11 results on '"Nowakowski, Tomasz J."'
Search Results
2. Massively parallel characterization of regulatory elements in the developing human cortex.
- Author
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Chengyu Deng, Whalen, Sean, Steyert, Marilyn, Ziffra, Ryan, Przytycki, Pawel F., Inoue, Fumitaka, Pereira, Daniela A., Capauto, Davide, Norton, Scott, Vaccarino, Flora M., Pollen, Alex A., Nowakowski, Tomasz J., Ahituv, Nadav, and Pollard, Katherine S.
- Published
- 2024
- Full Text
- View/download PDF
3. Spatiotemporal molecular dynamics of the developing human thalamus.
- Author
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Kim, Chang N., Shin, David, Wang, Albert, and Nowakowski, Tomasz J.
- Published
- 2023
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4. Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.
- Author
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Nowakowski, Tomasz J., Bhaduri, Aparna, Pollen, Alex A., Alvarado, Beatriz, Mostajo-Radji, Mohammed A., Di Lullo, Elizabeth, Haeussler, Maximilian, Sandoval-Espinosa, Carmen, Liu, Siyuan John, Velmeshev, Dmitry, Ounadjela, Johain Ryad, Shuga, Joe, Xiaohui Wang, Lim, Daniel A., West, Jay A., Leyrat, Anne A., Kent, W. James, and Kriegstein, Arnold R.
- Subjects
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SPATIOTEMPORAL processes , *GENE expression , *DEVELOPMENTAL neurobiology , *HIERARCHIES , *NEUROGLIA , *CELL differentiation - Abstract
Systematic analyses of spatiotemporal gene expression trajectories during organogenesis have been challenging because diverse cell types at different stages of maturation and differentiation coexist in the emerging tissues. We identified discrete cell types as well as temporally and spatially restricted trajectories of radial glia maturation and neurogenesis in developing human telencephalon. These lineage-specific trajectories reveal the expression of neurogenic transcription factors in early radial glia and enriched activation of mammalian target of rapamycin signaling in outer radial glia. Across cortical areas, modest transcriptional differences among radial glia cascade into robust typological distinctions among maturing neurons. Together, our results support a mixed model of topographical, typological, and temporal hierarchies governing cell-type diversity in the developing human telencephalon, including distinct excitatory lineages emerging in rostral and caudal cerebral cortex. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
5. Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy.
- Author
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Danqing Zhu, Brookes, David H., Busia, Akosua, Carneiro, Ana, Fannjiang, Clara, Popova, Galina, Shin, David, Donohue, Kevin C., Lin, Li F., Miller, Zachary M., Williams, Evan R., Chang, Edward F., Nowakowski, Tomasz J., Listgarten, Jennifer, and Schaffer, David V.
- Subjects
- *
ADENO-associated virus , *GENE therapy , *MACHINE learning , *PEPTIDES - Abstract
Adeno-associated viruses (AAVs) hold tremendous promise as delivery vectors for gene therapies. AAVs have been successfully engineered--for instance, for more efficient and/or cell-specific delivery to numerous tissues--by creating large, diverse starting libraries and selecting for desired properties. However, these starting libraries often contain a high proportion of variants unable to assemble or package their genomes, a prerequisite for any gene delivery goal. Here, we present and showcase a machine learning (ML) method for designing AAV peptide insertion libraries that achieve fivefold higher packaging fitness than the standard NNK library with negligible reduction in diversity. To demonstrate our ML-designed library's utility for downstream engineering goals, we show that it yields approximately 10-fold more successful variants than the NNK library after selection for infection of human brain tissue, leading to a promising glial-specific variant. Moreover, our design approach can be applied to other types of libraries for AAV and beyond. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
6. Massively parallel characterization of regulatory elements in the developing human cortex.
- Author
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Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen AA, Nowakowski TJ, Ahituv N, and Pollard KS
- Subjects
- Humans, Chromatin metabolism, Chromatin genetics, Deep Learning, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Neurons metabolism, Regulatory Sequences, Nucleic Acid, Promoter Regions, Genetic, Regulatory Elements, Transcriptional, Cerebral Cortex embryology, Cerebral Cortex metabolism, Neurogenesis genetics, Organoids metabolism
- Abstract
Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.
- Published
- 2024
- Full Text
- View/download PDF
7. Optimal trade-off control in machine learning-based library design, with application to adeno-associated virus (AAV) for gene therapy.
