1
|
Chen X, Yang HT, Zhang B, Phillips JW, Cheng D, Rigo F, Witte ON, Xing Y, Black DL. The RNA-binding proteins hnRNP H and F regulate splicing of a MYC-dependent HRAS exon in prostate cancer cells. Proc Natl Acad Sci U S A 2023; 120:e2220190120. [PMID: 37399401 DOI: 10.1073/pnas.2220190120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/31/2023] [Indexed: 07/05/2023] Open
Abstract
The MYC proto-oncogene contributes to the pathogenesis of more than half of human cancers. Malignant transformation by MYC transcriptionally up-regulates the core pre-mRNA splicing machinery and causes misregulation of alternative splicing. However, our understanding of how splicing changes are directed by MYC is limited. We performed a signaling pathway-guided splicing analysis to identify MYC-dependent splicing events. These included an HRAS cassette exon repressed by MYC across multiple tumor types. To molecularly dissect the regulation of this HRAS exon, we used antisense oligonucleotide tiling to identify splicing enhancers and silencers in its flanking introns. RNA-binding motif prediction indicated multiple binding sites for hnRNP H and hnRNP F within these cis-regulatory elements. Using siRNA knockdown and cDNA expression, we found that both hnRNP H and F activate the HRAS cassette exon. Mutagenesis and targeted RNA immunoprecipitation implicate two downstream G-rich elements in this splicing activation. Analyses of ENCODE RNA-seq datasets confirmed hnRNP H regulation of HRAS splicing. Analyses of RNA-seq datasets across multiple cancers showed a negative correlation of HNRNPH gene expression with MYC hallmark enrichment, consistent with the effect of hnRNP H on HRAS splicing. Interestingly, HNRNPF expression showed a positive correlation with MYC hallmarks and thus was not consistent with the observed effects of hnRNP F. Loss of hnRNP H/F altered cell cycle progression and induced apoptosis in the PC3 prostate cancer cell line. Collectively, our results reveal mechanisms for MYC-dependent regulation of splicing and point to possible therapeutic targets in prostate cancers.
Collapse
Affiliation(s)
- Xinyuan Chen
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA 90095
| | - Harry Taegyun Yang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA 90095
| | - Beatrice Zhang
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - John W Phillips
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
| | - Donghui Cheng
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
| | - Frank Rigo
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010
| | - Owen N Witte
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, CA 90095
| |
Collapse
|
2
|
Pan Y, Phillips JW, Zhang BD, Noguchi M, Kutschera E, McLaughlin J, Nesterenko PA, Mao Z, Bangayan NJ, Wang R, Tran W, Yang HT, Wang Y, Xu Y, Obusan MB, Cheng D, Lee AH, Kadash-Edmondson KE, Champhekar A, Puig-Saus C, Ribas A, Prins RM, Seet CS, Crooks GM, Witte ON, Xing Y. IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing. Proc Natl Acad Sci U S A 2023; 120:e2221116120. [PMID: 37192158 PMCID: PMC10214192 DOI: 10.1073/pnas.2221116120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/05/2023] [Indexed: 05/18/2023] Open
Abstract
Alternative splicing (AS) is prevalent in cancer, generating an extensive but largely unexplored repertoire of novel immunotherapy targets. We describe Isoform peptides from RNA splicing for Immunotherapy target Screening (IRIS), a computational platform capable of discovering AS-derived tumor antigens (TAs) for T cell receptor (TCR) and chimeric antigen receptor T cell (CAR-T) therapies. IRIS leverages large-scale tumor and normal transcriptome data and incorporates multiple screening approaches to discover AS-derived TAs with tumor-associated or tumor-specific expression. In a proof-of-concept analysis integrating transcriptomics and immunopeptidomics data, we showed that hundreds of IRIS-predicted TCR targets are presented by human leukocyte antigen (HLA) molecules. We applied IRIS to RNA-seq data of neuroendocrine prostate cancer (NEPC). From 2,939 NEPC-associated AS events, IRIS predicted 1,651 epitopes from 808 events as potential TCR targets for two common HLA types (A*02:01 and A*03:01). A more stringent screening test prioritized 48 epitopes from 20 events with "neoantigen-like" NEPC-specific expression. Predicted epitopes are often encoded by microexons of ≤30 nucleotides. To validate the immunogenicity and T cell recognition of IRIS-predicted TCR epitopes, we performed in vitro T cell priming in combination with single-cell TCR sequencing. Seven TCRs transduced into human peripheral blood mononuclear cells (PBMCs) showed high activity against individual IRIS-predicted epitopes, providing strong evidence of isolated TCRs reactive to AS-derived peptides. One selected TCR showed efficient cytotoxicity against target cells expressing the target peptide. Our study illustrates the contribution of AS to the TA repertoire of cancer cells and demonstrates the utility of IRIS for discovering AS-derived TAs and expanding cancer immunotherapies.
Collapse
Affiliation(s)
- Yang Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA90095
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - John W. Phillips
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Beatrice D. Zhang
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Miyako Noguchi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Jami McLaughlin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | | | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Nathanael J. Bangayan
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Robert Wang
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Wendy Tran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Harry T. Yang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA90095
| | - Yuanyuan Wang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA90095
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Yang Xu
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Matthew B. Obusan
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
| | - Alex H. Lee
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Kathryn E. Kadash-Edmondson
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Ameya Champhekar
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Cristina Puig-Saus
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Robert M. Prins
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Christopher S. Seet
- Molecular Biology Institute, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
| | - Gay M. Crooks
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Owen N. Witte
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| |
Collapse
|
3
|
Koch C, Svoboda K, Bernard A, Basso MA, Churchland AK, Fairhall AL, Groblewski PA, Lecoq JA, Mainen ZF, Mathis MW, Olsen SR, Phillips JW, Pouget A, Saxena S, Siegle JH, Zador AM. Next-generation brain observatories. Neuron 2022; 110:3661-3666. [PMID: 36240770 DOI: 10.1016/j.neuron.2022.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/16/2022] [Accepted: 09/26/2022] [Indexed: 11/05/2022]
Abstract
We propose centralized brain observatories for large-scale recordings of neural activity in mice and non-human primates coupled with cloud-based data analysis and sharing. Such observatories will advance reproducible systems neuroscience and democratize access to the most advanced tools and data.
Collapse
Affiliation(s)
- Christof Koch
- MindScope Program, Allen Institute, Seattle, WA, USA
| | - Karel Svoboda
- Allen Institute for Neural Dynamics, Seattle, WA, USA.
| | | | - Michele A Basso
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Mackenzie W Mathis
- Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Shawn R Olsen
- MindScope Program, Allen Institute, Seattle, WA, USA
| | | | - Alexandre Pouget
- Department of Basic Neuroscience, University of Geneva, Geneva, Switzerland
| | | | - Josh H Siegle
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | | |
Collapse
|
4
|
Ta LH, Carr-Ascher JR, Deng W, Tsai BL, Tran W, Gun D, Cheng D, Sha J, Hwang Y, Phillips JW, Obusan MB, Bangayan NJ, Noguchi M, Mao Z, Chen CC, Wang L, Varuzhanyan G, Gordon JD, Wohlschlegel JW, Witte ON. Abstract 2438: Determining the role of non-mutated C-Raf kinase in metastatic disease. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Many aggressive epithelial cancers do not carry targetable driver mutations (Mendiratta et al. 2021, NCI-MATCH Clinical trial NCT02465060). Commonly altered signaling pathways highlight the propensity for tumors to depend on such pathways for growth and survival where genomic alterations may not be required for pathway activation. The Raf family kinases are crucial mediators of the Ras/Raf/MEK/ERK (MAPK) cascade, which has been shown to be upregulated in a subset of metastatic cancers and are mutated in many epithelial cancers. A recent study suggests non-mutated C-Raf can drive metastasis to the lungs, bone, and various other tissues (Faltermeir et al. 2016). Though the mechanism of C-Raf driven metastasis is likely through MAPK activation, C-Raf has been demonstrated to possess MAPK independent roles that may also contribute to this phenotype. In this study, we explored various C-Raf functions as drivers of metastasis in an intracardiac mouse model system. Using a series of Raf knock-out cell lines and mutants targeting functional residues in C-Raf, we demonstrated that C-Raf dimerization is necessary to drive metastasis. We further showed that the metastasis-promoting activity of C-Raf is dependent on co-expression of its family member, B-Raf, for an accelerated metastatic phenotype. However, overexpression of a kinase-dead C-Raf mutant was still able to produce metastases albeit with lower efficiency, suggesting C-Raf possesses non-kinase dependent functions that also contributed to metastasis. Together, these results point to the importance of Raf non-canonical roles in oncogenic processes that may be unappreciated in metastatic disease.
Citation Format: Lisa H. Ta, Janai R. Carr-Ascher, Weixian Deng, Brandon L. Tsai, Wendy Tran, Donny Gun, Donghui Cheng, Jihui Sha, Yeonjoo Hwang, John W. Phillips, Matthew B. Obusan, Nathanael J. Bangayan, Miyako Noguchi, Zhiyuan Mao, Chia-Chun Chen, Liang Wang, Grigor Varuzhanyan, John D. Gordon, James W. Wohlschlegel, Owen N. Witte. Determining the role of non-mutated C-Raf kinase in metastatic disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2438.
Collapse
|
5
|
Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification. Nature 2022; 601:E12. [PMID: 34992294 PMCID: PMC8770134 DOI: 10.1038/s41586-021-04322-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
| |
Collapse
|
6
|
Ding S, Royall JJ, Lesnar P, Facer BA, Smith KA, Wei Y, Brouner K, Dalley RA, Dee N, Dolbeare TA, Ebbert A, Glass IA, Keller NH, Lee F, Lemon TA, Nyhus J, Pendergraft J, Reid R, Sarreal M, Shapovalova NV, Szafer A, Phillips JW, Sunkin SM, Hohmann JG, Jones AR, Hawrylycz MJ, Hof PR, Ng L, Bernard A, Lein ES. Cover Image, Volume 530, Issue 1. J Comp Neurol 2021. [DOI: 10.1002/cne.25287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
7
|
Nesterenko PA, McLaughlin J, Tsai BL, Burton Sojo G, Cheng D, Zhao D, Mao Z, Bangayan NJ, Obusan MB, Su Y, Ng RH, Chour W, Xie J, Li YR, Lee D, Noguchi M, Carmona C, Phillips JW, Kim JT, Yang L, Heath JR, Boutros PC, Witte ON. HLA-A ∗02:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses. Cell Rep 2021; 37:110167. [PMID: 34919800 PMCID: PMC8660260 DOI: 10.1016/j.celrep.2021.110167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/15/2021] [Accepted: 12/02/2021] [Indexed: 12/14/2022] Open
Abstract
Cross-reactivity and direct killing of target cells remain underexplored for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific CD8+ T cells. Isolation of T cell receptors (TCRs) and overexpression in allogeneic cells allows for extensive T cell reactivity profiling. We identify SARS-CoV-2 RNA-dependent RNA polymerase (RdRp/NSP12) as highly conserved, likely due to its critical role in the virus life cycle. We perform single-cell TCRαβ sequencing in human leukocyte antigen (HLA)-A∗02:01-restricted, RdRp-specific T cells from SARS-CoV-2-unexposed individuals. Human T cells expressing these TCRαβ constructs kill target cell lines engineered to express full-length RdRp. Three TCR constructs recognize homologous epitopes from common cold coronaviruses, indicating CD8+ T cells can recognize evolutionarily diverse coronaviruses. Analysis of individual TCR clones may help define vaccine epitopes that can induce long-term immunity against SARS-CoV-2 and other coronaviruses.
