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6 results on '"Christine Cuhaciyan"'

1. Neuropathological and transcriptomic characteristics of the aged brain

Author

Jeremy A Miller, Angela Guillozet-Bongaarts, Laura E Gibbons, Nadia Postupna, Anne Renz, Allison E Beller, Susan M Sunkin, Lydia Ng, Shannon E Rose, Kimberly A Smith, Aaron Szafer, Chris Barber, Darren Bertagnolli, Kristopher Bickley, Krissy Brouner, Shiella Caldejon, Mike Chapin, Mindy L Chua, Natalie M Coleman, Eiron Cudaback, Christine Cuhaciyan, Rachel A Dalley, Nick Dee, Tsega Desta, Tim A Dolbeare, Nadezhda I Dotson, Michael Fisher, Nathalie Gaudreault, Garrett Gee, Terri L Gilbert, Jeff Goldy, Fiona Griffin, Caroline Habel, Zeb Haradon, Nika Hejazinia, Leanne L Hellstern, Steve Horvath, Kim Howard, Robert Howard, Justin Johal, Nikolas L Jorstad, Samuel R Josephsen, Chihchau L Kuan, Florence Lai, Eric Lee, Felix Lee, Tracy Lemon, Xianwu Li, Desiree A Marshall, Jose Melchor, Shubhabrata Mukherjee, Julie Nyhus, Julie Pendergraft, Lydia Potekhina, Elizabeth Y Rha, Samantha Rice, David Rosen, Abharika Sapru, Aimee Schantz, Elaine Shen, Emily Sherfield, Shu Shi, Andy J Sodt, Nivretta Thatra, Michael Tieu, Angela M Wilson, Thomas J Montine, Eric B Larson, Amy Bernard, Paul K Crane, Richard G Ellenbogen, C Dirk Keene, and Ed Lein

Subjects
Alzheimer's disease, aging, dementia, gene expression, Medicine, Science, Biology (General), QH301-705.5
Abstract

As more people live longer, age-related neurodegenerative diseases are an increasingly important societal health issue. Treatments targeting specific pathologies such as amyloid beta in Alzheimer’s disease (AD) have not led to effective treatments, and there is increasing evidence of a disconnect between traditional pathology and cognitive abilities with advancing age, indicative of individual variation in resilience to pathology. Here, we generated a comprehensive neuropathological, molecular, and transcriptomic characterization of hippocampus and two regions cortex in 107 aged donors (median = 90) from the Adult Changes in Thought (ACT) study as a freely-available resource (http://aging.brain-map.org/). We confirm established associations between AD pathology and dementia, albeit with increased, presumably aging-related variability, and identify sets of co-expressed genes correlated with pathological tau and inflammation markers. Finally, we demonstrate a relationship between dementia and RNA quality, and find common gene signatures, highlighting the importance of properly controlling for RNA quality when studying dementia.

Published
2017
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2. Classification of electrophysiological and morphological neuron types in the mouse visual cortex

Author

David Sandman, Brian Lee, Michael Hawrylycz, Sara Kebede, Tom Egdorf, David Reid, Rob Young, Nivretta Thatra, Stefan Mihalas, David Feng, John W. Phillips, Rebecca de Frates, DiJon Hill, Cliff Slaughterbeck, Samuel R Josephsen, Tamara Casper, Xiaoxiao Liu, Hanchuan Peng, Peter Chong, Colin Farrell, Zhi Zhou, Sheana Parry, Jed Perkins, Brian Long, Susan M. Sunkin, Matthew Kroll, Krissy Brouner, Melissa Gorham, Aaron Szafer, Wayne Wakeman, Hong Gu, Marissa Garwood, Daniel Park, Kristen Hadley, Michael S. Fisher, Lydia Potekhina, Ed Lein, Alice Mukora, Hongkui Zeng, Nick Dee, Aaron Oldre, Lindsay Ng, Thomas Braun, Grace Williams, Tracy Lemon, Julie A. Harris, Medea McGraw, Nadezhda Dotson, Philip R. Nicovich, Amanda Gary, Rusty Mann, Alex M. Henry, Caroline Habel, Samuel Dingman, Katherine E. Link, Nathalie Gaudreault, Gilberto J. Soler-Llavina, Thuc Nghi Nguyen, Nicole Blesie, Bosiljka Tasic, Lydia Ng, Christine Cuhaciyan, Tim Jarsky, Keith B. Godfrey, Costas A. Anastassiou, Kirsten Crichton, Josef Sulc, Martin Schroedter, Dan Castelli, Miranda Robertson, Amy Bernard, Lisa Kim, Songlin Ding, Alyse Doperalski, Nathan W. Gouwens, Herman Tung, Tsega Desta, Corinne Teeter, James Harrington, Jonathan T. Ting, Kris Bickley, Anton Arkhipov, Kiet Ngo, Changkyu Lee, Jim Berg, Agata Budzillo, Emma Garren, Tanya L. Daigle, Christof Koch, Rachel A. Dalley, Eliza Barkan, Staci A. Sorensen, Gabe J. Murphy, Shiella Caldejon, and Naz Taskin

