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Leng K, Cadwell CR, Devine WP, Tihan T, Qi Z, Singhal NS, Glenn OA, Kamiya S, Wiita AP, Berger AC, Shieh JT, Titus EW, Paredes MF, Upadhyay V. Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy. Neurol Genet 2024; 10:e200142. [PMID: 38586598 PMCID: PMC10997208 DOI: 10.1212/nxg.0000000000200142] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/24/2024] [Indexed: 04/09/2024]
Abstract
Objectives Mosaic gain of chromosome 1q (chr1q) has been associated with malformation of cortical development (MCD) and epilepsy. Hyaline protoplasmic astrocytopathy (HPA) is a rare neuropathologic finding seen in cases of epilepsy with MCD. The cell-type specificity of mosaic chr1q gain in the brain and the molecular signatures of HPA are unknown. Methods We present the case of a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and HPA. We performed single-nuclei RNA sequencing (snRNA-seq) of brain tissue from the second resection. Results snRNA-seq showed increased expression of chr1q genes specifically in subsets of neurons and astrocytes. Differentially expressed genes associated with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subpopulation of astrocytes demonstrated marked enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in HPA. Discussion snRNA-seq may be used to infer the cell-type specificity of mosaic chromosomal copy number changes and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of HPA.
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Affiliation(s)
- Kun Leng
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Cathryn R Cadwell
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Walter P Devine
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Tarik Tihan
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Zhongxia Qi
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Nilika S Singhal
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Orit A Glenn
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Sherry Kamiya
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Arun P Wiita
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Amy C Berger
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Joseph T Shieh
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Erron W Titus
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Mercedes F Paredes
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
| | - Vaibhav Upadhyay
- From the Medical Scientist Training Program (K.L., E.W.T.); Department of Pathology (C.R.C., W.P.D., T.T., S.K.); Department of Neurological Surgery (C.R.C.); Weill Institute for Neuroscience (C.R.C., M.F.P.); Department of Laboratory Medicine (Z.Q., A.P.W., E.W.T.); Division of Epilepsy (N.S.S., M.F.P.), Department of Neurology; Department of Radiology and Biomedical Imaging (O.A.G.); Department of Bioengineering and Therapeutic Sciences (A.P.W.), University of California, San Francisco; Chan Zuckerberg Biohub (A.P.W.), San Francisco; Department of Medicine (A.C.B., V.U.), University of California San Francisco; Denali Therapeutics (A.C.B.), South San Francisco; Medical Genetics (J.T.S.), Department of Pediatrics, University of California, San Francisco
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Shin D, Kim CN, Ross J, Hennick KM, Wu SR, Paranjape N, Leonard R, Wang JC, Keefe MG, Pavlovic BJ, Donohue KC, Moreau C, Wigdor EM, Larson HH, Allen DE, Cadwell CR, Bhaduri A, Popova G, Bearden CE, Pollen AA, Jacquemont S, Sanders SJ, Haussler D, Wiita AP, Frost NA, Sohal VS, Nowakowski TJ. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. Cell Stem Cell 2024; 31:421-432.e8. [PMID: 38382530 PMCID: PMC10939828 DOI: 10.1016/j.stem.2024.01.010] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/14/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Thalamic dysfunction has been implicated in multiple psychiatric disorders. We sought to study the mechanisms by which abnormalities emerge in the context of the 22q11.2 microdeletion, which confers significant genetic risk for psychiatric disorders. We investigated early stages of human thalamus development using human pluripotent stem cell-derived organoids and show that the 22q11.2 microdeletion underlies widespread transcriptional dysregulation associated with psychiatric disorders in thalamic neurons and glia, including elevated expression of FOXP2. Using an organoid co-culture model, we demonstrate that the 22q11.2 microdeletion mediates an overgrowth of thalamic axons in a FOXP2-dependent manner. Finally, we identify ROBO2 as a candidate molecular mediator of the effects of FOXP2 overexpression on thalamic axon overgrowth. Together, our study suggests that early steps in thalamic development are dysregulated in a model of genetic risk for schizophrenia and contribute to neural phenotypes in 22q11.2 deletion syndrome.
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Affiliation(s)
- David Shin
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jayden Ross
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kelsey M Hennick
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sih-Rong Wu
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Neha Paranjape
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Rachel Leonard
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jerrick C Wang
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew G Keefe
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bryan J Pavlovic
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevin C Donohue
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Clara Moreau
- Sainte Justine Research Center, University of Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada; Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Emilie M Wigdor
- Institute of Developmental and Regenerative Medicine, University of Oxford, Headington, Oxford OX3 7TY, UK
| | - H Hanh Larson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Denise E Allen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Cathryn R Cadwell
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Galina Popova
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carrie E Bearden
- Integrative Center for Neurogenetics, Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Alex A Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sebastien Jacquemont
- Sainte Justine Research Center, University of Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute of Developmental and Regenerative Medicine, University of Oxford, Headington, Oxford OX3 7TY, UK
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Nicholas A Frost
- Department of Neurology, University of Utah, Salt Lake City, UT 84108, USA
| | - Vikaas S Sohal
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA.
