs) from a female patient with TSC with one or two mutations in  into neurons using induced expression of NGN2 to examine neuronal dysregulation associated with the neurological symptoms in TSC. Using this method, neuronal differentiation was comparable between the three genotypes of iPSCs. We observed that  neurons show mTOR complex 1 (mTORC1) hyperactivation and associated increased cell body size and process outgrowth, as well as exacerbation of the abnormalities by loss of the second allele of  in  neurons. Interestingly, iPSC-derived neurons with either a single or biallelic mutation in  demonstrated hypersynchrony and downregulation of FMRP targets. However, only neurons with biallelic mutations of  demonstrated hyperactivity and transcriptional dysregulation observed in cortical tubers. These data demonstrate that loss of one allele of  is sufficient to cause some morphological and physiological changes in human neurons but that biallelic mutations in  are necessary to induce gene expression dysregulation present in cortical tubers. Finally, we found that treatment of iPSC-derived neurons with rapamycin reduced neuronal activity and partially reversed gene expression abnormalities, demonstrating that mTOR dysregulation contributes to both phenotypes. Therefore, biallelic mutations in  and associated molecular dysfunction, including mTOR hyperactivation, may play a role in the development of cortical tubers. In this study, we examined neurons derived from induced pluripotent stem cells with two, one, or no functional  (tuberous sclerosis complex 2) alleles and found that loss of one or both alleles of  results in mTORC1 hyperactivation and specific neuronal abnormalities. However, only biallelic mutations in  resulted in elevated neuronal activity and upregulation of cell adhesion genes that is also observed in cortical tubers. These data suggest that loss of heterozygosity of  or  may play an important role in the development of cortical tubers, and potentially epilepsy, in patients with TSC.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29449635,

title = {Purkinje cells derived from TSC patients display hypoexcitability and synaptic deficits associated with reduced FMRP levels and reversed by rapamycin},

author = {Maria Sundberg and Ivan Tochitsky and David E Buchholz and Kellen Winden and Ville Kujala and Kush Kapur and Deniz Cataltepe and Daria Turner and Min-Joon Han and Clifford J Woolf and Mary E Hatten and Mustafa Sahin},

doi = {10.1038/s41380-018-0018-4},

issn = {1476-5578},

year  = {2018},

date = {2018-11-01},

journal = {Mol Psychiatry},

volume = {23},

number = {11},

pages = {2167--2183},

abstract = {Accumulating evidence suggests that cerebellar dysfunction early in life is associated with autism spectrum disorder (ASD), but the molecular mechanisms underlying the cerebellar deficits at the cellular level are unclear. Tuberous sclerosis complex (TSC) is a neurocutaneous disorder that often presents with ASD. Here, we developed a cerebellar Purkinje cell (PC) model of TSC with patient-derived human induced pluripotent stem cells (hiPSCs) to characterize the molecular mechanisms underlying cerebellar abnormalities in ASD and TSC. Our results show that hiPSC-derived PCs from patients with pathogenic TSC2 mutations displayed mTORC1 pathway hyperactivation, defects in neuronal differentiation and RNA regulation, hypoexcitability and reduced synaptic activity when compared with those derived from controls. Our gene expression analyses revealed downregulation of several components of fragile X mental retardation protein (FMRP) targets in TSC2-deficient hiPSC-PCs. We detected decreased expression of FMRP, glutamate receptor δ2 (GRID2), and pre- and post-synaptic markers such as synaptophysin and PSD95 in the TSC2-deficient hiPSC-PCs. The mTOR inhibitor rapamycin rescued the deficits in differentiation, synaptic dysfunction, and hypoexcitability of TSC2 mutant hiPSC-PCs in vitro. Our findings suggest that these gene expression changes and cellular abnormalities contribute to aberrant PC function during development in TSC affected individuals.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid29490194,