Collapse
Affiliation(s)
- Pavlo A Nesterenko
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jami McLaughlin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon L Tsai
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Giselle Burton Sojo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Zhao
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathanael J Bangayan
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew B Obusan
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Rachel H Ng
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jingyi Xie
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Yan-Ruide Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Derek Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Miyako Noguchi
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Camille Carmona
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John W Phillips
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jocelyn T Kim
- Division of Infectious Diseases, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lili Yang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA 98109, USA; Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Owen N Witte
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
8
|
Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES. Human neocortical expansion involves glutamatergic neuron diversification. Nature 2021; 598:151-158. [PMID: 34616067 PMCID: PMC8494638 DOI: 10.1038/s41586-021-03813-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/07/2021] [Indexed: 11/09/2022]
Abstract
The neocortex is disproportionately expanded in human compared with mouse1,2, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers composed of neurons that selectively make connections within the neocortex and with other telencephalic structures. Single-cell transcriptomic analyses of human and mouse neocortex show an increased diversity of glutamatergic neuron types in supragranular layers in human neocortex and pronounced gradients as a function of cortical depth3. Here, to probe the functional and anatomical correlates of this transcriptomic diversity, we developed a robust platform combining patch clamp recording, biocytin staining and single-cell RNA-sequencing (Patch-seq) to examine neurosurgically resected human tissues. We demonstrate a strong correspondence between morphological, physiological and transcriptomic phenotypes of five human glutamatergic supragranular neuron types. These were enriched in but not restricted to layers, with one type varying continuously in all phenotypes across layers 2 and 3. The deep portion of layer 3 contained highly distinctive cell types, two of which express a neurofilament protein that labels long-range projection neurons in primates that are selectively depleted in Alzheimer's disease4,5. Together, these results demonstrate the explanatory power of transcriptomic cell-type classification, provide a structural underpinning for increased complexity of cortical function in humans, and implicate discrete transcriptomic neuron types as selectively vulnerable in disease.
Collapse
Affiliation(s)
- Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Kyla Berry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Peter Chong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Szabina Furdan
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Clare Gamlin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex M Henry
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Djai B Heyer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chris Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Madie Hupp
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Desiree Marshall
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica Melief
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Eline J Mertens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Leona Mezei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Norbert Mihut
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gaspar Olah
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Attila Ozsvar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Viktor Szemenyei
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - René Wilbers
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Philip C de Witt Hamer
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander Idema
- Cancer Center Amsterdam, Brain Tumor Center, Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop P Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Idan Segev
- Edmond and Lily Safra Center for Brain Sciences and Department of Neurobiology, The Hebrew University Jerusalem, Jerusalem, Israel
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Huibert D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, The Netherlands
| | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
| |
Collapse
|
9
|
Ding SL, Royall JJ, Lesnar P, Facer BAC, Smith KA, Wei Y, Brouner K, Dalley RA, Dee N, Dolbeare TA, Ebbert A, Glass IA, Keller NH, Lee F, Lemon TA, Nyhus J, Pendergraft J, Reid R, Sarreal M, Shapovalova NV, Szafer A, Phillips JW, Sunkin SM, Hohmann JG, Jones AR, Hawrylycz MJ, Hof PR, Ng L, Bernard A, Lein ES. Cellular resolution anatomical and molecular atlases for prenatal human brains. J Comp Neurol 2021; 530:6-503. [PMID: 34525221 PMCID: PMC8716522 DOI: 10.1002/cne.25243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/12/2022]
Abstract
Increasing interest in studies of prenatal human brain development, particularly using new single‐cell genomics and anatomical technologies to create cell atlases, creates a strong need for accurate and detailed anatomical reference atlases. In this study, we present two cellular‐resolution digital anatomical atlases for prenatal human brain at postconceptional weeks (PCW) 15 and 21. Both atlases were annotated on sequential Nissl‐stained sections covering brain‐wide structures on the basis of combined analysis of cytoarchitecture, acetylcholinesterase staining, and an extensive marker gene expression dataset. This high information content dataset allowed reliable and accurate demarcation of developing cortical and subcortical structures and their subdivisions. Furthermore, using the anatomical atlases as a guide, spatial expression of 37 and 5 genes from the brains, respectively, at PCW 15 and 21 was annotated, illustrating reliable marker genes for many developing brain structures. Finally, the present study uncovered several novel developmental features, such as the lack of an outer subventricular zone in the hippocampal formation and entorhinal cortex, and the apparent extension of both cortical (excitatory) and subcortical (inhibitory) progenitors into the prenatal olfactory bulb. These comprehensive atlases provide useful tools for visualization, segmentation, targeting, imaging, and interpretation of brain structures of prenatal human brain, and for guiding and interpreting the next generation of cell census and connectome studies.
Collapse
Affiliation(s)
- Song-Lin Ding
- Allen Institute for Brain Science, Seattle, WA, 98109
| | | | - Phil Lesnar
- Allen Institute for Brain Science, Seattle, WA, 98109
| | | | | | - Yina Wei
- Zhejiang Lab, Hangzhou, Zhejiang, China
| | | | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, 98109
| | | | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, WA, 98109
| | - Ian A Glass
- Department of Pediatrics and Medicine, University of Washington School of Medicine, Seattle, WA, 98105
| | - Nika H Keller
- Allen Institute for Brain Science, Seattle, WA, 98109
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, WA, 98109
| | - Tracy A Lemon
- Allen Institute for Brain Science, Seattle, WA, 98109
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, 98109
| | | | - Robert Reid
- Allen Institute for Brain Science, Seattle, WA, 98109
| | | | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, 98109
| | | | | | | | - Allan R Jones
- Allen Institute for Brain Science, Seattle, WA, 98109
| | | | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 11029
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, 98109
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, 98109
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, 98109
| |
Collapse
|
10
|
Ding SL, Yao Z, Hirokawa KE, Nguyen TN, Graybuck LT, Fong O, Bohn P, Ngo K, Smith KA, Koch C, Phillips JW, Lein ES, Harris JA, Tasic B, Zeng H. Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis. Cell Rep 2021; 31:107648. [PMID: 32433957 DOI: 10.1016/j.celrep.2020.107648] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/23/2020] [Accepted: 04/22/2020] [Indexed: 01/02/2023] Open
Abstract
Subicular regions play important roles in spatial processing and many cognitive functions, and these are mainly attributed to the subiculum (Sub) rather than the prosubiculum (PS). Using single-cell RNA sequencing, we identify 27 transcriptomic cell types residing in sub-domains of the Sub and PS. Based on in situ expression of reliable transcriptomic markers, the precise boundaries of the Sub and PS are consistently defined along the dorsoventral axis. Using these borders to evaluate Cre-line specificity and tracer injections, we find bona fide Sub projections topographically to structures important for spatial processing and navigation. In contrast, the PS sends its outputs to widespread brain regions crucial for motivation, emotion, reward, stress, anxiety, and fear. The Sub and PS, respectively, dominate dorsal and ventral subicular regions and receive different afferents. These results reveal two molecularly and anatomically distinct circuits centered in the Sub and PS, respectively, providing a consistent explanation for historical data and a clearer foundation for future studies.
Collapse
Affiliation(s)
- Song-Lin Ding
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Phillip Bohn
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| |
Collapse
|
11
|
Siegle JH, Jia X, Durand S, Gale S, Bennett C, Graddis N, Heller G, Ramirez TK, Choi H, Luviano JA, Groblewski PA, Ahmed R, Arkhipov A, Bernard A, Billeh YN, Brown D, Buice MA, Cain N, Caldejon S, Casal L, Cho A, Chvilicek M, Cox TC, Dai K, Denman DJ, de Vries SEJ, Dietzman R, Esposito L, Farrell C, Feng D, Galbraith J, Garrett M, Gelfand EC, Hancock N, Harris JA, Howard R, Hu B, Hytnen R, Iyer R, Jessett E, Johnson K, Kato I, Kiggins J, Lambert S, Lecoq J, Ledochowitsch P, Lee JH, Leon A, Li Y, Liang E, Long F, Mace K, Melchior J, Millman D, Mollenkopf T, Nayan C, Ng L, Ngo K, Nguyen T, Nicovich PR, North K, Ocker GK, Ollerenshaw D, Oliver M, Pachitariu M, Perkins J, Reding M, Reid D, Robertson M, Ronellenfitch K, Seid S, Slaughterbeck C, Stoecklin M, Sullivan D, Sutton B, Swapp J, Thompson C, Turner K, Wakeman W, Whitesell JD, Williams D, Williford A, Young R, Zeng H, Naylor S, Phillips JW, Reid RC, Mihalas S, Olsen SR, Koch C. Survey of spiking in the mouse visual system reveals functional hierarchy. Nature 2021; 592:86-92. [PMID: 33473216 PMCID: PMC10399640 DOI: 10.1038/s41586-020-03171-x] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically1. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory2-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas3. We find that four classical hierarchical measures-response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale-are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.
Collapse
Affiliation(s)
| | - Xiaoxuan Jia
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | | - Sam Gale
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Nile Graddis
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Hannah Choi
- Allen Institute for Brain Science, Seattle, WA, USA.,Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Dillan Brown
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Nicolas Cain
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Linzy Casal
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Andrew Cho
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Timothy C Cox
- University of Missouri-Kansas City School of Dentistry, Kansas City, MO, USA
| | - Kael Dai
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Daniel J Denman
- Allen Institute for Brain Science, Seattle, WA, USA.,The University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | | | | | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Brian Hu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ross Hytnen
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - India Kato
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Jerome Lecoq
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Yang Li
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Fuhui Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kyla Mace
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Kat North
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Jed Perkins
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Sam Seid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Ben Sutton
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jackie Swapp
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Rob Young
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sarah Naylor
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - R Clay Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Shawn R Olsen
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | |
Collapse
|
12
|
Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell 2020; 181:936-953.e20. [PMID: 32386544 PMCID: PMC8152789 DOI: 10.1016/j.cell.2020.04.007] [Citation(s) in RCA: 454] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 12/12/2019] [Accepted: 04/03/2020] [Indexed: 01/25/2023]
Abstract
Recent large-scale collaborations are generating major surveys of cell types and connections in the mouse brain, collecting large amounts of data across modalities, spatial scales, and brain areas. Successful integration of these data requires a standard 3D reference atlas. Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 μm z-sampling from 1,675 young adult C57BL/6J mice. Then, using multimodal reference data, we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures. CCFv3 can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D and is openly accessible (https://atlas.brain-map.org/).