- Author
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Zhu D, Brookes DH, Busia A, Carneiro A, Fannjiang C, Popova G, Shin D, Donohue KC, Lin LF, Miller ZM, Williams ER, Chang EF, Nowakowski TJ, Listgarten J, and Schaffer DV
- Subjects
- Humans, Peptide Library, Brain, Machine Learning, Dependovirus genetics, Genetic Therapy
- Abstract
Adeno-associated viruses (AAVs) hold tremendous promise as delivery vectors for gene therapies. AAVs have been successfully engineered-for instance, for more efficient and/or cell-specific delivery to numerous tissues-by creating large, diverse starting libraries and selecting for desired properties. However, these starting libraries often contain a high proportion of variants unable to assemble or package their genomes, a prerequisite for any gene delivery goal. Here, we present and showcase a machine learning (ML) method for designing AAV peptide insertion libraries that achieve fivefold higher packaging fitness than the standard NNK library with negligible reduction in diversity. To demonstrate our ML-designed library's utility for downstream engineering goals, we show that it yields approximately 10-fold more successful variants than the NNK library after selection for infection of human brain tissue, leading to a promising glial-specific variant. Moreover, our design approach can be applied to other types of libraries for AAV and beyond.
- Published
- 2024
- Full Text
- View/download PDF
8. Microglial GPR56 is the molecular target of maternal immune activation-induced parvalbumin-positive interneuron deficits.
- Author
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Yu D, Li T, Delpech JC, Zhu B, Kishore P, Koshi T, Luo R, Pratt KJB, Popova G, Nowakowski TJ, Villeda SA, and Piao X
- Subjects
- Animals, Disease Models, Animal, Interneurons metabolism, Microglia metabolism, Parvalbumins metabolism, Autism Spectrum Disorder genetics, Autism Spectrum Disorder metabolism, Autistic Disorder metabolism
- Abstract
Parvalbumin-positive (PV
+ ) interneurons play a critical role in maintaining circuit rhythm in the brain, and their reduction is implicated in autism spectrum disorders. Animal studies demonstrate that maternal immune activation (MIA) leads to reduced PV+ interneurons in the somatosensory cortex and autism-like behaviors. However, the underlying molecular mechanisms remain largely unknown. Here, we show that MIA down-regulates microglial Gpr56 expression in fetal brains in an interleukin-17a-dependent manner and that conditional deletion of microglial Gpr56 [ Gpr56 conditional knockout (cKO)] mimics MIA-induced PV+ interneuron defects and autism-like behaviors in offspring. We further demonstrate that elevated microglial tumor necrosis factor-α expression is the underlying mechanism by which MIA and Gpr56 cKO impair interneuron generation. Genetically restoring Gpr56 expression in microglia ameliorates PV+ interneuron deficits and autism-like behaviors in MIA offspring. Together, our study demonstrates that microglial GPR56 plays an important role in PV+ interneuron development and serves as a salient target of MIA-induced neurodevelopmental disorders.- Published
- 2022
- Full Text
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9. A single-cell atlas of the normal and malformed human brain vasculature.
- Author
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Winkler EA, Kim CN, Ross JM, Garcia JH, Gil E, Oh I, Chen LQ, Wu D, Catapano JS, Raygor K, Narsinh K, Kim H, Weinsheimer S, Cooke DL, Walcott BP, Lawton MT, Gupta N, Zlokovic BV, Chang EF, Abla AA, Lim DA, and Nowakowski TJ
- Subjects
- Adult, Blood Vessels pathology, Blood Vessels physiology, Blood Vessels physiopathology, Cells, Cultured, Cerebral Cortex blood supply, Cerebral Hemorrhage pathology, Cerebral Hemorrhage physiopathology, Cerebrovascular Circulation, Endothelial Cells cytology, Endothelial Cells pathology, Endothelial Cells physiology, Fibroblasts cytology, Fibroblasts physiology, Humans, Inflammation, Intracranial Arteriovenous Malformations metabolism, Monocytes cytology, Monocytes physiology, Muscle, Smooth, Vascular cytology, Muscle, Smooth, Vascular pathology, Muscle, Smooth, Vascular physiology, Pericytes cytology, Pericytes physiology, RNA-Seq, Single-Cell Analysis, Blood Vessels cytology, Brain blood supply, Intracranial Arteriovenous Malformations pathology, Transcriptome
- Abstract
Cerebrovascular diseases are a leading cause of death and neurologic disability. Further understanding of disease mechanisms and therapeutic strategies requires a deeper knowledge of cerebrovascular cells in humans. We profiled transcriptomes of 181,388 cells to define a cell atlas of the adult human cerebrovasculature, including endothelial cell molecular signatures with arteriovenous segmentation and expanded perivascular cell diversity. By leveraging this reference, we investigated cellular and molecular perturbations in brain arteriovenous malformations, which are a leading cause of stroke in young people, and identified pathologic endothelial transformations with abnormal vascular patterning and the ontology of vascularly derived inflammation. We illustrate the interplay between vascular and immune cells that contributes to brain hemorrhage and catalog opportunities for targeting angiogenic and inflammatory programs in vascular malformations.