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Leng K, Cadwell CR, Patrick Devine W, Tihan T, Qi Z, Singhal N, Glenn O, Kamiya S, Wiita A, Berger A, Shieh JT, Titus EW, Paredes MF, Upadhyay V. Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy. bioRxiv 2024:2023.10.16.562560. [PMID: 38328093 PMCID: PMC10849466 DOI: 10.1101/2023.10.16.562560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Introduction Mosaic gain of chromosome 1q (chr1q) has been associated with malformation of cortical development (MCD) and epilepsy. Hyaline protoplasmic astrocytopathy (HPA) is a rare neuropathological finding seen in cases of epilepsy with MCD. The cell-type specificity of mosaic chr1q gain in the brain and the molecular signatures of HPA are unknown. Methods We present a child with pharmacoresistant epilepsy who underwent epileptic focus resections at age 3 and 5 years and was found to have mosaic chr1q gain and HPA. We performed single-nuclei RNA-sequencing (snRNA-seq) of brain tissue from the second resection. Results snRNA-seq showed increased expression of chr1q genes specifically in subsets of neurons and astrocytes. Differentially expressed genes associated with inferred chr1q gain included AKT3 and genes associated with cell adhesion or migration. A subpopulation of astrocytes demonstrated marked enrichment for synapse-associated transcripts, possibly linked to the astrocytic inclusions observed in HPA. Discussion snRNA-seq may be used to infer the cell type-specificity of mosaic chromosomal copy number changes and identify associated gene expression alterations, which in the case of chr1q gain may involve aberrations in cell migration. Future studies using spatial profiling could yield further insights on the molecular signatures of HPA.
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Affiliation(s)
- Kun Leng
- Medical Scientist Training Program, University of California, San Francisco
| | - Cathryn R. Cadwell
- Department of Pathology, University of California, San Francisco
- Department of Neurological Surgery, University of California San Francisco
- Weill Institute for Neuroscience, University of California, San Francisco
| | | | - Tarik Tihan
- Department of Pathology, University of California, San Francisco
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California, San Francisco
| | - Nilika Singhal
- Division of Epilepsy, Department of Neurology, University of California, San Francisco
| | - Orit Glenn
- Department of Radiology and Biomedical Imaging, University of California, San Francisco
| | - Sherry Kamiya
- Department of Pathology, University of California, San Francisco
| | - Arun Wiita
- Department of Laboratory Medicine, University of California, San Francisco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
- Chan Zuckerberg Biohub, San Francisco
| | - Amy Berger
- Department of Medicine, University of California, San Francisco
- Current affiliation: Denali Therapeutics
| | - Joseph T. Shieh
- Medical Genetics, Department of Pediatrics, University of California, San Francisco
| | - Erron W. Titus
- Medical Scientist Training Program, University of California, San Francisco
- Department of Laboratory Medicine, University of California, San Francisco
| | - Mercedes F. Paredes
- Weill Institute for Neuroscience, University of California, San Francisco
- Division of Epilepsy, Department of Neurology, University of California, San Francisco
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Cadwell CR, Tolias AS. Patch-seq: Multimodal Profiling of Single-Cell Morphology, Electrophysiology, and Gene Expression. Methods Mol Biol 2024; 2752:227-243. [PMID: 38194038 DOI: 10.1007/978-1-0716-3621-3_15] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Cells exhibit diverse morphologic phenotypes, biophysical and functional properties, and gene expression patterns. Understanding how these features are interrelated at the level of single cells has been challenging due to the lack of techniques for multimodal profiling of individual cells. We recently developed Patch-seq, a technique that combines whole-cell patch clamp recording, immunohistochemistry, and single-cell RNA-sequencing (scRNA-seq) to comprehensively profile single cells. Here we present a detailed step-by-step protocol for obtaining high-quality morphological, electrophysiological, and transcriptomic data from single cells. Patch-seq enables researchers to explore the rich, multidimensional phenotypic variability among cells and to directly correlate gene expression with phenotype at the level of single cells.
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Affiliation(s)
- Cathryn R Cadwell
- Departments of Neurological Surgery and Pathology, School of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
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Bartley CM, Ngo TT, Cadwell CR, Harroud A, Schubert RD, Alvarenga BD, Hawes IA, Zorn KC, Hunyh T, Teliska LH, Kung AF, Shah S, Gelfand JM, Chow FC, Rasband MN, Dubey D, Pittock SJ, DeRisi JL, Wilson MR, Pleasure SJ. Dual ankyrinG and subpial autoantibodies in a man with well-controlled HIV infection with steroid-responsive meningoencephalitis: A case report. Front Neurol 2023; 13:1102484. [PMID: 36756346 PMCID: PMC9900111 DOI: 10.3389/fneur.2022.1102484] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023] Open
Abstract
Neuroinvasive infection is the most common cause of meningoencephalitis in people living with human immunodeficiency virus (HIV), but autoimmune etiologies have been reported. We present the case of a 51-year-old man living with HIV infection with steroid-responsive meningoencephalitis whose comprehensive pathogen testing was non-diagnostic. Subsequent tissue-based immunofluorescence with acute-phase cerebrospinal fluid revealed anti-neural antibodies localizing to the axon initial segment (AIS), the node of Ranvier (NoR), and the subpial space. Phage display immunoprecipitation sequencing identified ankyrinG (AnkG) as the leading candidate autoantigen. A synthetic blocking peptide encoding the PhIP-Seq-identified AnkG epitope neutralized CSF IgG binding to the AIS and NoR, thereby confirming a monoepitopic AnkG antibody response. However, subpial immunostaining persisted, indicating the presence of additional autoantibodies. Review of archival tissue-based staining identified candidate AnkG autoantibodies in a 60-year-old woman with metastatic ovarian cancer and seizures that were subsequently validated by cell-based assay. AnkG antibodies were not detected by tissue-based assay and/or PhIP-Seq in control CSF (N = 39), HIV CSF (N = 79), or other suspected and confirmed neuroinflammatory CSF cases (N = 1,236). Therefore, AnkG autoantibodies in CSF are rare but extend the catalog of AIS and NoR autoantibodies associated with neurological autoimmunity.