title = {Abnormal mTOR Activation in Autism},

author = {Kellen D Winden and Darius Ebrahimi-Fakhari and Mustafa Sahin},

doi = {10.1146/annurev-neuro-080317-061747},

issn = {1545-4126},

year  = {2018},

date = {2018-07-01},

journal = {Annu Rev Neurosci},

volume = {41},

pages = {1--23},

abstract = {The mechanistic target of rapamycin (mTOR) is an important signaling hub that integrates environmental information regarding energy availability and stimulates anabolic molecular processes and cell growth. Abnormalities in this pathway have been identified in several syndromes in which autism spectrum disorder (ASD) is highly prevalent. Several studies have investigated mTOR signaling in developmental and neuronal processes that, when dysregulated, could contribute to the development of ASD. Although many potential mechanisms still remain to be fully understood, these associations are of great interest because of the clinical availability of mTOR inhibitors. Clinical trials evaluating the efficacy of mTOR inhibitors to improve neurodevelopmental outcomes have been initiated.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28183733,

title = {Neuronal CTGF/CCN2 negatively regulates myelination in a mouse model of tuberous sclerosis complex},

author = {Ebru Ercan and Juliette M Han and Alessia Di Nardo and Kellen Winden and Min-Joon Han and Leonie Hoyo and Afshin Saffari and Andrew Leask and Daniel H Geschwind and Mustafa Sahin},

doi = {10.1084/jem.20160446},

issn = {1540-9538},

year  = {2017},

date = {2017-03-01},

journal = {J Exp Med},

volume = {214},

number = {3},

pages = {681--697},

abstract = {Disruption of myelination during development has been implicated in a range of neurodevelopmental disorders including tuberous sclerosis complex (TSC). TSC patients with autism display impairments in white matter integrity. Similarly, mice lacking neuronal  have a hypomyelination phenotype. However, the mechanisms that underlie these phenotypes remain unknown. In this study, we demonstrate that neuronal TSC1/2 orchestrates a program of oligodendrocyte maturation through the regulated secretion of connective tissue growth factor (CTGF). We characterize oligodendrocyte maturation both in vitro and in vivo. We find that neuron-specific  deletion results in an increase in CTGF secretion that non-cell autonomously stunts oligodendrocyte development and decreases the total number of oligodendrocytes. Genetic deletion of CTGF from neurons, in turn, mitigates the TSC-dependent hypomyelination phenotype. These results show that the mechanistic target of rapamycin (mTOR) pathway in neurons regulates CTGF production and secretion, revealing a paracrine mechanism by which neuronal signaling regulates oligodendrocyte maturation and myelination in TSC. This study highlights the role of mTOR-dependent signaling between neuronal and nonneuronal cells in the regulation of myelin and identifies an additional therapeutic avenue for this disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid27005422,

title = {Cell-type-specific miR-431 dysregulation in a motor neuron model of spinal muscular atrophy},

author = {Mary H Wertz and Kellen Winden and Pierre Neveu and Shi-Yan Ng and Ebru Ercan and Mustafa Sahin},

doi = {10.1093/hmg/ddw084},

issn = {1460-2083},

year  = {2016},

date = {2016-06-01},

journal = {Hum Mol Genet},

volume = {25},

number = {11},

pages = {2168--2181},

abstract = {Spinal muscular atrophy (SMA) is an autosomal-recessive pediatric neurodegenerative disease characterized by selective loss of spinal motor neurons. It is caused by mutation in the survival of motor neuron 1, SMN1, gene and leads to loss of function of the full-length SMN protein. microRNAs (miRNAs) are small RNAs that are involved in post-transcriptional regulation of gene expression. Prior studies have implicated miRNAs in the pathogenesis of motor neuron disease. We hypothesized that motor neuron-specific miRNA expression changes are involved in their selective vulnerability in SMA. Therefore, we sought to determine the effect of SMN loss on miRNAs and their target mRNAs in spinal motor neurons. We used microarray and RNAseq to profile both miRNA and mRNA expression in primary spinal motor neuron cultures after acute SMN knockdown. By integrating the miRNA:mRNA profiles, a number of dysregulated miRNAs were identified with enrichment in differentially expressed putative mRNA targets. miR-431 expression was highly increased, and a number of its putative mRNA targets were significantly downregulated in motor neurons after SMN loss. Further, we found that miR-431 regulates motor neuron neurite length by targeting several molecules previously identified to play a role in motor neuron axon outgrowth, including chondrolectin. Together, our findings indicate that cell-type-specific dysregulation of miR-431 plays a role in the SMA motor neuron phenotype.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25818007,