Collapse
Affiliation(s)
- Quanxin Wang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Yang Li
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Josh Royall
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Phil Lesnar
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nile Graddis
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Maitham Naeemi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Benjamin Facer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anh Ho
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Seung Wook Oh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| |
Collapse
|
13
|
Hodge RD, Miller JA, Novotny M, Kalmbach BE, Ting JT, Bakken TE, Aevermann BD, Barkan ER, Berkowitz-Cerasano ML, Cobbs C, Diez-Fuertes F, Ding SL, McCorrison J, Schork NJ, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Yanny AM, Steemers FJ, Phillips JW, Bernard A, Koch C, Lasken RS, Scheuermann RH, Lein ES. Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons. Nat Commun 2020; 11:1172. [PMID: 32127543 PMCID: PMC7054400 DOI: 10.1038/s41467-020-14952-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
von Economo neurons (VENs) are bipolar, spindle-shaped neurons restricted to layer 5 of human frontoinsula and anterior cingulate cortex that appear to be selectively vulnerable to neuropsychiatric and neurodegenerative diseases, although little is known about other VEN cellular phenotypes. Single nucleus RNA-sequencing of frontoinsula layer 5 identifies a transcriptomically-defined cell cluster that contained VENs, but also fork cells and a subset of pyramidal neurons. Cross-species alignment of this cell cluster with a well-annotated mouse classification shows strong homology to extratelencephalic (ET) excitatory neurons that project to subcerebral targets. This cluster also shows strong homology to a putative ET cluster in human temporal cortex, but with a strikingly specific regional signature. Together these results suggest that VENs are a regionally distinctive type of ET neuron. Additionally, we describe the first patch clamp recordings of VENs from neurosurgically-resected tissue that show distinctive intrinsic membrane properties relative to neighboring pyramidal neurons.
Collapse
Affiliation(s)
| | | | | | - Brian E Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Charles Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, CA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
| |
Collapse
|
14
|
de Vries SEJ, Lecoq JA, Buice MA, Groblewski PA, Ocker GK, Oliver M, Feng D, Cain N, Ledochowitsch P, Millman D, Roll K, Garrett M, Keenan T, Kuan L, Mihalas S, Olsen S, Thompson C, Wakeman W, Waters J, Williams D, Barber C, Berbesque N, Blanchard B, Bowles N, Caldejon SD, Casal L, Cho A, Cross S, Dang C, Dolbeare T, Edwards M, Galbraith J, Gaudreault N, Gilbert TL, Griffin F, Hargrave P, Howard R, Huang L, Jewell S, Keller N, Knoblich U, Larkin JD, Larsen R, Lau C, Lee E, Lee F, Leon A, Li L, Long F, Luviano J, Mace K, Nguyen T, Perkins J, Robertson M, Seid S, Shea-Brown E, Shi J, Sjoquist N, Slaughterbeck C, Sullivan D, Valenza R, White C, Williford A, Witten DM, Zhuang J, Zeng H, Farrell C, Ng L, Bernard A, Phillips JW, Reid RC, Koch C. A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex. Nat Neurosci 2020; 23:138-151. [PMID: 31844315 PMCID: PMC6948932 DOI: 10.1038/s41593-019-0550-9] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/28/2019] [Indexed: 11/16/2022]
Abstract
To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes the cortical activity of nearly 60,000 neurons from six visual areas, four layers, and 12 transgenic mouse lines in a total of 243 adult mice, in response to a systematic set of visual stimuli. We classify neurons on the basis of joint reliabilities to multiple stimuli and validate this functional classification with models of visual responses. While most classes are characterized by responses to specific subsets of the stimuli, the largest class is not reliably responsive to any of the stimuli and becomes progressively larger in higher visual areas. These classes reveal a functional organization wherein putative dorsal areas show specialization for visual motion signals.
Collapse
Affiliation(s)
| | | | | | | | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Kate Roll
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Tom Keenan
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Shawn Olsen
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Chris Barber
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Linzy Casal
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Andrew Cho
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sissy Cross
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | - Sean Jewell
- Department of Statistics, University of Washington, Seattle, WA, USA
| | - Nika Keller
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ulf Knoblich
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Chris Lau
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eric Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lu Li
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Fuhui Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kyla Mace
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jed Perkins
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Sam Seid
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eric Shea-Brown
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Jianghong Shi
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | | | | | | | - Ryan Valenza
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Casey White
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Daniela M Witten
- Department of Statistics, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jun Zhuang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - R Clay Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | |
Collapse
|
15
|
Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES. Conserved cell types with divergent features in human versus mouse cortex. Nature 2019; 573:61-68. [PMID: 31435019 PMCID: PMC6919571 DOI: 10.1038/s41586-019-1506-7] [Citation(s) in RCA: 832] [Impact Index Per Article: 166.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 07/17/2019] [Indexed: 12/11/2022]
Abstract
Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease. Here we used single-nucleus RNA-sequencing analysis to perform a comprehensive study of cell types in the middle temporal gyrus of human cortex. We identified a highly diverse set of excitatory and inhibitory neuron types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to similar mouse cortex single-cell RNA-sequencing datasets revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of properties of human cell types. Despite this general conservation, we also found extensive differences between homologous human and mouse cell types, including marked alterations in proportions, laminar distributions, gene expression and morphology. These species-specific features emphasize the importance of directly studying human brain.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nelson Johansen
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Osnat Penn
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Höllt
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Allison Beller
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | | | | | - Charles Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
| | | | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ryder P Gwinn
- Epilepsy Surgery and Functional Neurosurgery, Swedish Neuroscience Institute, Seattle, WA, USA
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Andrew L Ko
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA
- Regional Epilepsy Center at Harborview Medical Center, Seattle, WA, USA
| | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ahmed Mahfouz
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, WA, USA
- Regional Epilepsy Center at Harborview Medical Center, Seattle, WA, USA
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sheana Parry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gerald Quon
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, San Diego, CA, USA
| | - Rafael Yuste
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Boudewijn Lelieveldt
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA.
| |
Collapse
|
16
|
Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin SM, Feng D, Anastassiou CA, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle TL, Dalley R, Dee N, Desta T, Ding SL, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris JA, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Link KE, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina G, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips JW, Zeng H, Koch C. Classification of electrophysiological and morphological neuron types in the mouse visual cortex. Nat Neurosci 2019; 22:1182-1195. [PMID: 31209381 PMCID: PMC8078853 DOI: 10.1038/s41593-019-0417-0] [Citation(s) in RCA: 219] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 04/25/2019] [Indexed: 12/21/2022]
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.
Collapse
Affiliation(s)
| | | | - Jim Berg
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jonathan Ting
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kris Bickley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Nicole Blesie
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Thomas Braun
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Agata Budzillo
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Tamara Casper
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Dan Castelli
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Peter Chong
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Tanya L Daigle
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Samuel Dingman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Michael Fisher
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Emma Garren
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Keith Godfrey
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Melissa Gorham
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Hong Gu
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Caroline Habel
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Julie A Harris
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Alex Henry
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sam Josephsen
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sara Kebede
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Brian Lee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Xiaoxiao Liu
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Medea McGraw
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Stefan Mihalas
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Daniel Park
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Sheana Parry
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Jed Perkins
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - David Reid
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - David Sandman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Corinne Teeter
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Grace Williams
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Rob Young
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Zhi Zhou
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Colin Farrell
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Hanchuan Peng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Anton Arkhipov
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington, USA.
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, Washington, USA
| |
Collapse
|
17
|
Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B. Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. PLoS One 2018; 13:e0209648. [PMID: 30586455 PMCID: PMC6306246 DOI: 10.1371/journal.pone.0209648] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 12/10/2018] [Indexed: 12/21/2022] Open
Abstract
Transcriptomic profiling of complex tissues by single-nucleus RNA-sequencing (snRNA-seq) affords some advantages over single-cell RNA-sequencing (scRNA-seq). snRNA-seq provides less biased cellular coverage, does not appear to suffer cell isolation-based transcriptional artifacts, and can be applied to archived frozen specimens. We used well-matched snRNA-seq and scRNA-seq datasets from mouse visual cortex to compare cell type detection. Although more transcripts are detected in individual whole cells (~11,000 genes) than nuclei (~7,000 genes), we demonstrate that closely related neuronal cell types can be similarly discriminated with both methods if intronic sequences are included in snRNA-seq analysis. We estimate that the nuclear proportion of total cellular mRNA varies from 20% to over 50% for large and small pyramidal neurons, respectively. Together, these results illustrate the high information content of nuclear RNA for characterization of cellular diversity in brain tissues.
Collapse
Affiliation(s)
- Trygve E. Bakken
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Rebecca D. Hodge
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Jeremy A. Miller
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Thuc Nghi Nguyen
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Brian Aevermann
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Darren Bertagnolli
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Lucas T. Graybuck
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Matthew Kroll
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Roger S. Lasken
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Sheana Parry
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Christine Rimorin
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | | | | | - Soraya I. Shehata
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - John W. Phillips
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Kimberly A. Smith
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, WA, United States of America
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA, United States of America
- * E-mail:
| |
Collapse
|
18
|
Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD. An anatomic transcriptional atlas of human glioblastoma. Science 2018; 360:660-663. [PMID: 29748285 DOI: 10.1126/science.aaf2666] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/30/2018] [Indexed: 12/20/2022]
Abstract
Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment.
