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Pérez RF, Tezanos P, Peñarroya A, González-Ramón A, Urdinguio RG, Gancedo-Verdejo J, Tejedor JR, Santamarina-Ojeda P, Alba-Linares JJ, Sainz-Ledo L, Roberti A, López V, Mangas C, Moro M, Cintado Reyes E, Muela Martínez P, Rodríguez-Santamaría M, Ortea I, Iglesias-Rey R, Castilla-Silgado J, Tomás-Zapico C, Iglesias-Gutiérrez E, Fernández-García B, Sanchez-Mut JV, Trejo JL, Fernández AF, Fraga MF. A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment. Nat Commun 2024; 15:5829. [PMID: 39013876 PMCID: PMC11252340 DOI: 10.1038/s41467-024-49608-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Abstract
Aging involves the deterioration of organismal function, leading to the emergence of multiple pathologies. Environmental stimuli, including lifestyle, can influence the trajectory of this process and may be used as tools in the pursuit of healthy aging. To evaluate the role of epigenetic mechanisms in this context, we have generated bulk tissue and single cell multi-omic maps of the male mouse dorsal hippocampus in young and old animals exposed to environmental stimulation in the form of enriched environments. We present a molecular atlas of the aging process, highlighting two distinct axes, related to inflammation and to the dysregulation of mRNA metabolism, at the functional RNA and protein level. Additionally, we report the alteration of heterochromatin domains, including the loss of bivalent chromatin and the uncovering of a heterochromatin-switch phenomenon whereby constitutive heterochromatin loss is partially mitigated through gains in facultative heterochromatin. Notably, we observed the multi-omic reversal of a great number of aging-associated alterations in the context of environmental enrichment, which was particularly linked to glial and oligodendrocyte pathways. In conclusion, our work describes the epigenomic landscape of environmental stimulation in the context of aging and reveals how lifestyle intervention can lead to the multi-layered reversal of aging-associated decline.
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Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Patricia Tezanos
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Alfonso Peñarroya
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Alejandro González-Ramón
- Laboratory of Functional Epi-Genomics of Aging and Alzheimer's disease, Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Alicante, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Javier Gancedo-Verdejo
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Lidia Sainz-Ledo
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Annalisa Roberti
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - Virginia López
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Cristina Mangas
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
| | - María Moro
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
| | - Elisa Cintado Reyes
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Pablo Muela Martínez
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
- Programa de Doctorado en Neurociencia, Universidad Autónoma de Madrid-Instituto Cajal, 28002, Madrid, Spain
| | - Mar Rodríguez-Santamaría
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain
- Bioterio y unidad de imagen preclínica, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Ignacio Ortea
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Proteomics Unit, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), 33011, Oviedo, Spain
| | - Ramón Iglesias-Rey
- Neuroimaging and Biotechnology Laboratory (NOBEL), Clinical Neurosciences Research Laboratory (LINC), Health Research Institute of Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
| | - Juan Castilla-Silgado
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Cristina Tomás-Zapico
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Eduardo Iglesias-Gutiérrez
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Benjamín Fernández-García
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain
- Departamento de Biología Funcional, Área de Fisiología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Jose Vicente Sanchez-Mut
- Laboratory of Functional Epi-Genomics of Aging and Alzheimer's disease, Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas (UMH-CSIC), 03550, Alicante, Spain
| | - José Luis Trejo
- Departamento de Neurociencia Translacional, Instituto Cajal-Consejo Superior de Investigaciones Científicas (IC-CSIC), 28002, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
| | - Mario F Fraga
- Cancer Epigenetics and Nanomedicine Laboratory, Centro de Investigación en Nanomateriales y Nanotecnología-Consejo Superior de Investigaciones Científicas (CINN-CSIC), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA-FINBA), Universidad de Oviedo, 33011, Oviedo, Spain.
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, 33003, Oviedo, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.
- Departamento de Biología de Organismos y Sistemas, Área de Fisiología Vegetal, Universidad de Oviedo, 33006, Oviedo, Spain.