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Affiliation(s)
- Christopher M. Bartley
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Thomas T. Ngo
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Cathryn R. Cadwell
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, United States
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States
| | - Adil Harroud
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Ryan D. Schubert
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Bonny D. Alvarenga
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Isobel A. Hawes
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Kelsey C. Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Trung Hunyh
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Lindsay H. Teliska
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Andrew F. Kung
- School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Shailee Shah
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, United States
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, United States
| | - Jeffrey M. Gelfand
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Felicia C. Chow
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Matthew N. Rasband
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Divyanshu Dubey
- Department of Neurology, Mayo Clinic Foundation, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation, Rochester, MN, United States
| | - Sean J. Pittock
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, United States
- Department of Neurology, Mayo Clinic Foundation, Rochester, MN, United States
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation, Rochester, MN, United States
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
| | - Samuel J. Pleasure
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
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6
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Lucas CHG, Davidson CJ, Alashari M, Putnam AR, Whipple NS, Bruggers CS, Mendez JS, Cheshier SH, Walker JB, Ramani B, Cadwell CR, Sullivan DV, Lu R, Mirchia K, Van Ziffle J, Devine P, Goldschmidt E, Hervey-Jumper SL, Gupta N, Oberheim Bush NA, Raleigh DR, Bollen A, Tihan T, Pekmezci M, Solomon DA, Phillips JJ, Perry A. Targeted Next-Generation Sequencing Reveals Divergent Clonal Evolution in Components of Composite Pleomorphic Xanthoastrocytoma-Ganglioglioma. J Neuropathol Exp Neurol 2022; 81:650-657. [PMID: 35703914 PMCID: PMC9297094 DOI: 10.1093/jnen/nlac044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 11/13/2022] Open
Abstract
Composite pleomorphic xanthoastrocytoma-ganglioglioma (PXA-GG) is an extremely rare central nervous system neoplasm with 2 distinct but intermingled components. Whether this tumor represents a "collision tumor" of separate neoplasms or a monoclonal neoplasm with divergent evolution is poorly understood. Clinicopathologic studies and capture-based next generation sequencing were performed on extracted DNA from all available PXA-GG at 2 medical centers. Five PXA-GG were diagnosed in 1 male and 4 female patients ranging from 13 to 25 years in age. Four arose within the cerebral hemispheres; 1 presented in the cerebellar vermis. DNA was sufficient for analysis in 4 PXA components and 3 GG components. Four paired PXA and GG components harbored BRAF p.V600E hotspot mutations. The 4 sequenced PXA components demonstrated CDKN2A homozygous deletion by sequencing with loss of p16 (protein product of CDKN2A) expression by immunohistochemistry, which was intact in all assessed GG components. The PXA components also demonstrated more frequent copy number alterations relative to paired GG components. In one PXA-GG, shared chromosomal copy number alterations were identified in both components. Our findings support divergent evolution of the PXA and GG components from a common BRAF p.V600E-mutant precursor lesion, with additional acquisition of CDKN2A homozygous deletion in the PXA component as is typically seen in conventional PXA.
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Affiliation(s)
- Calixto-Hope G Lucas
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | | | - Mouied Alashari
- Division of Pediatric Pathology, Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Angelica R Putnam
- Division of Pediatric Pathology, Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Nicholas S Whipple
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Carol S Bruggers
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Joe S Mendez
- Department of Neurosurgery, University of Utah/Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Samuel H Cheshier
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Huntsman Cancer Institute, University of Utah, Intermountain Primary Children's Hospital, Salt Lake City, Utah, USA
| | | | - Biswarathan Ramani
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Cathryn R Cadwell
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Daniel V Sullivan
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Rufei Lu
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Kanish Mirchia
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California, USA
| | - Patrick Devine
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California, USA
| | - Ezequiel Goldschmidt
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, USA
| | - Nancy Ann Oberheim Bush
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - David R Raleigh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, USA
| | - Andrew Bollen
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Tarik Tihan
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Melike Pekmezci
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - David A Solomon
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
- From the Department of Pathology, University of California, San Francisco, San Francisco, California, USA
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7
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Allen DE, Donohue KC, Cadwell CR, Shin D, Keefe MG, Sohal VS, Nowakowski TJ. Fate mapping of neural stem cell niches reveals distinct origins of human cortical astrocytes. Science 2022; 376:1441-1446. [PMID: 35587512 PMCID: PMC9233096 DOI: 10.1126/science.abm5224] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Progenitors of the developing human neocortex reside in the ventricular and outer subventricular zones (VZ and OSVZ, respectively). However, whether cells derived from these niches have similar developmental fates is unknown. By performing fate mapping in primary human tissue, we demonstrate that astrocytes derived from these niches populate anatomically distinct layers. Cortical plate astrocytes emerge from VZ progenitors and proliferate locally, while putative white matter astrocytes are morphologically heterogeneous and emerge from both VZ and OSVZ progenitors. Furthermore, via single-cell sequencing of morphologically defined astrocyte subtypes using Patch-seq, we identify molecular distinctions between VZ-derived cortical plate astrocytes and OSVZ-derived white matter astrocytes that persist into adulthood. Together, our study highlights a complex role for cell lineage in the diversification of human neocortical astrocytes.