title = {Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy},

author = {Kellen D Winden and Anatol Bragin and Jerome Engel and Dan H Geschwind},

doi = {10.1016/j.nbd.2015.02.011},

issn = {1095-953X},

year  = {2015},

date = {2015-06-01},

journal = {Neurobiol Dis},

volume = {78},

pages = {35--44},

abstract = {The molecular basis of epileptogenesis is poorly characterized. Studies in humans and animal models have identified an electrophysiological signature that precedes the onset of epilepsy, which has been termed fast ripples (FRs) based on its frequency. Multiple lines of evidence implicate regions generating FRs in epileptogenesis, and FRs appear to demarcate the seizure onset zone, suggesting a role in ictogenesis as well. We performed gene expression analysis comparing areas of the dentate gyrus that generate FRs to those that do not generate FRs in a well-characterized rat model of epilepsy. We identified a small cohort of genes that are differentially expressed in FR versus non-FR brain tissue and used quantitative PCR to validate some of those that modulate neuronal excitability. Gene expression network analysis demonstrated conservation of gene co-expression between non-FR and FR samples, but examination of gene connectivity revealed changes that were most pronounced in the cm-40 module, which contains several genes associated with synaptic function and the differentially expressed genes Kcna4, Kcnv1, and Npy1r that are down-regulated in FRs. We then demonstrate that the genes within the cm-40 module are regulated by seizure activity and enriched for the targets of the RNA binding protein Elavl4. Our data suggest that seizure activity induces co-expression of genes associated with synaptic transmission and that this pattern is attenuated in areas displaying FRs, implicating the failure of this mechanism in the generation of FRs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid26060907,

title = {Megalencephaly and Macrocephaly},

author = {Kellen D Winden and Christopher J Yuskaitis and Annapurna Poduri},

doi = {10.1055/s-0035-1552622},

issn = {1098-9021},

year  = {2015},

date = {2015-06-01},

journal = {Semin Neurol},

volume = {35},

number = {3},

pages = {277--287},

abstract = {Megalencephaly is a developmental disorder characterized by brain overgrowth secondary to increased size and/or numbers of neurons and glia. These disorders can be divided into metabolic and developmental categories based on their molecular etiologies. Metabolic megalencephalies are mostly caused by genetic defects in cellular metabolism, whereas developmental megalencephalies have recently been shown to be caused by alterations in signaling pathways that regulate neuronal replication, growth, and migration. These disorders often lead to epilepsy, developmental disabilities, and behavioral problems; specific disorders have associations with overgrowth or abnormalities in other tissues. The molecular underpinnings of many of these disorders are now understood, providing insight into how dysregulation of critical pathways leads to disease. The advances in molecular understanding are leading to improved diagnosis of these conditions, as well as providing new avenues for therapeutic interventions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid23551880,

title = {Stroke in primary hyperoxaluria type I},

author = {Neal M Rao and Anil Yallapragada and Kellen D Winden and Jeffrey Saver and David S Liebeskind},

doi = {10.1111/jon.12020},

issn = {1552-6569},

year  = {2014},

date = {2014-01-01},

journal = {J Neuroimaging},

volume = {24},

number = {4},

pages = {411--413},

abstract = {We report the case of a 27-year-old man with a history of previously undiagnosed renal disease that presented with multiple cerebrovascular infarctions. Workup for traditional causes of cerebrovascular infarction including cardiac telemetry, multiple echocardiograms, and hypercoagulative workup was negative. However, a transcranial Doppler detected circulating microemboli at the rate of 14 per hour. A serum oxalate level greater than the supersaturation point of calcium oxalate was detected, providing a potential source of the microemboli. Furthermore, serial imaging recorded rapid mineralization of the infarcted territories. In the absence of any proximal vessel irregularities, atherosclerosis, valvular abnormalities, arrhythmias, or systemic shunt as potential stroke etiology in this patient, we propose that circulating oxalate precipitate may be a potential mechanism for stroke in patients with primary oxalosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22920253,