Subjects
0301 basic medicine, Genetically modified mouse, Cell type, Patch-Clamp Techniques, Databases, Factual, Action Potentials, Datasets as Topic, Mice, Transgenic, Biology, Article, Neuron types, Mice, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Genes, Reporter, Biocytin, medicine, Animals, Cell shape, Cell Shape, Visual Cortex, Neurons, General Neuroscience, Laboratory mouse, Electrophysiology, 030104 developmental biology, Visual cortex, medicine.anatomical_structure, chemistry, Transcriptome, Neuroscience, 030217 neurology & neurosurgery
Abstract

Understanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To systematically profile morpho-electric properties of mammalian neurons, we established a single-cell characterization pipeline using standardized patch-clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly accessible online database, the Allen Cell Types Database, to display these datasets. Intrinsic physiological properties were measured from 1,938 neurons from the adult laboratory mouse visual cortex, morphological properties were measured from 461 reconstructed neurons, and 452 neurons had both measurements available. Quantitative features were used to classify neurons into distinct types using unsupervised methods. We established a taxonomy of morphologically and electrophysiologically defined cell types for this region of the cortex, with 17 electrophysiological types, 38 morphological types and 46 morpho-electric types. There was good correspondence with previously defined transcriptomic cell types and subclasses using the same transgenic mouse lines.

Published
2019

3. Classification of electrophysiological and morphological types in mouse visual cortex

Author

Tom Egdorf, Rebecca de Frates, Emma Garren, Sara Kebede, Peter Chong, John W. Phillips, Nivretta Thatra, Samuel R Josephsen, Philip R. Nicovich, Tim Jarsky, Xiaoxiao Liu, Susan M. Sunkin, Brian Lee, Keith B. Godfrey, Matthew Kroll, Nicole Blesie, Bosiljka Tasic, Amy Bernard, Lisa Kim, Costas A. Anastassiou, Kristen Hadley, Staci A. Sorensen, Thuc Nghi Nguyen, Martin Schroedter, Corinne Teeter, Kirsten Crichton, Josef Sulc, Rachel A. Dalley, David Feng, Tracy Lemon, Michael Hawrylycz, Miranda Robertson, Christine Cuhaciyan, Eliza Barkan, Shiella Caldejon, Tsega Desta, Kris Bickley, Dan Castelli, Wayne Wakeman, Herman Tung, Hongkui Zeng, Grace Williams, Nadezhda Dotson, Rusty Mann, Tamara Casper, Anton Arkhipov, Daniel Park, Sheana Parry, Jed Perkins, Alyse Doperalski, Brian Long, Thomas Braun, Christof Koch, Gabe J. Murphy, Aaron Oldre, Changkyu Lee, Colin Farrell, Medea McGraw, Amanda Gary, Kiet Ngo, Melissa Gorham, Naz Taskin, Jim Berg, Samuel Dingman, Tanya L. Daigle, Agata Budzillo, Marissa Garwood, Gilberto J. Soler-Llavina, Aaron Szafer, Nick Dee, Jonathan T. Ting, Lydia Ng, Alex M. Henry, James Harrington, Julie A. Harris, Michael S. Fisher, Lindsay Ng, Caroline Habel, Nathalie Gaudreault, Krissy Brouner, David Reid, Lydia Potekhina, Rob Young, DiJon Hill, Cliff Slaughterbeck, Ed Lein, Alice Mukora, David Sandman, Stefan Mihalas, Nathan W. Gouwens, Zhi Zhou, Hanchuan Peng, and Hong Gu

Subjects
Genetically modified mouse, Cell type, Cell, Laboratory mouse, Biology, Electrophysiology, chemistry.chemical_compound, Visual cortex, medicine.anatomical_structure, chemistry, Biocytin, medicine, Patch clamp, Neuroscience
Abstract

Understanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To profile morpho-electric properties of mammalian neurons systematically, we established a single cell characterization pipeline using standardized patch clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly-accessible online database, the Allen Cell Types Database, to display these data sets. Intrinsic physiological and morphological properties were measured from over 1,800 neurons from the adult laboratory mouse visual cortex. Quantitative features were used to classify neurons into distinct types using unsupervised methods. We establish a taxonomy of morphologically- and electrophysiologically-defined cell types for this region of cortex with 17 e-types and 35 m-types, as well as an initial correspondence with previously-defined transcriptomic cell types using the same transgenic mouse lines.