- Published
- 2022
- Full Text
- View/download PDF
10. Nests of dividing neuroblasts sustain interneuron production for the developing human brain.
- Author
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Paredes MF, Mora C, Flores-Ramirez Q, Cebrian-Silla A, Del Dosso A, Larimer P, Chen J, Kang G, Gonzalez Granero S, Garcia E, Chu J, Delgado R, Cotter JA, Tang V, Spatazza J, Obernier K, Ferrer Lozano J, Vento M, Scott J, Studholme C, Nowakowski TJ, Kriegstein AR, Oldham MC, Hasenstaub A, Garcia-Verdugo JM, Alvarez-Buylla A, and Huang EJ
- Subjects
- Animals, Animals, Newborn, Cell Movement, Cell Proliferation, Cerebral Cortex cytology, Cerebral Cortex embryology, Cerebral Cortex growth & development, GABAergic Neurons cytology, GABAergic Neurons physiology, Gene Expression Profiling, Gestational Age, Humans, Interneurons cytology, Median Eminence cytology, Median Eminence growth & development, Mice, Neural Stem Cells transplantation, Prosencephalon embryology, Prosencephalon growth & development, Transplantation, Heterologous, Interneurons physiology, Median Eminence embryology, Neural Stem Cells physiology, Neurogenesis, Prosencephalon cytology
- Abstract
The human cortex contains inhibitory interneurons derived from the medial ganglionic eminence (MGE), a germinal zone in the embryonic ventral forebrain. How this germinal zone generates sufficient interneurons for the human brain remains unclear. We found that the human MGE (hMGE) contains nests of proliferative neuroblasts with ultrastructural and transcriptomic features that distinguish them from other progenitors in the hMGE. When dissociated hMGE cells are transplanted into the neonatal mouse brain, they reform into nests containing proliferating neuroblasts that generate young neurons that migrate extensively into the mouse forebrain and mature into different subtypes of functional interneurons. Together, these results indicate that the nest organization and sustained proliferation of neuroblasts in the hMGE provide a mechanism for the extended production of interneurons for the human forebrain.
- Published
- 2022
- Full Text
- View/download PDF
11. The CHD8/CHD7/Kismet family links blood-brain barrier glia and serotonin to ASD-associated sleep defects.
- Author
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Coll-Tané M, Gong NN, Belfer SJ, van Renssen LV, Kurtz-Nelson EC, Szuperak M, Eidhof I, van Reijmersdal B, Terwindt I, Durkin J, Verheij MMM, Kim CN, Hudac CM, Nowakowski TJ, Bernier RA, Pillen S, Earl RK, Eichler EE, Kleefstra T, Kayser MS, and Schenck A
- Subjects
- Animals, Blood-Brain Barrier metabolism, DNA Helicases metabolism, Drosophila metabolism, Neuroglia metabolism, Quality of Life, Serotonin, Sleep, Transcription Factors metabolism, Autistic Disorder genetics, DNA-Binding Proteins metabolism
- Abstract
Sleep disturbances in autism and neurodevelopmental disorders are common and adversely affect patient's quality of life, yet the underlying mechanisms are understudied. We found that individuals with mutations in CHD8 , among the highest-confidence autism risk genes, or CHD7 suffer from disturbed sleep maintenance. These defects are recapitulated in Drosophila mutants affecting kismet , the sole CHD8/CHD7 ortholog. We show that Kismet is required in glia for early developmental and adult sleep architecture. This role localizes to subperineurial glia constituting the blood-brain barrier. We demonstrate that Kismet-related sleep disturbances are caused by high serotonin during development, paralleling a well-established but genetically unsolved autism endophenotype. Despite their developmental origin, Kismet's sleep architecture defects can be reversed in adulthood by a behavioral regime resembling human sleep restriction therapy. Our findings provide fundamental insights into glial regulation of sleep and propose a causal mechanistic link between the CHD8/CHD7/Kismet family, developmental hyperserotonemia, and autism-associated sleep disturbances., (Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)
- Published
- 2021
- Full Text
- View/download PDF
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