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2
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Bartelt LC, Fakhri M, Adamek G, Trybus M, Samelak-Czajka A, Jackowiak P, Fiszer A, Lowe CB, La Spada AR, Switonski PM. Antibody-assisted selective isolation of Purkinje cell nuclei from mouse cerebellar tissue. CELL REPORTS METHODS 2024; 4:100816. [PMID: 38981474 PMCID: PMC11294835 DOI: 10.1016/j.crmeth.2024.100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/08/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
We developed a method that utilizes fluorescent labeling of nuclear envelopes alongside cytometry sorting for the selective isolation of Purkinje cell (PC) nuclei. Beginning with SUN1 reporter mice, we GFP-tagged envelopes to confirm that PC nuclei could be accurately separated from other cell types. We then developed an antibody-based protocol to make PC nuclear isolation more robust and adaptable to cerebellar tissues of any genotypic background. Immunofluorescent labeling of the nuclear membrane protein RanBP2 enabled the isolation of PC nuclei from C57BL/6 cerebellum. By analyzing the expression of PC markers, nuclear size, and nucleoli number, we confirmed that our method delivers a pure fraction of PC nuclei. To demonstrate its applicability, we isolated PC nuclei from spinocerebellar ataxia type 7 (SCA7) mice and identified transcriptional changes in known and new disease-associated genes. Access to pure PC nuclei offers insights into PC biology and pathology, including the nature of selective neuronal vulnerability.
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Affiliation(s)
- Luke C Bartelt
- University Program in Genetics & Genomics, Duke University Medical Center, Durham, NC 27710, USA; Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mouad Fakhri
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Grazyna Adamek
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Trybus
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Samelak-Czajka
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Albert R La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
| | - Pawel M Switonski
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
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3
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Emery B, Wood TL. Regulators of Oligodendrocyte Differentiation. Cold Spring Harb Perspect Biol 2024; 16:a041358. [PMID: 38503504 PMCID: PMC11146316 DOI: 10.1101/cshperspect.a041358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Myelination has evolved as a mechanism to ensure fast and efficient propagation of nerve impulses along axons. Within the central nervous system (CNS), myelination is carried out by highly specialized glial cells, oligodendrocytes. The formation of myelin is a prolonged aspect of CNS development that occurs well into adulthood in humans, continuing throughout life in response to injury or as a component of neuroplasticity. The timing of myelination is tightly tied to the generation of oligodendrocytes through the differentiation of their committed progenitors, oligodendrocyte precursor cells (OPCs), which reside throughout the developing and adult CNS. In this article, we summarize our current understanding of some of the signals and pathways that regulate the differentiation of OPCs, and thus the myelination of CNS axons.
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Affiliation(s)
- Ben Emery
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Teresa L Wood
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
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4
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Moreno CS, Winham CL, Alemozaffar M, Klein ER, Lawal IO, Abiodun-Ojo OA, Patil D, Barwick BG, Huang Y, Schuster DM, Sanda MG, Osunkoya AO. Integrated Genomic Analysis of Primary Prostate Tumor Foci and Corresponding Lymph Node Metastases Identifies Mutations and Pathways Associated with Metastasis. Cancers (Basel) 2023; 15:5671. [PMID: 38067373 PMCID: PMC10705102 DOI: 10.3390/cancers15235671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 02/12/2024] Open
Abstract
Prostate cancer is a highly heterogeneous disease and mortality is mainly due to metastases but the initial steps of metastasis have not been well characterized. We have performed integrative whole exome sequencing and transcriptome analysis of primary prostate tumor foci and corresponding lymph node metastases (LNM) from 43 patients enrolled in clinical trial. We present evidence that, while there are some cases of clonally independent primary tumor foci, 87% of primary tumor foci and metastases are descended from a common ancestor. We demonstrate that genes related to oxidative phosphorylation are upregulated in LNM and in African-American patients relative to White patients. We further show that mutations in TP53, FLT4, EYA1, NCOR2, CSMD3, and PCDH15 are enriched in prostate cancer metastases. These findings were validated in a meta-analysis of 3929 primary tumors and 2721 metastases and reveal a pattern of molecular alterations underlying the pathology of metastatic prostate cancer. We show that LNM contain multiple subclones that are already present in primary tumor foci. We observed enrichment of mutations in several genes including understudied genes such as EYA1, CSMD3, FLT4, NCOR2, and PCDH15 and found that mutations in EYA1 and CSMD3 are associated with a poor outcome in prostate cancer.