title = {Human-specific transcriptional networks in the brain},

author = {Genevieve Konopka and Tara Friedrich and Jeremy Davis-Turak and Kellen Winden and Michael C Oldham and Fuying Gao and Leslie Chen and Guang-Zhong Wang and Rui Luo and Todd M Preuss and Daniel H Geschwind},

doi = {10.1016/j.neuron.2012.05.034},

issn = {1097-4199},

year  = {2012},

date = {2012-08-01},

journal = {Neuron},

volume = {75},

number = {4},

pages = {601--617},

abstract = {Understanding human-specific patterns of brain gene expression and regulation can provide key insights into human brain evolution and speciation. Here, we use next-generation sequencing, and Illumina and Affymetrix microarray platforms, to compare the transcriptome of human, chimpanzee, and macaque telencephalon. Our analysis reveals a predominance of genes differentially expressed within human frontal lobe and a striking increase in transcriptional complexity specific to the human lineage in the frontal lobe. In contrast, caudate nucleus gene expression is highly conserved. We also identify gene coexpression signatures related to either neuronal processes or neuropsychiatric diseases, including a human-specific module with CLOCK as its hub gene and another module enriched for neuronal morphological processes and genes coexpressed with FOXP2, a gene important for language evolution. These data demonstrate that transcriptional networks have undergone evolutionary remodeling even within a given brain region, providing a window through which to view the foundation of uniquely human cognitive capacities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21868380,

title = {Substrate sequence influences γ-secretase modulator activity, role of the transmembrane domain of the amyloid precursor protein},

author = {Sarah A Sagi and Christian B Lessard and Kellen D Winden and Hiroko Maruyama and Jeremy C Koo and Sascha Weggen and Thomas L Kukar and Todd E Golde and Edward H Koo},

doi = {10.1074/jbc.M111.277228},

issn = {1083-351X},

year  = {2011},

date = {2011-11-01},

journal = {J Biol Chem},

volume = {286},

number = {46},

pages = {39794--39803},

abstract = {A subset of non-steroidal anti-inflammatory drugs modulates the γ cleavage site in the amyloid precursor protein (APP) to selectively reduce production of Aβ42. It is unclear precisely how these γ-secretase modulators (GSMs) act to preferentially spare Aβ40 production as well as Notch processing and signaling. In an effort to determine the substrate requirements in NSAID/GSM activity, we determined the effects of sulindac sulfide and flurbiprofen on γ-cleavage of artificial constructs containing several γ-secretase substrates. Using FLAG-tagged constructs that expressed extracellularly truncated APP, Notch-1, or CD44, we found that these substrates have different sensitivities to sulindac sulfide. γ-Secretase cleavage of APP was altered by sulindac sulfide, but CD44 and Notch-1 were either insensitive or only minimally altered by this compound. Using chimeric APP constructs, we observed that the transmembrane domain (TMD) of APP played a pivotal role in determining drug sensitivity. Substituting the APP TMD with that of APLP2 retained the sensitivity to γ-cleavage modulation, but replacing TMDs from Notch-1 or ErbB4 rendered the resultant molecules insensitive to drug treatment. Specifically, the GXXXG motif within APP appeared to be critical to GSM activity. Consequently, the modulatory effects on γ-cleavage appears to be substrate-dependent. We hypothesize that the substrate present in the γ-secretase complex influences the conformation of the complex so that the binding site of GSMs is either stabilized or less favorable to influence the cleavage of the respective substrates.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21943601,

title = {Functional genomic analyses identify pathways dysregulated by progranulin deficiency, implicating Wnt signaling},

author = {Ezra Y Rosen and Eric M Wexler and Revital Versano and Giovanni Coppola and Fuying Gao and Kellen D Winden and Michael C Oldham and Lauren Herl Martens and Ping Zhou and Robert V Farese and Daniel H Geschwind},