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Affiliation(s)
- Denise E Allen
- Department of Anatomy, The University of California San Francisco, San Francisco, USA,Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Department of Neurological Surgery, The University of California San Francisco, San Francisco, USA,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, The University of California San Francisco, San Francisco, USA
| | - Kevin C Donohue
- Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,School of Medicine, The University of California San Francisco, San Francisco, USA,Center for Integrative Neuroscience, The University of California San Francisco; San Francisco, USA,Weill Institute for Neurosciences, The University of California San Francisco; San Francisco, USA,Kavli Institute for Fundamental Neuroscience, The University of California San Francisco, San Francisco, USA
| | - Cathryn R Cadwell
- Department of Pathology, The University of California San Francisco, San Francisco, USA
| | - David Shin
- Department of Anatomy, The University of California San Francisco, San Francisco, USA,Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Department of Neurological Surgery, The University of California San Francisco, San Francisco, USA,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, The University of California San Francisco, San Francisco, USA
| | - Matthew G Keefe
- Department of Anatomy, The University of California San Francisco, San Francisco, USA,Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Department of Neurological Surgery, The University of California San Francisco, San Francisco, USA,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, The University of California San Francisco, San Francisco, USA
| | - Vikaas S Sohal
- Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Weill Institute for Neurosciences, The University of California San Francisco; San Francisco, USA,Kavli Institute for Fundamental Neuroscience, The University of California San Francisco, San Francisco, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, The University of California San Francisco, San Francisco, USA,Department of Psychiatry and Behavioral Sciences, The University of California San Francisco, San Francisco, USA,Department of Neurological Surgery, The University of California San Francisco, San Francisco, USA,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, The University of California San Francisco, San Francisco, USA,Weill Institute for Neurosciences, The University of California San Francisco; San Francisco, USA,Corresponding author.
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8
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Tanner JA, Richie MB, Cadwell CR, Eliaz A, Kim S, Haq Z, Rasool N, Shah MP, Guterman EL. Amyloid-β related angiitis presenting as eosinophilic meningitis: a case report. BMC Neurol 2022; 22:116. [PMID: 35331158 PMCID: PMC8944059 DOI: 10.1186/s12883-022-02638-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/08/2021] [Accepted: 03/14/2022] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Eosinophilic meningitis is uncommon and often attributed to infectious causes. CASE PRESENTATION We describe a case of a 72-year-old man who presented with subacute onset eosinophilic meningitis, vasculitis, and intracranial hypertension with progressive and severe neurologic symptoms. Brain MRI demonstrated multifocal strokes and co-localized right temporo-parieto-occipital vasogenic edema, cortical superficial siderosis, and diffuse leptomeningeal enhancement. He ultimately underwent brain biopsy with immunohistochemical stains for amyloid-β and Congo red that were extensively positive in the blood vessel walls and in numerous diffuse and neuritic parenchymal confirming a diagnosis of amyloid-β related angiitis. He was treated with immunosuppression with clinical stabilization. CONCLUSIONS Amyloid-β related angiitis is an underrecognized cause of eosinophilic meningitis that can present fulminantly and is typically responsive to immunosuppression. The presence of eosinophils may provide additional clues to the underlying pathophysiology of amyloid-β related angiitis.
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Affiliation(s)
- Jeremy A Tanner
- Department of Neurology, University of California, San Francisco (UCSF), 505 Parnassus Avenue, M798 Box 0114, San Francisco, CA, 94143, USA
| | - Megan B Richie
- Department of Neurology, University of California, San Francisco (UCSF), 505 Parnassus Avenue, M798 Box 0114, San Francisco, CA, 94143, USA
| | - Cathryn R Cadwell
- Department of Anatomic Pathology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Amity Eliaz
- School of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Shannen Kim
- School of Medicine, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Zeeshan Haq
- Department of Ophthalmology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Nailyn Rasool
- Department of Neurology, University of California, San Francisco (UCSF), 505 Parnassus Avenue, M798 Box 0114, San Francisco, CA, 94143, USA
- Department of Ophthalmology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Maulik P Shah
- Department of Neurology, University of California, San Francisco (UCSF), 505 Parnassus Avenue, M798 Box 0114, San Francisco, CA, 94143, USA
| | - Elan L Guterman
- Department of Neurology, University of California, San Francisco (UCSF), 505 Parnassus Avenue, M798 Box 0114, San Francisco, CA, 94143, USA.