Collapse
Affiliation(s)
- Ralph B Puchalski
- Allen Institute for Brain Science, Seattle, WA 98109, USA. .,Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Nameeta Shah
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA. .,Mazumdar Shaw Center for Translational Research, Bangalore 560099, India
| | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Steve R Nomura
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jae-Guen Yoon
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Michael Lankerovich
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Andrew F Boe
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Mike Chapin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Suvro Datta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xu Feng
- Radia Inc., Lynnwood, WA 98036, USA
| | - Michael Fisher
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Garrett Gee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Guangyu Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - John Hohmann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Parvinder Hothi
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kevin Joines
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ali Kriedberg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chris Lau
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hwahyung Lee
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Fuhui Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Naveed Mastan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Erika Mott
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chantal Murthy
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Eric Olson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zack Riley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Rosen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Andrew Sodt
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Don Marsh
- White Marsh Forests, Seattle, WA 98119, USA
| | - Robert C Rostomily
- Department of Neurosurgery, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.,Department of Neurological Surgery, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Allan Jones
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Haley R Gittleman
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Patrick J Cimino
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | - Megha S Uppin
- Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, India
| | - C Dirk Keene
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | | | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael E Berens
- TGen, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Neurology, Columbia University, New York, NY 10032, USA.,Department of Pathology, Columbia University, New York, NY 10032, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Charles Cobbs
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Greg D Foltz
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| |
Collapse
|
19
|
Ding SL, Royall JJ, Sunkin SM, Ng L, Facer BAC, Lesnar P, Guillozet-Bongaarts A, McMurray B, Szafer A, Dolbeare TA, Stevens A, Tirrell L, Benner T, Caldejon S, Dalley RA, Dee N, Lau C, Nyhus J, Reding M, Riley ZL, Sandman D, Shen E, van der Kouwe A, Varjabedian A, Wright M, Zöllei L, Dang C, Knowles JA, Koch C, Phillips JW, Sestan N, Wohnoutka P, Zielke HR, Hohmann JG, Jones AR, Bernard A, Hawrylycz MJ, Hof PR, Fischl B, Lein ES. Comprehensive cellular-resolution atlas of the adult human brain. J Comp Neurol 2017; 524:3127-481. [PMID: 27418273 PMCID: PMC5054943 DOI: 10.1002/cne.24080] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/11/2016] [Accepted: 07/13/2016] [Indexed: 12/12/2022]
Abstract
Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole‐brain coverage, relatively low image resolution, and sparse structural annotation. We present the first digital human brain atlas to incorporate neuroimaging, high‐resolution histology, and chemoarchitecture across a complete adult female brain, consisting of magnetic resonance imaging (MRI), diffusion‐weighted imaging (DWI), and 1,356 large‐format cellular resolution (1 µm/pixel) Nissl and immunohistochemistry anatomical plates. The atlas is comprehensively annotated for 862 structures, including 117 white matter tracts and several novel cyto‐ and chemoarchitecturally defined structures, and these annotations were transferred onto the matching MRI dataset. Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations. Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains. This interactive online digital atlas is integrated with existing Allen Institute for Brain Science gene expression atlases and is publicly accessible as a resource for the neuroscience community. J. Comp. Neurol. 524:3127–3481, 2016. © 2016 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Song-Lin Ding
- Allen Institute for Brain Science, Seattle, Washington, 98109.
| | - Joshua J Royall
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | | | - Phil Lesnar
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | | | - Bergen McMurray
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Tim A Dolbeare
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Allison Stevens
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, 02129
| | - Lee Tirrell
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, 02129
| | - Thomas Benner
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, 02129
| | | | - Rachel A Dalley
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Christopher Lau
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Zackery L Riley
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - David Sandman
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Elaine Shen
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Andre van der Kouwe
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, 02129
| | - Ani Varjabedian
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, 02129
| | - Michelle Wright
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, 02129
| | - Lilla Zöllei
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, 02129
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - James A Knowles
- Zilkha Neurogenetic Institute, and Department of Psychiatry, University of Southern California, Los Angeles, California, 90033
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - John W Phillips
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Nenad Sestan
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut, 06510
| | - Paul Wohnoutka
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - H Ronald Zielke
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - John G Hohmann
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Allan R Jones
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington, 98109
| | | | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 11029
| | - Bruce Fischl
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts, 02129
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington, 98109.
| |
Collapse
|
20
|
Close JL, Yao Z, Levi BP, Miller JA, Bakken TE, Menon V, Ting JT, Wall A, Krostag AR, Thomsen ER, Nelson AM, Mich JK, Hodge RD, Shehata SI, Glass IA, Bort S, Shapovalova NV, Ngo NK, Grimley JS, Phillips JW, Thompson CL, Ramanathan S, Lein E. Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation. Neuron 2017; 93:1035-1048.e5. [PMID: 28279351 DOI: 10.1016/j.neuron.2017.02.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 11/12/2016] [Accepted: 01/30/2017] [Indexed: 12/31/2022]
Abstract
GABAergic interneurons are essential for neural circuit function, and their loss or dysfunction is implicated in human neuropsychiatric disease. In vitro methods for interneuron generation hold promise for studying human cellular and functional properties and, ultimately, for therapeutic cell replacement. Here we describe a protocol for generating cortical interneurons from hESCs and analyze the properties and maturation time course of cell types using single-cell RNA-seq. We find that the cell types produced mimic in vivo temporal patterns of neuron and glial production, with immature progenitors and neurons observed early and mature cortical neurons and glial cell types produced late. By comparing the transcriptomes of immature interneurons to those of more mature neurons, we identified genes important for human interneuron differentiation. Many of these genes were previously implicated in neurodevelopmental and neuropsychiatric disorders.
Collapse
Affiliation(s)
- Jennie L Close
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Abigail Wall
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Angel M Nelson
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | - John K Mich
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Susan Bort
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - N Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Sharad Ramanathan
- Molecular and Cellular Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| |
Collapse
|
21
|
Ding SL, Royall JJ, Sunkin SM, Ng L, Facer BAC, Lesnar P, Guillozet-Bongaarts A, McMurray B, Szafer A, Dolbeare TA, Stevens A, Tirrell L, Benner T, Caldejon S, Dalley RA, Dee N, Lau C, Nyhus J, Reding M, Riley ZL, Sandman D, Shen E, van der Kouwe A, Varjabedian A, Write M, Zollei L, Dang C, Knowles JA, Koch C, Phillips JW, Sestan N, Wohnoutka P, Zielke HR, Hohmann JG, Jones AR, Bernard A, Hawrylycz MJ, Hof PR, Fischl B, LeinReference ES. Comprehensive cellular-resolution atlas of the adult human brain. J Comp Neurol 2016; 525:407. [PMID: 27917481 DOI: 10.1002/cne.24130] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
22
|
Yao Z, Mich JK, Ku S, Menon V, Krostag AR, Martinez RA, Furchtgott L, Mulholland H, Bort S, Fuqua MA, Gregor BW, Hodge RD, Jayabalu A, May RC, Melton S, Nelson AM, Ngo NK, Shapovalova NV, Shehata SI, Smith MW, Tait LJ, Thompson CL, Thomsen ER, Ye C, Glass IA, Kaykas A, Yao S, Phillips JW, Grimley JS, Levi BP, Wang Y, Ramanathan S. A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development. Cell Stem Cell 2016; 20:120-134. [PMID: 28094016 DOI: 10.1016/j.stem.2016.09.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/18/2016] [Accepted: 09/29/2016] [Indexed: 01/29/2023]
Abstract
During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development. Bayesian analyses inferred a unified cell-type lineage tree that bifurcates between cortical and mid/hindbrain cell types. Two methods of clonal analyses confirmed these findings and further revealed the importance of Wnt/β-catenin signaling in controlling this lineage decision. Together, these findings provide a rich transcriptome-based lineage map for studying human brain development and modeling developmental disorders.
Collapse
Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - John K Mich
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Sherman Ku
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Leon Furchtgott
- Molecular and Cellular Biology Department, Harvard University, Cambridge, MA 02138, USA
| | | | - Susan Bort
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ben W Gregor
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Anu Jayabalu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ryan C May
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Samuel Melton
- School of Engineering and Applied Science, Harvard University, Cambridge, MA 02138, USA
| | | | - N Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Leah J Tait
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Chaoyang Ye
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ian A Glass
- Division of Genetic Medicine, University of Washington, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Ajamete Kaykas
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Shuyuan Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Yanling Wang
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Sharad Ramanathan
- Allen Institute for Brain Science, Seattle, WA 98109, USA; Molecular and Cellular Biology Department, Harvard University, Cambridge, MA 02138, USA; School of Engineering and Applied Science, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
23
|
Ding SL, Royall JJ, Sunkin SM, Ng L, Facer BA, Lesnar P, Guillozet-Bongaarts A, McMurray B, Szafer A, Dolbeare TA, Stevens A, Tirrell L, Benner T, Caldejon S, Dalley RA, Dee N, Lau C, Nyhus J, Reding M, Riley ZL, Sandman D, Shen E, van der Kouwe A, Varjabedian A, Write M, Zollei L, Dang C, Knowles JA, Koch C, Phillips JW, Sestan N, Wohnoutka P, Zielke HR, Hohmann JG, Jones AR, Bernard A, Hawrylycz MJ, Hof PR, Fischl B, Lein ES. Comprehensive cellular-resolution atlas of the adult human brain. J Comp Neurol 2016. [DOI: 10.1002/cne.24097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Song-Lin Ding
- Allen Institute for Brain Science; Seattle Washington 98109
| | | | | | - Lydia Ng
- Allen Institute for Brain Science; Seattle Washington 98109
| | | | - Phil Lesnar
- Allen Institute for Brain Science; Seattle Washington 98109
| | | | | | - Aaron Szafer
- Allen Institute for Brain Science; Seattle Washington 98109
| | | | - Allison Stevens
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital; Charlestown Massachusetts 02129
| | - Lee Tirrell
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital; Charlestown Massachusetts 02129
| | - Thomas Benner
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital; Charlestown Massachusetts 02129
| | | | | | - Nick Dee
- Allen Institute for Brain Science; Seattle Washington 98109
| | | | - Julie Nyhus
- Allen Institute for Brain Science; Seattle Washington 98109
| | - Melissa Reding
- Allen Institute for Brain Science; Seattle Washington 98109
| | | | - David Sandman
- Allen Institute for Brain Science; Seattle Washington 98109
| | - Elaine Shen
- Allen Institute for Brain Science; Seattle Washington 98109
| | - Andre van der Kouwe
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital; Charlestown Massachusetts 02129
| | - Ani Varjabedian
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital; Charlestown Massachusetts 02129
| | - Michelle Write
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital; Charlestown Massachusetts 02129
| | - Lilla Zollei
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital; Charlestown Massachusetts 02129
| | - Chinh Dang
- Allen Institute for Brain Science; Seattle Washington 98109
| | - James A. Knowles
- Zilkha Neurogenetic Institute, and Department of Psychiatry; University of Southern California; Los Angeles California 90033
| | - Christof Koch
- Allen Institute for Brain Science; Seattle Washington 98109
| | | | - Nenad Sestan
- Department of Neurobiology and Kavli Institute for Neuroscience; Yale University School of Medicine; New Haven Connecticut 06510
| | - Paul Wohnoutka
- Allen Institute for Brain Science; Seattle Washington 98109
| | - H. Ronald Zielke
- Department of Pediatrics; University of Maryland School of Medicine; Baltimore Maryland 21201
| | | | - Allan R. Jones
- Allen Institute for Brain Science; Seattle Washington 98109
| | - Amy Bernard
- Allen Institute for Brain Science; Seattle Washington 98109
| | | | - Patrick R. Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York 11029
| | - Bruce Fischl
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging; Massachusetts General Hospital; Charlestown Massachusetts 02129
| | - Ed S. Lein
- Allen Institute for Brain Science; Seattle Washington 98109
| |
Collapse
|
24
|
Bakken TE, Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Dalley RA, Royall JJ, Lemon T, Shapouri S, Aiona K, Arnold J, Bennett JL, Bertagnolli D, Bickley K, Boe A, Brouner K, Butler S, Byrnes E, Caldejon S, Carey A, Cate S, Chapin M, Chen J, Dee N, Desta T, Dolbeare TA, Dotson N, Ebbert A, Fulfs E, Gee G, Gilbert TL, Goldy J, Gourley L, Gregor B, Gu G, Hall J, Haradon Z, Haynor DR, Hejazinia N, Hoerder-Suabedissen A, Howard R, Jochim J, Kinnunen M, Kriedberg A, Kuan CL, Lau C, Lee CK, Lee F, Luong L, Mastan N, May R, Melchor J, Mosqueda N, Mott E, Ngo K, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry S, Pendergraft J, Potekhina L, Reding M, Riley ZL, Roberts T, Rogers B, Roll K, Rosen D, Sandman D, Sarreal M, Shapovalova N, Shi S, Sjoquist N, Sodt AJ, Townsend R, Velasquez L, Wagley U, Wakeman WB, White C, Bennett C, Wu J, Young R, Youngstrom BL, Wohnoutka P, Gibbs RA, Rogers J, Hohmann JG, Hawrylycz MJ, Hevner RF, Molnár Z, Phillips JW, Dang C, Jones AR, Amaral DG, Bernard A, Lein ES. A comprehensive transcriptional map of primate brain development. Nature 2016; 535:367-75. [PMID: 27409810 PMCID: PMC5325728 DOI: 10.1038/nature18637] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 06/10/2016] [Indexed: 12/20/2022]
Abstract
The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.