doi = {10.1016/j.neuron.2011.07.021},

issn = {1097-4199},

year  = {2011},

date = {2011-09-01},

journal = {Neuron},

volume = {71},

number = {6},

pages = {1030--1042},

abstract = {Progranulin (GRN) mutations cause frontotemporal dementia (FTD), but GRN's function in the CNS remains largely unknown. To identify the pathways downstream of GRN, we used weighted gene coexpression network analysis (WGCNA) to develop a systems-level view of transcriptional alterations in a human neural progenitor model of GRN-deficiency. This highlighted key pathways such as apoptosis and ubiquitination in GRN deficient human neurons, while revealing an unexpected major role for the Wnt signaling pathway, which was confirmed by analysis of gene expression data from postmortem FTD brain. Furthermore, we observed that the Wnt receptor Fzd2 was one of only a few genes upregulated at 6 weeks in a GRN knockout mouse, and that FZD2 reduction caused increased apoptosis, while its upregulation promoted neuronal survival in vitro. Together, these in vitro and in vivo data point to an adaptive role for altered Wnt signaling in GRN deficiency-mediated FTD, representing a potential therapeutic target.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21962519,

title = {Absence of CNTNAP2 leads to epilepsy, neuronal migration abnormalities, and core autism-related deficits},

author = {Olga Peñagarikano and Brett S Abrahams and Edward I Herman and Kellen D Winden and Amos Gdalyahu and Hongmei Dong and Lisa I Sonnenblick and Robin Gruver and Joel Almajano and Anatol Bragin and Peyman Golshani and Joshua T Trachtenberg and Elior Peles and Daniel H Geschwind},

doi = {10.1016/j.cell.2011.08.040},

issn = {1097-4172},

year  = {2011},

date = {2011-09-01},

journal = {Cell},

volume = {147},

number = {1},

pages = {235--246},

abstract = {Although many genes predisposing to autism spectrum disorders (ASD) have been identified, the biological mechanism(s) remain unclear. Mouse models based on human disease-causing mutations provide the potential for understanding gene function and novel treatment development. Here, we characterize a mouse knockout of the Cntnap2 gene, which is strongly associated with ASD and allied neurodevelopmental disorders. Cntnap2(-/-) mice show deficits in the three core ASD behavioral domains, as well as hyperactivity and epileptic seizures, as have been reported in humans with CNTNAP2 mutations. Neuropathological and physiological analyses of these mice before the onset of seizures reveal neuronal migration abnormalities, reduced number of interneurons, and abnormal neuronal network activity. In addition, treatment with the FDA-approved drug risperidone ameliorates the targeted repetitive behaviors in the mutant mice. These data demonstrate a functional role for CNTNAP2 in brain development and provide a new tool for mechanistic and therapeutic research in ASD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21695113,

title = {A systems level, functional genomics analysis of chronic epilepsy},

author = {Kellen D Winden and Stanislav L Karsten and Anatol Bragin and Lili C Kudo and Lauren Gehman and Josephine Ruidera and Daniel H Geschwind and Jerome Engel},

doi = {10.1371/journal.pone.0020763},

issn = {1932-6203},

year  = {2011},

date = {2011-01-01},

journal = {PLoS One},

volume = {6},

number = {6},

pages = {e20763},

abstract = {Neither the molecular basis of the pathologic tendency of neuronal circuits to generate spontaneous seizures (epileptogenicity) nor anti-epileptogenic mechanisms that maintain a seizure-free state are well understood. Here, we performed transcriptomic analysis in the intrahippocampal kainate model of temporal lobe epilepsy in rats using both Agilent and Codelink microarray platforms to characterize the epileptic processes. The experimental design allowed subtraction of the confounding effects of the lesion, identification of expression changes associated with epileptogenicity, and genes upregulated by seizures with potential homeostatic anti-epileptogenic effects. Using differential expression analysis, we identified several hundred expression changes in chronic epilepsy, including candidate genes associated with epileptogenicity such as Bdnf and Kcnj13. To analyze these data from a systems perspective, we applied weighted gene co-expression network analysis (WGCNA) to identify groups of co-expressed genes (modules) and their central (hub) genes. One such module contained genes upregulated in the epileptogenic region, including multiple epileptogenicity candidate genes, and was found to be involved the protection of glial cells against oxidative stress, implicating glial oxidative stress in epileptogenicity. Another distinct module corresponded to the effects of chronic seizures and represented changes in neuronal synaptic vesicle trafficking. We found that the network structure and connectivity of one hub gene, Sv2a, showed significant changes between normal and epileptogenic tissue, becoming more highly connected in epileptic brain. Since Sv2a is a target of the antiepileptic levetiracetam, this module may be important in controlling seizure activity. Bioinformatic analysis of this module also revealed a potential mechanism for the observed transcriptional changes via generation of longer alternatively polyadenlyated transcripts through the upregulation of the RNA binding protein HuD. In summary, combining conventional statistical methods and network analysis allowed us to interpret the differentially regulated genes from a systems perspective, yielding new insight into several biological pathways underlying homeostatic anti-epileptogenic effects and epileptogenicity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19907493,