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Affiliation(s)
- Carlos S. Moreno
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA; (C.L.W.); (A.O.O.)
- Department of Biomedical Informatics, Emory University, Atlanta, GA 30322, USA
| | - Cynthia L. Winham
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA; (C.L.W.); (A.O.O.)
| | - Mehrdad Alemozaffar
- Department of Urology, Emory University, Atlanta, GA 30322, USA (D.P.); (M.G.S.)
| | - Emma R. Klein
- Emory College of Arts and Sciences, Atlanta, GA 30322, USA
| | - Ismaheel O. Lawal
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA 30322, USA (O.A.A.-O.); (D.M.S.)
| | - Olayinka A. Abiodun-Ojo
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA 30322, USA (O.A.A.-O.); (D.M.S.)
| | - Dattatraya Patil
- Department of Urology, Emory University, Atlanta, GA 30322, USA (D.P.); (M.G.S.)
| | - Benjamin G. Barwick
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Yijian Huang
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA;
| | - David M. Schuster
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA 30322, USA (O.A.A.-O.); (D.M.S.)
| | - Martin G. Sanda
- Department of Urology, Emory University, Atlanta, GA 30322, USA (D.P.); (M.G.S.)
| | - Adeboye O. Osunkoya
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA; (C.L.W.); (A.O.O.)
- Department of Urology, Emory University, Atlanta, GA 30322, USA (D.P.); (M.G.S.)
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5
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Rexach JE, Cheng Y, Chen L, Polioudakis D, Lin LC, Mitri V, Elkins A, Yin A, Calini D, Kawaguchi R, Ou J, Huang J, Williams C, Robinson J, Gaus SE, Spina S, Lee EB, Grinberg LT, Vinters H, Trojanowski JQ, Seeley WW, Malhotra D, Geschwind DH. Disease-specific selective vulnerability and neuroimmune pathways in dementia revealed by single cell genomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560245. [PMID: 37808727 PMCID: PMC10557766 DOI: 10.1101/2023.09.29.560245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The development of successful therapeutics for dementias requires an understanding of their shared and distinct molecular features in the human brain. We performed single-nuclear RNAseq and ATACseq in Alzheimer disease (AD), Frontotemporal degeneration (FTD), and Progressive Supranuclear Palsy (PSP), analyzing 40 participants, yielding over 1.4M cells from three brain regions ranging in vulnerability and pathological burden. We identify 35 shared disease-associated cell types and 14 that are disease-specific, replicating those previously identified in AD. Disease - specific cell states represent molecular features of disease-specific glial-immune mechanisms and neuronal vulnerability in each disorder, layer 4/5 intra-telencephalic neurons in AD, layer 2/3 intra-telencephalic neurons in FTD, and layer 5/6 near-projection neurons in PSP. We infer intrinsic disease-associated gene regulatory networks, which we empirically validate by chromatin footprinting. We find that causal genetic risk acts in specific neuronal and glial cells that differ across disorders, primarily non-neuronal cells in AD and specific neuronal subtypes in FTD and PSP. These data illustrate the heterogeneous spectrum of glial and neuronal composition and gene expression alterations in different dementias and identify new therapeutic targets by revealing shared and disease-specific cell states.