Collapse
Affiliation(s)
- Trygve E Bakken
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jeremy A Miller
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Song-Lin Ding
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Kimberly A Smith
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Rachel A Dalley
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Joshua J Royall
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Sheila Shapouri
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Kaylynn Aiona
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - James Arnold
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jeffrey L Bennett
- Department of Psychiatry and Behavioral Science, California National Primate Research Center, The M.I.N.D. Institute, University of California, Davis, Sacramento, California 95817, USA
| | | | | | - Andrew Boe
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Stephanie Butler
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Emi Byrnes
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Shiella Caldejon
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Anita Carey
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Shelby Cate
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Mike Chapin
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jefferey Chen
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Tim A Dolbeare
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Nadia Dotson
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Erich Fulfs
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Garrett Gee
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Terri L Gilbert
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Lindsey Gourley
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Ben Gregor
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Guangyu Gu
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jon Hall
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Zeb Haradon
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - David R Haynor
- Department of Radiology, University of Washington, Seattle, Washington 98195, USA
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Anna Hoerder-Suabedissen
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jay Jochim
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Marty Kinnunen
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Ali Kriedberg
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Chihchau L Kuan
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Christopher Lau
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Chang-Kyu Lee
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Lon Luong
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Naveed Mastan
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Ryan May
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jose Melchor
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Nerick Mosqueda
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Erika Mott
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Eric Olson
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jody Parente
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Patrick D Parker
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Sheana Parry
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | | | - Lydia Potekhina
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Zackery L Riley
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Tyson Roberts
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Brandon Rogers
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Kate Roll
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - David Rosen
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Melaine Sarreal
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | | | - Shu Shi
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Nathan Sjoquist
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Andy J Sodt
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Robbie Townsend
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | | | - Udi Wagley
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Wayne B Wakeman
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Cassandra White
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Crissa Bennett
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Jennifer Wu
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Rob Young
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | | | - Paul Wohnoutka
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - John G Hohmann
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | | | - Robert F Hevner
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98101, USA
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - John W Phillips
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Allan R Jones
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - David G Amaral
- Department of Psychiatry and Behavioral Science, California National Primate Research Center, The M.I.N.D. Institute, University of California, Davis, Sacramento, California 95817, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington 98109, USA
| |
Collapse
|
25
|
Lee JK, Phillips JW, Smith BA, Park JW, Stoyanova T, McCaffrey EF, Baertsch R, Sokolov A, Meyerowitz JG, Mathis C, Cheng D, Stuart JM, Shokat KM, Gustafson WC, Huang J, Witte ON. N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells. Cancer Cell 2016; 29:536-547. [PMID: 27050099 PMCID: PMC4829466 DOI: 10.1016/j.ccell.2016.03.001] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/15/2015] [Accepted: 03/01/2016] [Indexed: 02/06/2023]
Abstract
MYCN amplification and overexpression are common in neuroendocrine prostate cancer (NEPC). However, the impact of aberrant N-Myc expression in prostate tumorigenesis and the cellular origin of NEPC have not been established. We define N-Myc and activated AKT1 as oncogenic components sufficient to transform human prostate epithelial cells to prostate adenocarcinoma and NEPC with phenotypic and molecular features of aggressive, late-stage human disease. We directly show that prostate adenocarcinoma and NEPC can arise from a common epithelial clone. Further, N-Myc is required for tumor maintenance, and destabilization of N-Myc through Aurora A kinase inhibition reduces tumor burden. Our findings establish N-Myc as a driver of NEPC and a target for therapeutic intervention.
Collapse
Affiliation(s)
- John K Lee
- Division of Hematology and Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John W Phillips
- Department of Microbiology, Immunology, and Medical Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bryan A Smith
- Department of Microbiology, Immunology, and Medical Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jung Wook Park
- Department of Microbiology, Immunology, and Medical Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tanya Stoyanova
- Department of Microbiology, Immunology, and Medical Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Erin F McCaffrey
- Department of Microbiology, Immunology, and Medical Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert Baertsch
- Center for Biomolecular Science and Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Artem Sokolov
- Center for Biomolecular Science and Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Justin G Meyerowitz
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Departments of Neurology and Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Colleen Mathis
- Department of Microbiology, Immunology, and Medical Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua M Stuart
- Center for Biomolecular Science and Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kevan M Shokat
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - W Clay Gustafson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics, UCSF Benioff Children's Hospital, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiaoti Huang
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Owen N Witte
- Department of Microbiology, Immunology, and Medical Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
26
|
Lee JK, Smith BA, Phillips JW, Park J, Stoyanova TI, Baertsch R, Sokolov A, Mathis C, Cheng D, Stuart JM, Huang J, Witte ON. Abstract A28: N-Myc drives small cell neuroendocrine cancer initiated from human prostate basal cells. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.myc15-a28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Human small cell prostate carcinoma (SCPC) represents up to 25% of lethal castration-resistant prostate cancer. Molecular characterization of a panel of SCPCs recently identified frequent genomic amplification of both MYCN and AURKA. The oncogenic function of N-Myc has been characterized in many cancer types but its role in the initiation of human SCPC has not been defined. To investigate the function of N-Myc in human prostate transformation, we utilized a tissue regeneration model of human prostate cancer. Human prostate basal epithelial cells were isolated from benign primary prostate tissue from four independent human donors, infected with lentiviruses expressing the oncogenes N-Myc and activated (myristoylated) AKT1, mixed with mouse urogenital sinus mesenchyme, and grafted subcutaneously in immunodeficient NOD-SCID-IL2Rγnull mice. Palpable tumors were appreciated within 2-3 months and histological evaluation revealed regions of mixed high-grade adenocarcinoma and small cell carcinoma. The small cell carcinoma histology showed typical findings of high nuclear-to-cytoplasmic ratio, nuclear molding, stippled chromatin, and frequent mitotic and apoptotic features. Immunohistochemical analysis demonstrated low to absent androgen receptor (AR) staining in both the adenocarcinoma and small cell carcinoma. Further, we found heterogeneous staining for neuroendocrine markers including neural cell adhesion molecule 1, chromogranin A, synaptophysin, thyroid transcription factor 1, and forkhead box A2 in the regions of small cell carcinoma in support of the histological diagnosis. To assess the androgen dependence of tumor growth, regenerated N-Myc and activated AKT1 tumors derived from the lentiviral infection of primary human prostate basal cells were passaged in either intact or castrate immunodeficient mice. Tumors were propagated both in the presence and absence of androgens and showed a small but progressive enrichment of the small cell carcinoma over the adenocarcinoma with successive passage in castrate hosts. Molecular profiling by RNA-Seq of three regenerated N-Myc and activated AKT1 tumors showed a significant resemblance to a subset of human SCPC clinical specimens. Further, the adenocarcinoma and small cell carcinoma components of each tumor were remarkably similar at the transcriptional level despite their differences in histological appearance. In conclusion, we have established a novel model of human small cell prostate cancer arising from benign human prostate basal cells. Overexpression of N-Myc and activated AKT1 in basal cells produces tumors that recapitulate the histology, immunophenotype, and transcriptional profile of human SCPC. These findings support a direct role for N-Myc in the neuroendocrine transformation of basal cells in the human prostate. Further studies are ongoing to elucidate the mechanisms by which N-Myc induces a neuroendocrine differentiation program in prostate cancer.
Citation Format: John K. Lee, Bryan A. Smith, John W. Phillips, Jungwook Park, Tanya I. Stoyanova, Robert Baertsch, Artem Sokolov, Colleen Mathis, Donghui Cheng, Joshua M. Stuart, Jiaoti Huang, Owen N. Witte. N-Myc drives small cell neuroendocrine cancer initiated from human prostate basal cells. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr A28.
Collapse
|
27
|
Martínez TF, Phillips JW, Karanja KK, Polaczek P, Wang CM, Li BC, Campbell JL, Dervan PB. Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response. Nucleic Acids Res 2014; 42:11546-59. [PMID: 25249630 PMCID: PMC4191428 DOI: 10.1093/nar/gku866] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pyrrole–imidazole polyamides targeted to the androgen response element were cytotoxic in multiple cell lines, independent of intact androgen receptor signaling. Polyamide treatment induced accumulation of S-phase cells and of PCNA replication/repair foci. Activation of a cell cycle checkpoint response was evidenced by autophosphorylation of ATR, the S-phase checkpoint kinase, and by recruitment of ATR and the ATR activators RPA, 9-1-1, and Rad17 to chromatin. Surprisingly, ATR activation was accompanied by only a slight increase in single-stranded DNA, and the ATR targets RPA2 and Chk1, a cell cycle checkpoint kinase, were not phosphorylated. However, ATR activation resulted in phosphorylation of the replicative helicase subunit MCM2, an ATR effector. Polyamide treatment also induced accumulation of monoubiquitinated FANCD2, which is recruited to stalled replication forks and interacts transiently with phospho-MCM2. This suggests that polyamides induce replication stress that ATR can counteract independently of Chk1 and that the FA/BRCA pathway may also be involved in the response to polyamides. In biochemical assays, polyamides inhibit DNA helicases, providing a plausible mechanism for S-phase inhibition.