Published
2018
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4. Neuropathological and transcriptomic characteristics of the aged brain

Author

Terri L. Gilbert, Thomas J. Montine, Aaron Szafer, Eiron Cudaback, Nick Dee, Christine Cuhaciyan, Xianwu Li, Kimberly A. Smith, Samuel R Josephsen, Tim A. Dolbeare, Paul K. Crane, Amy Bernard, Nadezhda Dotson, Michael Tieu, Fiona Griffin, Shannon E. Rose, Ed S. Lein, Jeff Goldy, Laura E. Gibbons, Julie Pendergraft, Felix Lee, Nivretta Thatra, Elaine Shen, Elizabeth Rha, Susan M. Sunkin, Garrett Gee, Lydia Potekhina, Nadia Postupna, Darren Bertagnolli, Andy J. Sodt, Nikolas L. Jorstad, Angela L. Guillozet-Bongaarts, Samantha Rice, Jeremy A. Miller, Natalie M Coleman, Zeb Haradon, Tsega Desta, David Rosen, Angela M. Wilson, Justin Johal, Shubhabrata Mukherjee, Kristopher Bickley, Anne Renz, Abharika Sapru, Robert Howard, Desiree A. Marshall, Tracy Lemon, Nika Hejazinia, Rachel A. Dalley, Shu Shi, Steve Horvath, Mindy L Chua, Aimee Schantz, Eric B. Larson, Allison Beller, Michael S. Fisher, Julie Nyhus, C. Dirk Keene, Lydia Ng, Kim Howard, Caroline Habel, Nathalie Gaudreault, Krissy Brouner, Leanne L Hellstern, Shiella Caldejon, Jose Melchor, Emily Sherfield, Chihchau L. Kuan, Mike Chapin, Richard G. Ellenbogen, Chris Barber, Florence Lai, and Eric Lee

Subjects
0301 basic medicine, Male, Amyloid beta, QH301-705.5, Science, Hippocampus, Disease, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Alzheimer Disease, medicine, Dementia, Humans, Biology (General), Gene, Pathological, Aged, Aged, 80 and over, Cerebral Cortex, General Immunology and Microbiology, biology, business.industry, General Neuroscience, Gene Expression Profiling, aging, Cognition, General Medicine, Alzheimer's disease, medicine.disease, 3. Good health, Tools and Resources, 030104 developmental biology, biology.protein, gene expression, Medicine, Female, business, Neuroscience, 030217 neurology & neurosurgery, Human, dementia
Abstract

As more people live longer, age-related neurodegenerative diseases are an increasingly important societal health issue. Treatments targeting specific pathologies such as amyloid beta in Alzheimer’s disease (AD) have not led to effective treatments, and there is increasing evidence of a disconnect between traditional pathology and cognitive abilities with advancing age, indicative of individual variation in resilience to pathology. Here, we generated a comprehensive neuropathological, molecular, and transcriptomic characterization of hippocampus and two regions cortex in 107 aged donors (median = 90) from the Adult Changes in Thought (ACT) study as a freely-available resource (http://aging.brain-map.org/). We confirm established associations between AD pathology and dementia, albeit with increased, presumably aging-related variability, and identify sets of co-expressed genes correlated with pathological tau and inflammation markers. Finally, we demonstrate a relationship between dementia and RNA quality, and find common gene signatures, highlighting the importance of properly controlling for RNA quality when studying dementia.