title = {Human-specific transcriptional regulation of CNS development genes by FOXP2},

author = {Genevieve Konopka and Jamee M Bomar and Kellen Winden and Giovanni Coppola and Zophonias O Jonsson and Fuying Gao and Sophia Peng and Todd M Preuss and James A Wohlschlegel and Daniel H Geschwind},

doi = {10.1038/nature08549},

issn = {1476-4687},

year  = {2009},

date = {2009-11-01},

journal = {Nature},

volume = {462},

number = {7270},

pages = {213--217},

abstract = {The signalling pathways controlling both the evolution and development of language in the human brain remain unknown. So far, the transcription factor FOXP2 (forkhead box P2) is the only gene implicated in Mendelian forms of human speech and language dysfunction. It has been proposed that the amino acid composition in the human variant of FOXP2 has undergone accelerated evolution, and this two-amino-acid change occurred around the time of language emergence in humans. However, this remains controversial, and whether the acquisition of these amino acids in human FOXP2 has any functional consequence in human neurons remains untested. Here we demonstrate that these two human-specific amino acids alter FOXP2 function by conferring differential transcriptional regulation in vitro. We extend these observations in vivo to human and chimpanzee brain, and use network analysis to identify novel relationships among the differentially expressed genes. These data provide experimental support for the functional relevance of changes in FOXP2 that occur on the human lineage, highlighting specific pathways with direct consequences for human brain development and disease in the central nervous system (CNS). Because FOXP2 has an important role in speech and language in humans, the identified targets may have a critical function in the development and evolution of language circuitry in humans.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19638972,

title = {The organization of the transcriptional network in specific neuronal classes},

author = {Kellen D Winden and Michael C Oldham and Karoly Mirnics and Philip J Ebert and Christo H Swan and Pat Levitt and John L Rubenstein and Steve Horvath and Daniel H Geschwind},

doi = {10.1038/msb.2009.46},

issn = {1744-4292},

year  = {2009},

date = {2009-01-01},

journal = {Mol Syst Biol},

volume = {5},

pages = {291},

abstract = {Genome-wide expression profiling has aided the understanding of the molecular basis of neuronal diversity, but achieving broad functional insight remains a considerable challenge. Here, we perform the first systems-level analysis of microarray data from single neuronal populations using weighted gene co-expression network analysis to examine how neuronal transcriptome organization relates to neuronal function and diversity. We systematically validate network predictions using published proteomic and genomic data. Several network modules of co-expressed genes correspond to interneuron development programs, in which the hub genes are known to be critical for interneuron specification. Other co-expression modules relate to fundamental cellular functions, such as energy production, firing rate, trafficking, and synapses, suggesting that fundamental aspects of neuronal diversity are produced by quantitative variation in basic metabolic processes. We identify two transcriptionally distinct mitochondrial modules and demonstrate that one corresponds to mitochondria enriched in neuronal processes and synapses, whereas the other represents a population restricted to the soma. Finally, we show that galectin-1 is a new interneuron marker, and we validate network predictions in vivo using Rgs4 and Dlx1/2 knockout mice. These analyses provide a basis for understanding how specific aspects of neuronal phenotypic diversity are organized at the transcriptional level.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}