Collapse
Affiliation(s)
- Thomas F Martínez
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John W Phillips
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kenneth K Karanja
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Piotr Polaczek
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chieh-Mei Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Benjamin C Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
28
|
Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, Caldejon S, Carey A, Cuhaciyan C, Dalley RA, Dee N, Dolbeare TA, Facer BAC, Feng D, Fliss TP, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Howard RE, Jochim JM, Kuan CL, Lau C, Lee CK, Lee F, Lemon TA, Lesnar P, McMurray B, Mastan N, Mosqueda N, Naluai-Cecchini T, Ngo NK, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry SE, Stevens A, Pletikos M, Reding M, Roll K, Sandman D, Sarreal M, Shapouri S, Shapovalova NV, Shen EH, Sjoquist N, Slaughterbeck CR, Smith M, Sodt AJ, Williams D, Zöllei L, Fischl B, Gerstein MB, Geschwind DH, Glass IA, Hawrylycz MJ, Hevner RF, Huang H, Jones AR, Knowles JA, Levitt P, Phillips JW, Sestan N, Wohnoutka P, Dang C, Bernard A, Hohmann JG, Lein ES. Transcriptional landscape of the prenatal human brain. Nature 2014; 508:199-206. [PMID: 24695229 PMCID: PMC4105188 DOI: 10.1038/nature13185] [Citation(s) in RCA: 820] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 02/26/2014] [Indexed: 12/21/2022]
Abstract
The anatomical and functional architecture of the human brain is largely determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of 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 postmitotic 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 human-expanded outer subventricular zones. Both germinal and postmitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in 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.
Collapse
Affiliation(s)
- Jeremy A Miller
- 1] Allen Institute for Brain Science, Seattle, Washington 98103, USA [2]
| | - Song-Lin Ding
- 1] Allen Institute for Brain Science, Seattle, Washington 98103, USA [2]
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Kimberly A Smith
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Zackery L Riley
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Joshua J Royall
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Kaylynn Aiona
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - James M Arnold
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Crissa Bennet
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Stephanie Butler
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Shiella Caldejon
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Anita Carey
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Rachel A Dalley
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Tim A Dolbeare
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - David Feng
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Tim P Fliss
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Garrett Gee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Lindsey Gourley
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Guangyu Gu
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Robert E Howard
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jayson M Jochim
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Chihchau L Kuan
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Christopher Lau
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Chang-Kyu Lee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Tracy A Lemon
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Phil Lesnar
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Bergen McMurray
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Naveed Mastan
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nerick Mosqueda
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Theresa Naluai-Cecchini
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 1959 North East Pacific Street, Box 356320, Seattle, Washington 98195, USA
| | - Nhan-Kiet Ngo
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Aaron Oldre
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Eric Olson
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Jody Parente
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Patrick D Parker
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Sheana E Parry
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Allison Stevens
- 1] Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Computer Science and AI Lab, MIT, Cambridge, Massachusetts 02139, USA
| | - Mihovil Pletikos
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Kate Roll
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Melaine Sarreal
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Sheila Shapouri
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Elaine H Shen
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nathan Sjoquist
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | - Michael Smith
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Andy J Sodt
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Derric Williams
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Lilla Zöllei
- Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - Bruce Fischl
- 1] Department of Radiology, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA [2] Computer Science and AI Lab, MIT, Cambridge, Massachusetts 02139, USA
| | - Mark B Gerstein
- 1] Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA [2] Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology and Semel Institute David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA
| | - Ian A Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 1959 North East Pacific Street, Box 356320, Seattle, Washington 98195, USA
| | | | - Robert F Hevner
- 1] Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington 98101, USA [2] Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington 98105, USA
| | - Hao Huang
- Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Allan R Jones
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - James A Knowles
- Zilkha Neurogenetic Institute, and Department of Psychiatry, University of Southern California, Los Angeles, California 90033, USA
| | - Pat Levitt
- 1] Department of Pediatrics, Children's Hospital, Los Angeles, California 90027, USA [2] Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - John W Phillips
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Nenad Sestan
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Paul Wohnoutka
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - John G Hohmann
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| |
Collapse
|
29
|
Ondeyka J, Buevich AV, Williamson RT, Zink DL, Polishook JD, Occi J, Vicente F, Basilio A, Bills GF, Donald RGK, Phillips JW, Goetz MA, Singh SB. Isolation, structure elucidation, and biological activity of altersolanol P using Staphylococcus aureus fitness test based genome-wide screening. J Nat Prod 2014; 77:497-502. [PMID: 24428261 DOI: 10.1021/np400759f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bacteria continue to evade existing antibiotics by acquiring resistance by various mechanisms, leading to loss of antibiotic effectiveness. To avoid an epidemic from infections of incurable drug-resistant bacteria, new antibiotics with new modes of action are desperately needed. Using a genome-wide mechanism of action-guided whole cell screening approach based on antisense Staphylococcus aureus fitness test technology, we report herein the discovery of altersolanol P (1), a new tetrahydroanthraquinone from an unknown fungus from the Hypocreales isolated from forest litter collected in Puerto Rico. The structure was elucidated by high-resolution mass spectrometry and 2D NMR spectroscopy. Relative stereochemistry was established by NOESY correlations, and absolute configuration was deduced by the application of MPA ester-based methodology. Observed (1)H and (13)C NMR shifts were well aligned with the corresponding chemical shifts predicted by DFT calculations. Altersolanol P exhibited Gram-positive antibacterial activity (MIC range 1-8 μg/mL) and inhibited the growth of Gram-negative Haemophilus influenzae (MIC 2 μg/mL). The isolation, structure elucidation, and antibacterial activity of altersolanol P are described.
Collapse
Affiliation(s)
- John Ondeyka
- Merck Research Laboratories , Rahway, New Jersey 07065 and Kenilworth, New Jersey 07033, United States
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Miller JA, Menon V, Goldy J, Kaykas A, Lee CK, Smith KA, Shen EH, Phillips JW, Lein ES, Hawrylycz MJ. Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq. BMC Genomics 2014; 15:154. [PMID: 24564186 PMCID: PMC4007560 DOI: 10.1186/1471-2164-15-154] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/30/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput sequencing is gradually replacing microarrays as the preferred method for studying mRNA expression levels, providing nucleotide resolution and accurately measuring absolute expression levels of almost any transcript, known or novel. However, existing microarray data from clinical, pharmaceutical, and academic settings represent valuable and often underappreciated resources, and methods for assessing and improving the quality of these data are lacking. RESULTS To quantitatively assess the quality of microarray probes, we directly compare RNA-Seq to Agilent microarrays by processing 231 unique samples from the Allen Human Brain Atlas using RNA-Seq. Both techniques provide highly consistent, highly reproducible gene expression measurements in adult human brain, with RNA-Seq slightly outperforming microarray results overall. We show that RNA-Seq can be used as ground truth to assess the reliability of most microarray probes, remove probes with off-target effects, and scale probe intensities to match the expression levels identified by RNA-Seq. These sequencing scaled microarray intensities (SSMIs) provide more reliable, quantitative estimates of absolute expression levels for many genes when compared with unscaled intensities. Finally, we validate this result in two human cell lines, showing that linear scaling factors can be applied across experiments using the same microarray platform. CONCLUSIONS Microarrays provide consistent, reproducible gene expression measurements, which are improved using RNA-Seq as ground truth. We expect that our strategy could be used to improve probe quality for many data sets from major existing repositories.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mike J Hawrylycz
- Allen Institute for Brain Science, 551 N 34th Street, Seattle, WA 98103, USA.
| |
Collapse
|
31
|
Singh SB, Goetz MA, Smith SK, Zink DL, Polishook J, Onishi R, Salowe S, Wiltsie J, Allocco J, Sigmund J, Dorso K, de la Cruz M, Martín J, Vicente F, Genilloud O, Donald RG, Phillips JW. Kibdelomycin A, a congener of kibdelomycin, derivatives and their antibacterial activities. Bioorg Med Chem Lett 2012; 22:7127-30. [DOI: 10.1016/j.bmcl.2012.09.071] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/17/2012] [Accepted: 09/19/2012] [Indexed: 11/17/2022]
|
32
|
Huber J, Donald RG, Lee SH, Jarantow LW, Salvatore MJ, Meng X, Painter R, Onishi RH, Occi J, Dorso K, Young K, Park YW, Skwish S, Szymonifka MJ, Waddell TS, Miesel L, Phillips JW, Roemer T. Chemical Genetic Identification of Peptidoglycan Inhibitors Potentiating Carbapenem Activity against Methicillin-Resistant Staphylococcus aureus. ACTA ACUST UNITED AC 2009; 16:837-48. [DOI: 10.1016/j.chembiol.2009.05.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 05/25/2009] [Accepted: 05/28/2009] [Indexed: 10/20/2022]
|
33
|
Donald RG, Skwish S, Forsyth RA, Anderson JW, Zhong T, Burns C, Lee S, Meng X, LoCastro L, Jarantow LW, Martin J, Lee SH, Taylor I, Robbins D, Malone C, Wang L, Zamudio CS, Youngman PJ, Phillips JW. A Staphylococcus aureus Fitness Test Platform for Mechanism-Based Profiling of Antibacterial Compounds. ACTA ACUST UNITED AC 2009; 16:826-36. [DOI: 10.1016/j.chembiol.2009.07.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 05/25/2009] [Accepted: 07/09/2009] [Indexed: 10/20/2022]
|
34
|
Chenoweth DM, Harki DA, Phillips JW, Dose C, Dervan PB. Cyclic pyrrole-imidazole polyamides targeted to the androgen response element. J Am Chem Soc 2009; 131:7182-8. [PMID: 19413319 DOI: 10.1021/ja901309z] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hairpin pyrrole-imidazole (Py-Im) polyamides are a class of cell-permeable DNA-binding small molecules that can disrupt transcription factor-DNA binding and regulate endogenous gene expression. The covalent linkage of antiparallel Py-Im ring pairs with an gamma-amino acid turn unit affords the classical hairpin Py-Im polyamide structure. Closing the hairpin with a second turn unit yields a cyclic polyamide, a lesser-studied architecture mainly attributable to synthetic inaccessibility. We have applied our methodology for solution-phase polyamide synthesis to cyclic polyamides with an improved high-yield cyclization step. Cyclic 8-ring Py-Im polyamides 1-3 target the DNA sequence 5'-WGWWCW-3', which corresponds to the androgen response element (ARE) bound by the androgen receptor transcription factor to modulate gene expression. We find that cyclic Py-Im polyamides 1-3 bind DNA with exceptionally high affinities and regulate the expression of AR target genes in cell culture studies, from which we infer that the cycle is cell permeable.