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9
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Cadwell CR, Bowman S, Laszik ZG, Pekmezci M. Loss of fidelity in scanned digital images compared to glass slides of brain tumors resected using cavitron ultrasonic surgical aspirator. Brain Pathol 2021; 31:e12938. [PMID: 33576118 PMCID: PMC8412125 DOI: 10.1111/bpa.12938] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/18/2020] [Accepted: 01/04/2021] [Indexed: 11/30/2022] Open
Abstract
Conversion of glass slides to digital images is necessary to capitalize on advances in computational pathology and could potentially transform our approach to primary diagnosis, research, and medical education. Most slide scanners have a limited maximum scannable area and utilize proprietary tissue detection algorithms to selectively scan regions that contain tissue, allowing for increased scanning speed and reduced file size compared to scanning the entire slide at high resolution. However, very small and faintly stained tissue fragments may not be recognized by these algorithms, leading to loss of fidelity in the digital image compared to the glass slides. Cavitron ultrasonic surgical aspirator (CUSA) is frequently used in brain tumor resections, resulting in highly fragmented specimens that are used for primary diagnosis. Here we evaluated the rate of loss of fidelity in 296 digital images from 40 CUSA-resected brain tumors scanned using a Philips Ultra Fast Scanner. Overall, 54% of the slides (at least one from every case) showed loss of fidelity, with at least one tissue fragment not scanned at high resolution. The majority of the missed tissue fragments were small (<0.5 mm), but rare slides were missing fragments greater than 5 mm in greatest dimension. In addition, 19% of the slides with missing tissue showed no indication of loss of fidelity in the digital image itself; the missing tissue could only be appreciated upon review of the glass slides. These results highlight a potential liability in the use of digital images for primary diagnosis in CUSA-resected brain tumor specimens.
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Affiliation(s)
- Cathryn R Cadwell
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sarah Bowman
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Zoltan G Laszik
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
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10
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Lipovsek M, Bardy C, Cadwell CR, Hadley K, Kobak D, Tripathy SJ. Patch-seq: Past, Present, and Future. J Neurosci 2021; 41:937-946. [PMID: 33431632 PMCID: PMC7880286 DOI: 10.1523/jneurosci.1653-20.2020] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 06/30/2020] [Revised: 11/11/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
Single-cell transcriptomic approaches are revolutionizing neuroscience. Integrating this wealth of data with morphology and physiology, for the comprehensive study of neuronal biology, requires multiplexing gene expression data with complementary techniques. To meet this need, multiple groups in parallel have developed "Patch-seq," a modification of whole-cell patch-clamp protocols that enables mRNA sequencing of cell contents after electrophysiological recordings from individual neurons and morphologic reconstruction of the same cells. In this review, we first outline the critical technical developments that enabled robust Patch-seq experimental efforts and analytical solutions to interpret the rich multimodal data generated. We then review recent applications of Patch-seq that address novel and long-standing questions in neuroscience. These include the following: (1) targeted study of specific neuronal populations based on their anatomic location, functional properties, lineage, or a combination of these factors; (2) the compilation and integration of multimodal cell type atlases; and (3) the investigation of the molecular basis of morphologic and functional diversity. Finally, we highlight potential opportunities for further technical development and lines of research that may benefit from implementing the Patch-seq technique. As a multimodal approach at the intersection of molecular neurobiology and physiology, Patch-seq is uniquely positioned to directly link gene expression to brain function.
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Affiliation(s)
- Marcela Lipovsek
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Cedric Bardy
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI), Adelaide 5000, SA, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park 5042, SA, Australia
| | - Cathryn R Cadwell
- Department of Pathology, University of California San Francisco, San Francisco, California 94143
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, Washington 98109
| | - Dmitry Kobak
- Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Shreejoy J Tripathy
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, Ontario M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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11
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Cadwell CR, Yuksek GE, Hirbe AC, Srihari D, LeBoit P, Dahiya S, Pekmezci M. Preferentially Expressed Antigen in Melanoma (PRAME) Expression in Malignant, but Not Benign, Peripheral Nerve Sheath Tumors. J Neuropathol Exp Neurol 2020; 80:384-386. [PMID: 33212492 DOI: 10.1093/jnen/nlaa125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Cathryn R Cadwell
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California
| | - Gul E Yuksek
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California
| | - Angela C Hirbe
- Division of Medical Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Divya Srihari
- Division of Medical Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Phillip LeBoit
- Division of Dermatopathology, Departments of Pathology and Dermatology, University of California San Francisco, San Francisco, California
| | - Sonika Dahiya
- Division of Neuropathology, Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri
| | - Melike Pekmezci
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California
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12
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Lucas CHG, Gupta R, Doo P, Lee JC, Cadwell CR, Ramani B, Hofmann JW, Sloan EA, Kleinschmidt-DeMasters BK, Lee HS, Wood MD, Grafe M, Born D, Vogel H, Salamat S, Puccetti D, Scharnhorst D, Samuel D, Cooney T, Cham E, Jin LW, Khatib Z, Maher O, Chamyan G, Brathwaite C, Bannykh S, Mueller S, Kline CN, Banerjee A, Reddy A, Taylor JW, Clarke JL, Oberheim Bush NA, Butowski N, Gupta N, Auguste KI, Sun PP, Roland JL, Raffel C, Aghi MK, Theodosopoulos P, Chang E, Hervey-Jumper S, Phillips JJ, Pekmezci M, Bollen AW, Tihan T, Chang S, Berger MS, Perry A, Solomon DA. Comprehensive analysis of diverse low-grade neuroepithelial tumors with FGFR1 alterations reveals a distinct molecular signature of rosette-forming glioneuronal tumor. Acta Neuropathol Commun 2020; 8:151. [PMID: 32859279 PMCID: PMC7456392 DOI: 10.1186/s40478-020-01027-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/19/2020] [Indexed: 01/09/2023] Open
Abstract