Published
2017

5. Author response: Neuropathological and transcriptomic characteristics of the aged brain

Author

Lydia Ng, Shubhabrata Mukherjee, Amy Bernard, Mindy L Chua, Jeff Goldy, Fiona Griffin, Darren Bertagnolli, Shu Shi, Ed S. Lein, Susan M. Sunkin, Nika Hejazinia, Justin Johal, Krissy Brouner, Jeremy A. Miller, Steve Horvath, Zeb Haradon, Natalie M Coleman, Jose Melchor, Desiree A. Marshall, Samuel R Josephsen, Paul K. Crane, Kristopher Bickley, Tim A. Dolbeare, Kim Howard, Michael S. Fisher, C. Dirk Keene, Angela M. Wilson, Tracy Lemon, Aaron Szafer, Eiron Cudaback, Nick Dee, Eric B. Larson, Elizabeth Rha, Chris Barber, Julie Nyhus, Michael Tieu, Lydia Potekhina, Caroline Habel, Nathalie Gaudreault, Kimberly A. Smith, Shannon E. Rose, Nikolas L. Jorstad, Angela L. Guillozet-Bongaarts, Terri L. Gilbert, Felix Lee, Nivretta Thatra, Florence Lai, Julie Pendergraft, Elaine Shen, Eric Lee, Christine Cuhaciyan, Chihchau L. Kuan, Mike Chapin, Richard G. Ellenbogen, Andy J. Sodt, Leanne L Hellstern, Shiella Caldejon, Nadia Postupna, David Rosen, Emily Sherfield, Tsega Desta, Anne Renz, Xianwu Li, Abharika Sapru, Robert Howard, Rachel A. Dalley, Aimee Schantz, Allison Beller, Samantha Rice, Nadezhda Dotson, Laura E. Gibbons, Garrett Gee, and Thomas J. Montine

Subjects
0301 basic medicine, Transcriptome, 03 medical and health sciences, 030104 developmental biology, business.industry, Medicine, business, Neuroscience
Published
2017

6. Transcriptional landscape of the prenatal human brain

Author

Amy Bernard, Phil Lesnar, Daniel H. Geschwind, Sheana Parry, Ed S. Lein, Benjamin W. Gregor, Theresa Naluai-Cecchini, John W. Phillips, Elaine H. Shen, Julie Nyhus, Chinh Dang, Rachel A. Dalley, Susan M. Sunkin, Nerick Mosqueda, Mark Gerstein, Lydia Ng, Hao Huang, Guangyu Gu, Lindsey Gourley, Tim A. Dolbeare, Darren Bertagnolli, Ian A. Glass, Bergen McMurray, Melaine Sarreal, Allison Stevens, Tim P. Fliss, Crissa Bennet, Clifford R. Slaughterbeck, Aaron Szafer, Mihovil Pletikos, Nenad Sestan, Benjamin A.C. Facer, Nick Dee, David Feng, Jody Parente, Paul Wohnoutka, Andy J. Sodt, Robert Howard, Christopher Lau, Tracy Lemon, Aaron Oldre, Robert F. Hevner, Nathan Sjoquist, Michael Hawrylycz, Nadiya V. Shapovalova, Joshua J. Royall, Pat Levitt, Zackery L. Riley, Anita Carey, John G. Hohmann, Kaylynn Aiona, Bruce Fischl, James A. Knowles, Felix Lee, Lilla Zöllei, Sheila Shapouri, Eric Olson, Melissa Reding, Christine Cuhaciyan, Shiella Caldejon, Songlin Ding, Derric Williams, Chihchau L. Kuan, Jayson M. Jochim, Michael W. Smith, Krissy Brouner, Allan R. Jones, Patrick D. Parker, Garrett Gee, Kate Roll, David Sandman, Stephanie Butler, James M. Arnold, Kimberly A. Smith, Jeremy A. Miller, Jeff Goldy, Nhan Kiet Ngo, Amanda Ebbert, Changkyu Lee, and Naveed Mastan

Subjects
Evolution, General Science & Technology, 1.1 Normal biological development and functioning, Neocortex, Biology, Human brain, Microarray, Development, Article, Transcriptome, Mice, Fetus, Atlases as Topic, Species Specificity, Stem Cell Research - Nonembryonic - Human, Underpinning research, Subplate, medicine, Genetics, Animals, Humans, Artistic, Developmental, Gene Regulatory Networks, Anatomy, Artistic, Conserved Sequence, Regulation of gene expression, Pediatric, Multidisciplinary, Microarray analysis techniques, Neurosciences, Gene Expression Regulation, Developmental, Brain, Stem Cell Research, Human Fetal Tissue, medicine.anatomical_structure, Frontal lobe, Gene Expression Regulation, Cerebral cortex, Neurological, Gene expression, Anatomy, Neuroscience, Biotechnology
Abstract

The anatomical and functional architecture of the human brain is mainly determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of the mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and post-mitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and outer subventricular zones even though the outer zone is expanded in humans. Both germinal and post-mitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in the frontal lobe. Finally, many neurodevelopmental disorder and human-evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

Published
2014

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