Collapse
Affiliation(s)
- David M Chenoweth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | | | | | | | | |
Collapse
|
35
|
Wigg AJ, Barritt GJ, Young GP, Phillips JW. Inhibition of oxidative stress and apoptosis enables extended maintenance of integrity and function of isolated hepatocytes in suspension. J Gastroenterol Hepatol 2009; 24:1082-8. [PMID: 19638086 DOI: 10.1111/j.1440-1746.2009.05798.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
AIMS Isolated hepatocytes in suspension may offer an alternative culture system for bioartificial liver devices. However, maintenance of isolated hepatocyte suspensions in conventional media leads to rapid loss of cell integrity. The aim of this study was to develop a modified medium to better maintain hepatocyte integrity. METHODS Isolated rat hepatocytes were prepared by collagenase digestion. Hepatocytes were purified in a Percoll gradient, suspended in bicarbonate buffered isotonic saline supplemented with d-alpha-tocopherol succinate and glucose and medium changed at 24 h (modified medium). The properties of cells treated this way were compared with those prepared by collagenase digestion and suspension in bicarbonate buffered isotonic saline (basic medium). Both media were maintained at 30 degrees C for 48 h on an orbital shaker. Markers for oxidative stress, apoptosis and metabolic function were measured enzymatically. Cell morphology was assessed by electron microscopy. RESULTS When compared to collagenase-isolated hepatocytes maintained in basic medium, hepatocytes purified by Percoll (Amersham Biosciences, Castle Hill, Australia) and maintained in modified medium demonstrated significantly increased glutathione (GSH) and GSH : glutathione disulphide (GSSH) ratios, decreased lipid peroxidation product formation, decreased caspase-3 protease activity, reduced uptake of trypan blue and loss of lactate dehydrogenase (LDH) and increase preservation of cellular adenosine triphosphate concentration ([ATP]), urea synthesis, ammonia removal and glycogen content. Cell morphology was substantially preserved following 48 h of maintenance in the modified medium. CONCLUSIONS The use of Percoll and modified medium reduces cell injury and apoptosis and greatly improves maintenance of cell function and morphology. The modifications reported here and the use of isolated hepatocyte suspensions in bioartificial liver devices are worthy of further investigation.
Collapse
Affiliation(s)
- Alan J Wigg
- Department of Gastroenterology and Hepatology, Flinders Medical Centre, Bedford Park, South Australia, Australia.
| | | | | | | |
Collapse
|
36
|
Hsu CF, Phillips JW, Trauger JW, Farkas ME, Belitsky JM, Heckel A, Olenyuk BZ, Puckett JW, Wang CCC, Dervan PB. Completion of a Programmable DNA-Binding Small Molecule Library. Tetrahedron 2007; 63:6146-6151. [PMID: 18596841 DOI: 10.1016/j.tet.2007.03.041] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Hairpin pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells and downregulate endogenous gene expression. We complete here a library of 27 hairpin Py-Im polyamides which bind 7-base-pair sequences of the general form 5'-WWGNNNW-3' (where W = A or T, N = W, G, or C). Their equilibrium association constants (K(a)) range from K(a) = 1×10(8) M(-1) to 4×10(10) M(-1) with good sequence specificity. A table of binding affinities and sequence contexts for this completed 27-member library has been assembled for the benefit of the chemical biology community interested in molecular control of transcription.
Collapse
Affiliation(s)
- Carey F Hsu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Singh SB, Phillips JW, Wang J. Highly sensitive target-based whole-cell antibacterial discovery strategy by antisense RNA silencing. Curr Opin Drug Discov Devel 2007; 10:160-6. [PMID: 17436551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Examples of drug-resistant bacteria are increasing while the discovery of new antibiotics with new mechanisms of action has been essentially nonexistent. The antisense-based sensitization of bacterial targets in Staphylococcus aureus is one of the new approaches that provides increased sensitivity for the detection of target-specific antibiotics and whole-cell screening assays based on differential sensitivity of target-depleted strains. The screening of natural product extracts using this type of assay designed for condensing enzyme (FabH/FabF) targets of the fatty acid biosynthesis pathway led to the discovery of a number of target-specific inhibitors including the novel antibiotic platensimycin, which has displayed activity against various drug-resistant bacteria. The antisense-based discovery strategy, rationale and design of screening assays, and the application of such assays for screening of natural product extracts and the discovery of fatty acid condensing enzyme inhibitors are reviewed in this article.
Collapse
Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, RY80Y-350, 126 E Lincoln Avenue, Rahway, NJ 07065, USA.
| | | | | |
Collapse
|
38
|
Monks SA, Leonardson A, Zhu H, Cundiff P, Pietrusiak P, Edwards S, Phillips JW, Sachs A, Schadt EE. Genetic inheritance of gene expression in human cell lines. Am J Hum Genet 2004; 75:1094-105. [PMID: 15514893 PMCID: PMC1182144 DOI: 10.1086/426461] [Citation(s) in RCA: 296] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Accepted: 10/01/2004] [Indexed: 11/03/2022] Open
Abstract
Combining genetic inheritance information, for both molecular profiles and complex traits, is a promising strategy not only for detecting quantitative trait loci (QTLs) for complex traits but for understanding which genes, pathways, and biological processes are also under the influence of a given QTL. As a primary step in determining the feasibility of such an approach in humans, we present the largest survey to date, to our knowledge, of the heritability of gene-expression traits in segregating human populations. In particular, we measured expression for 23,499 genes in lymphoblastoid cell lines for members of 15 Centre d'Etude du Polymorphisme Humain (CEPH) families. Of the total set of genes, 2,340 were found to be expressed, of which 31% had significant heritability when a false-discovery rate of 0.05 was used. QTLs were detected for 33 genes on the basis of at least one P value <.000005. Of these, 13 genes possessed a QTL within 5 Mb of their physical location. Hierarchical clustering was performed on the basis of both Pearson correlation of gene expression and genetic correlation. Both reflected biologically relevant activity taking place in the lymphoblastoid cell lines, with greater coherency represented in Kyoto Encyclopedia of Genes and Genomes database (KEGG) pathways than in Gene Ontology database pathways. However, more pathway coherence was observed in KEGG pathways when clustering was based on genetic correlation than when clustering was based on Pearson correlation. As more expression data in segregating populations are generated, viewing clusters or networks based on genetic correlation measures and shared QTLs will offer potentially novel insights into the relationship among genes that may underlie complex traits.
Collapse
Affiliation(s)
- S A Monks
- Department of Statistics, Oklahoma State University, Stillwater, OK 74078-1056, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Lum PY, Armour CD, Stepaniants SB, Cavet G, Wolf MK, Butler JS, Hinshaw JC, Garnier P, Prestwich GD, Leonardson A, Garrett-Engele P, Rush CM, Bard M, Schimmack G, Phillips JW, Roberts CJ, Shoemaker DD. Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 2004; 116:121-37. [PMID: 14718172 DOI: 10.1016/s0092-8674(03)01035-3] [Citation(s) in RCA: 362] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Modern medicine faces the challenge of developing safer and more effective therapies to treat human diseases. Many drugs currently in use were discovered without knowledge of their underlying molecular mechanisms. Understanding their biological targets and modes of action will be essential to design improved second-generation compounds. Here, we describe the use of a genome-wide pool of tagged heterozygotes to assess the cellular effects of 78 compounds in Saccharomyces cerevisiae. Specifically, lanosterol synthase in the sterol biosynthetic pathway was identified as a target of the antianginal drug molsidomine, which may explain its cholesterol-lowering effects. Further, the rRNA processing exosome was identified as a potential target of the cell growth inhibitor 5-fluorouracil. This genome-wide screen validated previously characterized targets or helped identify potentially new modes of action for over half of the compounds tested, providing proof of this principle for analyzing the modes of action of clinically relevant compounds.
Collapse
Affiliation(s)
- Pek Yee Lum
- Rosetta Inpharmatics LLC, a wholly-owned subsidiary of Merck & Co, Inc, 12040 115th Avenue NE, Kirkland, WA 98034, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Abstract
Isolated hepatocytes in suspension provide a number of advantages for use in bioartificial liver device, however, poor stability of this cell preparation at physiological temperatures is an apparent barrier preventing their use. We therefore investigated the integrity and differentiated function of isolated rat hepatocytes under conditions of mild hypothermia. Isolated hepatocytes were suspended in a bicarbonate buffered saline medium, supplemented with glucose and bovine serum albumin (BSA), and maintained for 48 h at 25 degrees C on a rotary shaker under an atmosphere of 95% O2 and 5% CO2. Under these conditions there was no significant decline in cell viability and good preservation of cellular morphology on transmission electron microscopy for at least 24 h. Isolated hepatocytes in suspension at 25 degrees C were also able to maintain normal Na+ and K+ ion gradients. The cellular energy status ([ATP], ATP/ADP ratio, cytoplasmic and mitochondrial redox potentials), metabolic function (urea synthesis and ammonia removal), albumin synthesis and phase I and phase II drug detoxification activity of these cells were also maintained for at least 24 h post isolation. These observations demonstrate the robust nature of mildly hypothermic isolated hepatocytes in suspension and encourage further studies re-examining the feasibility of using this cell preparation in bioartificial livers.
Collapse
Affiliation(s)
- Alan J Wigg
- Departments of Gastroenterology and Hepatology, Flinders Medical Centre, Flinders University, Adelaide, Australia.
| | | | | |
Collapse
|
41
|
Abstract
The assessment of cell concentration and viability of freshly isolated hepatocyte preparations has been traditionally performed using manual counting with a Neubauer counting chamber and staining for trypan blue exclusion. Despite the simple and rapid nature of this assessment, concerns about the accuracy of these methods exist. Simple flow cytometry techniques which determine cell concentration and viability are available yet surprisingly have not been extensively used or validated with isolated hepatocyte preparations. We therefore investigated the use of flow cytometry using TRUCOUNT Tubes and propidium iodide staining to measure cell concentration and viability of isolated rat hepatocytes in suspension. Analysis using TRUCOUNT Tubes provided more accurate and reproducible measurement of cell concentration than manual cell counting. Hepatocyte viability, assessed using propidium iodide, correlated more closely than did trypan blue exclusion with all indicators of hepatocyte integrity and function measured (lactate dehydrogenase leakage, cytochrome p450 content, cellular ATP concentration, ammonia and lactate removal, urea and albumin synthesis). We conclude that flow cytometry techniques can be used to measure cell concentration and viability of isolated hepatocyte preparations. The techniques are simple, rapid, and more accurate than manual cell counting and trypan blue staining and the results are not affected by protein-containing media.