The FGFR1 gene encoding fibroblast growth factor receptor 1 has emerged as a frequently altered oncogene in the pathogenesis of multiple low-grade neuroepithelial tumor (LGNET) subtypes including pilocytic astrocytoma, dysembryoplastic neuroepithelial tumor (DNT), rosette-forming glioneuronal tumor (RGNT), and extraventricular neurocytoma (EVN). These activating FGFR1 alterations in LGNET can include tandem duplication of the exons encoding the intracellular tyrosine kinase domain, in-frame gene fusions most often with TACC1 as the partner, or hotspot missense mutations within the tyrosine kinase domain (either at p.N546 or p.K656). However, the specificity of these different FGFR1 events for the various LGNET subtypes and accompanying genetic alterations are not well defined. Here we performed comprehensive genomic and epigenomic characterization on a diverse cohort of 30 LGNET with FGFR1 alterations. We identified that RGNT harbors a distinct epigenetic signature compared to other LGNET with FGFR1 alterations, and is uniquely characterized by FGFR1 kinase domain hotspot missense mutations in combination with either PIK3CA or PIK3R1 mutation, often with accompanying NF1 or PTPN11 mutation. In contrast, EVN harbors its own distinct epigenetic signature and is characterized by FGFR1-TACC1 fusion as the solitary pathogenic alteration. Additionally, DNT and pilocytic astrocytoma are characterized by either kinase domain tandem duplication or hotspot missense mutations, occasionally with accompanying NF1 or PTPN11 mutation, but lacking the accompanying PIK3CA or PIK3R1 mutation that characterizes RGNT. The glial component of LGNET with FGFR1 alterations typically has a predominantly oligodendroglial morphology, and many of the pilocytic astrocytomas with FGFR1 alterations lack the biphasic pattern, piloid processes, and Rosenthal fibers that characterize pilocytic astrocytomas with BRAF mutation or fusion. Together, this analysis improves the classification and histopathologic stratification of LGNET with FGFR1 alterations.
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13
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Cadwell CR, Scala F, Fahey PG, Kobak D, Mulherkar S, Sinz FH, Papadopoulos S, Tan ZH, Johnsson P, Hartmanis L, Li S, Cotton RJ, Tolias KF, Sandberg R, Berens P, Jiang X, Tolias AS. Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex. eLife 2020; 9:e52951. [PMID: 32134385 PMCID: PMC7162653 DOI: 10.7554/elife.52951] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 10/22/2019] [Accepted: 03/02/2020] [Indexed: 11/24/2022] Open
Abstract
Clones of excitatory neurons derived from a common progenitor have been proposed to serve as elementary information processing modules in the neocortex. To characterize the cell types and circuit diagram of clonally related excitatory neurons, we performed multi-cell patch clamp recordings and Patch-seq on neurons derived from Nestin-positive progenitors labeled by tamoxifen induction at embryonic day 10.5. The resulting clones are derived from two radial glia on average, span cortical layers 2-6, and are composed of a random sampling of transcriptomic cell types. We find an interaction between shared lineage and connection type: related neurons are more likely to be connected vertically across cortical layers, but not laterally within the same layer. These findings challenge the view that related neurons show uniformly increased connectivity and suggest that integration of vertical intra-clonal input with lateral inter-clonal input may represent a developmentally programmed connectivity motif supporting the emergence of functional circuits.
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Affiliation(s)
- Cathryn R Cadwell
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
- Department of Anatomic Pathology, University of California San FranciscoSan FranciscoUnited States
| | - Federico Scala
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
| | - Paul G Fahey
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
| | - Dmitry Kobak
- Institute for Ophthalmic Research, University of TübingenTübingenGermany
| | - Shalaka Mulherkar
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
| | - Fabian H Sinz
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
- Department of Computer Science, University of TübingenTübingenGermany
- Interfaculty Institute for Biomedical Informatics, University of TübingenTübingenGermany
| | - Stelios Papadopoulos
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
| | - Zheng H Tan
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
| | - Per Johnsson
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Leonard Hartmanis
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Shuang Li
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
| | - Ronald J Cotton
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
| | - Kimberley F Tolias
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHoustonUnited States
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Philipp Berens
- Institute for Ophthalmic Research, University of TübingenTübingenGermany
- Department of Computer Science, University of TübingenTübingenGermany
| | - Xiaolong Jiang
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
- Jan and Dan Duncan Neurological Research Institute at Texas Children's HospitalHoustonUnited States
| | - Andreas Savas Tolias
- Department of Neuroscience, Baylor College of MedicineHoustonUnited States
- Center for Neuroscience and Artificial Intelligence, Baylor College of MedicineHoustonUnited States
- Department of Electrical and Computer Engineering, Rice UniversityHoustonUnited States
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14
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Cadwell CR, Scala F, Li S, Livrizzi G, Shen S, Sandberg R, Jiang X, Tolias AS. Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq. Nat Protoc 2017; 12:2531-2553. [PMID: 29189773 PMCID: PMC6422019 DOI: 10.1038/nprot.2017.120] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [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] [Indexed: 11/09/2022]
Abstract
Neurons exhibit a rich diversity of morphological phenotypes, electrophysiological properties, and gene-expression patterns. Understanding how these different characteristics are interrelated at the single-cell level has been difficult because of the lack of techniques for multimodal profiling of individual cells. We recently developed Patch-seq, a technique that combines whole-cell patch-clamp recording, immunohistochemistry, and single-cell RNA-sequencing (scRNA-seq) to comprehensively profile single neurons from mouse brain slices. Here, we present a detailed step-by-step protocol, including modifications to the patching mechanics and recording procedure, reagents and recipes, procedures for immunohistochemistry, and other tips to assist researchers in obtaining high-quality morphological, electrophysiological, and transcriptomic data from single neurons. Successful implementation of Patch-seq allows researchers to explore the multidimensional phenotypic variability among neurons and to correlate gene expression with phenotype at the level of single cells. The entire procedure can be completed in ∼2 weeks through the combined efforts of a skilled electrophysiologist, molecular biologist, and biostatistician.
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Affiliation(s)
- Cathryn R. Cadwell
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Federico Scala
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Shuang Li
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Giulia Livrizzi
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Shan Shen
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Rickard Sandberg
- Ludwig Institute for Cancer Research, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Xiaolong Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, Texas, USA
| | - Andreas S. Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, Texas, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas, USA
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15
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Abstract
Individual neurons vary widely in terms of their gene expression, morphology, and electrophysiological properties. While many techniques exist to study single-cell variability along one or two of these dimensions, very few techniques can assess all three features for a single cell. We recently developed Patch-seq, which combines whole-cell patch clamp recording with single-cell RNA-sequencing and immunohistochemistry to comprehensively profile the transcriptomic, morphologic, and physiologic features of individual neurons. Patch-seq can be broadly applied to characterize cell types in complex tissues such as the nervous system, and to study the transcriptional signatures underlying the multidimensional phenotypes of single cells.
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Affiliation(s)
- Cathryn R Cadwell
- Department of Neuroscience, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA
| | - Rickard Sandberg
- Ludwig Institute for Cancer Research, Stockholm, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, Nobels väg 3, 171 65 Solna, Stockholm, Sweden
| | - Xiaolong Jiang
- Department of Neuroscience, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, 1250 Moursund Street, Suite 1025.18, Houston, Texas, 77030, USA
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77030, USA. .,Department of Electrical and Computer Engineering, Rice University, Houston, Texas, USA.
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16
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Jiang X, Shen S, Sinz F, Reimer J, Cadwell CR, Berens P, Ecker AS, Patel S, Denfield GH, Froudarakis E, Li S, Walker E, Tolias AS. Response to Comment on “Principles of connectivity among morphologically defined cell types in adult neocortex”. Science 2016; 353:1108. [DOI: 10.1126/science.aaf6102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/03/2016] [Indexed: 11/02/2022]
Affiliation(s)
- Xiaolong Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Shan Shen
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Fabian Sinz
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Jacob Reimer
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Cathryn R. Cadwell
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Philipp Berens
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Bernstein Centre for Computational Neuroscience, Tübingen, Germany
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Werner Reichardt Center for Integrative Neuroscience and Institute of Theoretical Physics, University of Tübingen, Tübingen, Germany
| | - Alexander S. Ecker
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Bernstein Centre for Computational Neuroscience, Tübingen, Germany
- Werner Reichardt Center for Integrative Neuroscience and Institute of Theoretical Physics, University of Tübingen, Tübingen, Germany
| | - Saumil Patel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - George H. Denfield
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | | | - Shuang Li
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Edgar Walker
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Andreas S. Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Bernstein Centre for Computational Neuroscience, Tübingen, Germany
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17
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Jiang X, Shen S, Cadwell CR, Berens P, Sinz F, Ecker AS, Patel S, Tolias AS. Principles of connectivity among morphologically defined cell types in adult neocortex. Science 2015; 350:aac9462. [PMID: 26612957 DOI: 10.1126/science.aac9462] [Citation(s) in RCA: 519] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Since the work of Ramón y Cajal in the late 19th and early 20th centuries, neuroscientists have speculated that a complete understanding of neuronal cell types and their connections is key to explaining complex brain functions. However, a complete census of the constituent cell types and their wiring diagram in mature neocortex remains elusive. By combining octuple whole-cell recordings with an optimized avidin-biotin-peroxidase staining technique, we carried out a morphological and electrophysiological census of neuronal types in layers 1, 2/3, and 5 of mature neocortex and mapped the connectivity between more than 11,000 pairs of identified neurons. We categorized 15 types of interneurons, and each exhibited a characteristic pattern of connectivity with other interneuron types and pyramidal cells. The essential connectivity structure of the neocortical microcircuit could be captured by only a few connectivity motifs.
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Affiliation(s)
- Xiaolong Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
| | - Shan Shen
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Cathryn R Cadwell
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Philipp Berens
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA. Bernstein Centre for Computational Neuroscience, Tübingen, Germany. Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany. Werner Reichardt Center for Integrative Neuroscience and Institute of Theoretical Physics, University of Tübingen, Tübingen, Germany
| | - Fabian Sinz
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Alexander S Ecker
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA. Bernstein Centre for Computational Neuroscience, Tübingen, Germany. Werner Reichardt Center for Integrative Neuroscience and Institute of Theoretical Physics, University of Tübingen, Tübingen, Germany. Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Saumil Patel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA. Bernstein Centre for Computational Neuroscience, Tübingen, Germany.