Collapse
Affiliation(s)
- Alan J Wigg
- Department of Medical Biochemistry, Flinders University, Bedford Park, South Australia 5042, Australia.
| | | | | | | |
Collapse
|
42
|
|
43
|
|
44
|
Abstract
We have used a random walk model of glycolysis and gluconeogenesis to investigate the bioenergetic implications of considering the cell cytoplasm to be a uniform well-mixed compartment. Radiotracer studies conducted on hepatocytes harvested from fasted rats and incubated with 40 mM glucose and 10 mM lactate demonstrated simultaneous glycolysis and gluconeogenesis, with net glycolysis. Tracer introduced as glycerol was incorporated both into glucose (via gluconeogenesis) and into pyruvate (via glycolysis). The data allow us to place a lower bound on the energetic cost of futile cycles involving adenosine triphosphate (ATP) hydrolysis in the early phosphorylation steps of glycolysis. Applying the Markov Chain model for glucose undergoing metabolism to pyruvate, the expected number of ATP molecules hydrolysed is not less than 15 ATP molecules per glucose molecule. The data suggest that, in hepatocytes under the circumstances of this experiment, either glycolysis is a net consumer of ATP, or glycolysis and gluconeogenesis are compartmentalized to a greater extent than is generally supposed.
Collapse
Affiliation(s)
- M E Jones
- The School of Medicine, 6E-124, Flinders University of South Australia, 2100, Adelaide, 5001, SA, Australia.
| | | | | |
Collapse
|
45
|
Bruns SD, McGee JM, Phillips JW. Current treatment of cutaneous melanoma and the sentinel lymph node. J Okla State Med Assoc 2002; 95:332-5. [PMID: 12043108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Affiliation(s)
- Stephen D Bruns
- University of Oklahoma-Tulsa, Schustermann Health Sciences Center, Oklahoma, USA
| | | | | |
Collapse
|
46
|
Phillips JW, Jones ME, Berry MN. Implications of the simultaneous occurrence of hepatic glycolysis from glucose and gluconeogenesis from glycerol. Eur J Biochem 2002; 269:792-7. [PMID: 11846780 DOI: 10.1046/j.0014-2956.2001.02687.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Glycolysis from [6-(3)H]glucose and gluconeogenesis from [U-(14)C]glycerol were examined in isolated hepatocytes from fasted rats. A 5 mm bolus of glycerol inhibited phosphorylation of 40 mm glucose by 50% and glycolysis by more than 60%, and caused cellular ATP depletion and glycerol 3-phosphate accumulation. Gluconeogenesis from 5 mm glycerol was unaffected by the presence of 40 mm glucose. When nonsaturating concentrations of glycerol (< 200 microm) were maintained in the medium by infusion of glycerol, cellular ATP concentrations remained normal. The rate of uptake of infused glycerol was unaffected by 40 mm glucose, but carbohydrate synthesis from glycerol was inhibited 25%, a corresponding amount of glycerol being diverted to glycolytic products, whereas 10 mm glucose had no inhibitory effect on conversion of infused glycerol into carbohydrate. Glycerol infusion depressed glycolysis from 10 mm and 40 mm glucose by 15 and 25%, respectively; however, the overall rates of glycolysis were unchanged because of a concomitant increase in glycolysis from the infused glycerol. These studies show that exposure of hepatocytes to glucose and low quasi-steady-state concentrations of glycerol result in the simultaneous occurrence, at substantial rates, of glycolysis from glucose and gluconeogenesis from the added glycerol. We interpret our results as demonstrating that, in hepatocytes from normal rats, segments of the pathways of glycolysis from glucose and gluconeogenesis from glycerol are compartmentalized and that this segregation prevents substantial cross-over of phosphorylated intermediates from one pathway to the other. The competition between glucose and glycerol implies that glycolysis and phosphorylation of glycerol take place in the same cells, and that the occurrence of simultaneous glycolysis and gluconeogenesis may indicate channelling within the cytoplasm of individual hepatocytes.
Collapse
Affiliation(s)
- John W Phillips
- Departments of Medical Biochemistry, Anatomy and Histology and Human Physiology, School of Medicine, The Flinders University of South Australia, Adelaide, South Australia, Australia
| | | | | |
Collapse
|
47
|
Phillips JW, Phillips SD. In defense of surrogate parenting: a critical analysis of the recent Kentucky experience. KY Law J 2001; 69:877-931. [PMID: 11658606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
|
48
|
Levine PB, Mitchell OS, Phillips JW. A benefit of one's own: older women's entitlement to Social Security retirement. Soc Secur Bull 2001; 63:47-53. [PMID: 11439706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
This article explores differences in Social Security eligibility and benefit levels for older men and women using survey data from the Health and Retirement Study combined with administrative records on actual work histories and Social Security rules. We are able to determine the fully insured status of those persons, how close they are to meeting eligibility criteria when they are not fully insured, and their prospects for benefits. Around three-quarters of older women nearing retirement today will be fully insured for Social Security old-age benefits on the basis of their own accounts, but the rest would need substantial extra employment to rise above the eligibility threshold. Further, two-thirds of older married women who are fully insured have sufficient lifetime earnings to translate into an age-65 primary insurance amount worth at least half their husband's, but the other one-third can expect no additional retirement benefit from contributing to Social Security late in life. Finally, most wives will not be able to improve their benefits by working more under current rules. These results have mixed implications regarding the potential impact of women's rising labor force attachment on eventual retirement benefits. Working more years could increase women's chances of becoming eligible for Social Security benefits, but that effect is likely to be small. Furthermore, even when women do become fully insured according to the rules, not many wives will receive a higher benefit at the margin. The reason is that married women still receive higher Social Security benefits as a spouse than they do on the basis of their own work record. In fact, the net benefit from Social Security due to additional work is negative once one takes into account the Social Security contributions the women paid while employed. Benefits paid to widows are even more likely to be based on the spouse's work history rather than on the woman's. Hence, the rising labor market attachment of women in the future may increase their eligibility for benefits but will produce only modest (and often negative) impacts on their old-age Social Security benefits under current rules.
Collapse
Affiliation(s)
- P B Levine
- Department of Economics, Wellesley College, USA
| | | | | |
Collapse
|
49
|
Daugherty BL, Straley KS, Sanders JM, Phillips JW, Disdier M, McEver RP, Green SA. AP-3 adaptor functions in targeting P-selectin to secretory granules in endothelial cells. Traffic 2001; 2:406-13. [PMID: 11389768 DOI: 10.1034/j.1600-0854.2001.002006406.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
P-selectin, a cell adhesion protein participating in the early stages of inflammation, contains multiple sorting signals that regulate its cell surface expression. Targeting to secretory granules regulates delivery of P-selectin to the cell surface. Internalization followed by sorting from early to late endosomes mediates rapid removal of P-selectin from the surface. We show here that the P-selectin cytoplasmic domain bound AP-2 and AP-3 adaptor complexes in vitro. The amino acid substitution L768A, which abolishes endosomal sorting and impairs granule targeting of P-selectin, reduced binding of AP-3 adaptors but not AP-2 adaptors. Turnover of P-selectin was 2.4-fold faster than turnover of transferrin receptor in AP-3-deficient mocha fibroblasts, similar to turnover of these two proteins in AP-3-competent cells, demonstrating that AP-3 function is not required for endosomal sorting. However, sorting P-selectin to secretory granules was defective in endothelial cells from AP-3-deficient pearl mice, demonstrating a role for AP-3 adaptors in granule assembly in endothelial cells. P-selectin sorting to platelet alpha-granules was normal in pearl mice, consistent with earlier evidence that granule targeting of P-selectin is mechanistically distinct in endothelial cells and platelets. These observations establish that AP-3 adaptor functions in assembly of conventional secretory granules, in addition to lysosomes and the 'lysosome-like' secretory granules of platelets and melanocytes.
Collapse
Affiliation(s)
- B L Daugherty
- Department of Cell Biology, UVa Health System, School of Medicine, PO Box 800732, Charlottesville, VA 22908-0732, USA
| | | | | | | | | | | | | |
Collapse
|
50
|
Finn JP, Ebert TR, Withers RT, Carey MF, Mackay M, Phillips JW, Febbraio MA. Effect of creatine supplementation on metabolism and performance in humans during intermittent sprint cycling. Eur J Appl Physiol 2001; 84:238-43. [PMID: 11320642 DOI: 10.1007/s004210170011] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This double blind study investigated the effect of oral creatine supplementation (CrS) on 4 x 20 s of maximal sprinting on an air-braked cycle ergometer. Each sprint was separated by 20 s of recovery. A group of 16 triathletes [mean age 26.6 (SD 5.1) years. mean body mass 77.0 (SD 5.8) kg, mean body fat 12.9 (SD 4.6)%, maximal oxygen uptake 4.86 (SD 0.7) l.min-1] performed an initial 4 x 20 s trial after a muscle biopsy sample had been taken at rest. The subjects were then matched on their total intramuscular creatine content (TCr) before being randomly assigned to groups to take by mouth either a creatine supplement (CRE) or a placebo (CON) before a second 4 x 20 s trial. A muscle biopsy sample was also taken immediately before this second trial. The CrS of 100 g comprised 4 x 5 g for 5 days. The initial mean TCr were 112.5 (SD 8.7) and 112.5 (SD 10.7) mmol.kg-1 dry mass for CRE and CON, respectively. After creatine loading and placebo ingestion respectively, CRE [128.7 (SD 11.8) mmol.kg-1 dry mass] had a greater (P = 0.01) TCr than CON [112.0 (SD 10.0) mmol.kg-1 dry mass]. While the increase in free creatine for CRE was statistically significant (P = 0.034), this was not so for the changes in phosphocreatine content [trial 1: 75.7 (SD 6.9), trial 2: 84.7 (SD 11.0) mmol.kg-1 dry mass, P = 0.091]. There were no significant differences between CRE and CON for citrate synthase activity (P = 0.163). There was a tendency towards improved performance in terms of 1 s peak power (in watts P = 0.07; in watts per kilogram P = 0.05), 5 s peak power (in watts P = 0.08) and fatigue index (P = 0.08) after CrS for sprint 1 of the second trial. However, there was no improvement for mean power (in watts P = 0.15; in watts per kilogram P = 0.1) in sprint 1 or for any performance values in subsequent sprints. Our results suggest that, while CrS elevates the intramuscular stores of free creatine, this does not have an ergogenic effect on 4 x 20 s all-out cycle sprints with intervening 20-s rest periods.
Collapse
Affiliation(s)
- J P Finn
- School of Health, Education and Community Services, Northern Territory University, Darwin, NT 0909, Australia.
| | | | | | | | | | | | | |
Collapse
|