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18
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McGinley MJ, Vinck M, Reimer J, Batista-Brito R, Zagha E, Cadwell CR, Tolias AS, Cardin JA, McCormick DA. Waking State: Rapid Variations Modulate Neural and Behavioral Responses. Neuron 2015; 87:1143-1161. [PMID: 26402600 DOI: 10.1016/j.neuron.2015.09.012] [Citation(s) in RCA: 446] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The state of the brain and body constantly varies on rapid and slow timescales. These variations contribute to the apparent noisiness of sensory responses at both the neural and the behavioral level. Recent investigations of rapid state changes in awake, behaving animals have provided insight into the mechanisms by which optimal sensory encoding and behavioral performance are achieved. Fluctuations in state, as indexed by pupillometry, impact both the "signal" (sensory evoked response) and the "noise" (spontaneous activity) of cortical responses. By taking these fluctuations into account, neural response (co)variability is significantly reduced, revealing the brain to be more reliable and predictable than previously thought.
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Affiliation(s)
- Matthew J McGinley
- Department of Neurobiology, Kavli Institute for Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Martin Vinck
- Department of Neurobiology, Kavli Institute for Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Jacob Reimer
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Renata Batista-Brito
- Department of Neurobiology, Kavli Institute for Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Edward Zagha
- Department of Neurobiology, Kavli Institute for Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Cathryn R Cadwell
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Jessica A Cardin
- Department of Neurobiology, Kavli Institute for Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
| | - David A McCormick
- Department of Neurobiology, Kavli Institute for Neuroscience, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
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19
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Cadwell CR, Palasantza A, Jiang X, Berens P, Deng Q, Yilmaz M, Reimer J, Shen S, Bethge M, Tolias KF, Sandberg R, Tolias AS. Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq. Nat Biotechnol 2015; 34:199-203. [PMID: 26689543 DOI: 10.1038/nbt.3445] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 12/02/2015] [Indexed: 01/21/2023]
Abstract
Despite the importance of the mammalian neocortex for complex cognitive processes, we still lack a comprehensive description of its cellular components. To improve the classification of neuronal cell types and the functional characterization of single neurons, we present Patch-seq, a method that combines whole-cell electrophysiological patch-clamp recordings, single-cell RNA-sequencing and morphological characterization. Following electrophysiological characterization, cell contents are aspirated through the patch-clamp pipette and prepared for RNA-sequencing. Using this approach, we generate electrophysiological and molecular profiles of 58 neocortical cells and show that gene expression patterns can be used to infer the morphological and physiological properties such as axonal arborization and action potential amplitude of individual neurons. Our results shed light on the molecular underpinnings of neuronal diversity and suggest that Patch-seq can facilitate the classification of cell types in the nervous system.
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Affiliation(s)
- Cathryn R Cadwell
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Athanasia Palasantza
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - Xiaolong Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Philipp Berens
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Bernstein Center for Computational Neuroscience, Tübingen, Germany.,Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.,Werner Reichardt Center for Integrative Neuroscience and Institute of Theoretical Physics, University of Tübingen, Tübingen, Germany
| | - Qiaolin Deng
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - Marlene Yilmaz
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - Jacob Reimer
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Shan Shen
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Matthias Bethge
- Bernstein Center for Computational Neuroscience, Tübingen, Germany.,Werner Reichardt Center for Integrative Neuroscience and Institute of Theoretical Physics, University of Tübingen, Tübingen, Germany.,Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Kimberley F Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Rickard Sandberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.,Ludwig Institute for Cancer Research, Stockholm, Sweden
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.,Bernstein Center for Computational Neuroscience, Tübingen, Germany
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20
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Reimer J, Froudarakis E, Cadwell CR, Yatsenko D, Denfield GH, Tolias AS. Pupil fluctuations track fast switching of cortical states during quiet wakefulness. Neuron 2014; 84:355-62. [PMID: 25374359 DOI: 10.1016/j.neuron.2014.09.033] [Citation(s) in RCA: 409] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2014] [Indexed: 11/16/2022]
Abstract
Neural responses are modulated by brain state, which varies with arousal, attention, and behavior. In mice, running and whisking desynchronize the cortex and enhance sensory responses, but the quiescent periods between bouts of exploratory behaviors have not been well studied. We found that these periods of "quiet wakefulness" were characterized by state fluctuations on a timescale of 1-2 s. Small fluctuations in pupil diameter tracked these state transitions in multiple cortical areas. During dilation, the intracellular membrane potential was desynchronized, sensory responses were enhanced, and population activity was less correlated. In contrast, constriction was characterized by increased low-frequency oscillations and higher ensemble correlations. Specific subtypes of cortical interneurons were differentially activated during dilation and constriction, consistent with their participation in the observed state changes. Pupillometry has been used to index attention and mental effort in humans, but the intracellular dynamics and differences in population activity underlying this phenomenon were previously unknown.
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Affiliation(s)
- Jacob Reimer
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA.
| | | | - Cathryn R Cadwell
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dimitri Yatsenko
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - George H Denfield
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Computational and Applied Mathematics, Rice University, Houston, TX 77005, USA.
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