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6
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Ramos SI, Mussa ZM, Falk EN, Pai B, Giotti B, Allette K, Cai P, Dekio F, Sebra R, Beaumont KG, Tsankov AM, Tsankova NM. An atlas of late prenatal human neurodevelopment resolved by single-nucleus transcriptomics. Nat Commun 2022; 13:7671. [PMID: 36509746 PMCID: PMC9744747 DOI: 10.1038/s41467-022-34975-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/10/2022] [Indexed: 12/14/2022] Open
Abstract
Late prenatal development of the human neocortex encompasses a critical period of gliogenesis and cortical expansion. However, systematic single-cell analyses to resolve cellular diversity and gliogenic lineages of the third trimester are lacking. Here, we present a comprehensive single-nucleus RNA sequencing atlas of over 200,000 nuclei derived from the proliferative germinal matrix and laminating cortical plate of 15 prenatal, non-pathological postmortem samples from 17 to 41 gestational weeks, and 3 adult controls. This dataset captures prenatal gliogenesis with high temporal resolution and is provided as a resource for further interrogation. Our computational analysis resolves greater complexity of glial progenitors, including transient glial intermediate progenitor cell (gIPC) and nascent astrocyte populations in the third trimester of human gestation. We use lineage trajectory and RNA velocity inference to further characterize specific gIPC subpopulations preceding both oligodendrocyte (gIPC-O) and astrocyte (gIPC-A) lineage differentiation. We infer unique transcriptional drivers and biological pathways associated with each developmental state, validate gIPC-A and gIPC-O presence within the human germinal matrix and cortical plate in situ, and demonstrate gIPC states being recapitulated across adult and pediatric glioblastoma tumors.
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Affiliation(s)
- Susana I Ramos
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zarmeen M Mussa
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elisa N Falk
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Balagopal Pai
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Peiwen Cai
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Fumiko Dekio
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kristin G Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nadejda M Tsankova
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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7
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Gaspar LM, Gonçalves CI, Fonseca F, Carvalho D, Cortez L, Palha A, Barros IF, Nobre E, Duarte JS, Amaral C, Bugalho MJ, Marques O, Pereira BD, Lemos MC. A Common Variant in the CDK8 Gene Is Associated with Sporadic Pituitary Adenomas in the Portuguese Population: A Case-Control Study. Int J Mol Sci 2022; 23:ijms231911749. [PMID: 36233050 PMCID: PMC9570112 DOI: 10.3390/ijms231911749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/21/2022] [Accepted: 10/01/2022] [Indexed: 11/16/2022] Open
Abstract
The majority of pituitary adenomas occur in a sporadic context, and in the absence of known genetic predisposition. Three common variants at the NEBL (rs2359536), PCDH15 (rs10763170) and CDK8 (rs17083838) loci were previously associated with sporadic pituitary adenomas in the Han Chinese population, but these findings have not yet been replicated in any other population. The aim of this case-control study was to assess if these variants are associated with susceptibility to sporadic pituitary adenomas in the Portuguese population. Genotype and allele frequencies were determined in 570 cases and in 546 controls. The CDK8 rs17083838 minor allele (A allele) was significantly associated with sporadic pituitary adenomas, under an additive (odds ratio (OR) 1.73, 95% confidence interval (CI) 1.19–2.50, p = 0.004) and dominant (OR 1.82, 95% CI 1.24–2.68, p = 0.002) inheritance model. The NEBL rs2359536 and PCDH15 rs10763170 variants were not associated with the overall risk for the disease, although a borderline significant association was observed between the PCDH15 rs10763170 minor allele (T allele) and somatotrophinomas (dominant model, OR 1.55, 95% CI 1.02–2.35, p = 0.035). These findings suggest that the CDK8 rs17083838 variant, and possibly the PCDH15 rs10763170 variant, may increase susceptibility to sporadic pituitary adenomas in the Portuguese population.
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Affiliation(s)
- Leonor M. Gaspar
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Catarina I. Gonçalves
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Fernando Fonseca
- Serviço de Endocrinologia, Hospital de Curry Cabral, Centro Hospitalar Universitário Lisboa Central, 1050-099 Lisboa, Portugal
| | - Davide Carvalho
- Serviço de Endocrinologia, Diabetes e Metabolismo, Centro Hospitalar de São João, Faculdade de Medicina e Instituto de Investigação e Inovação em Saúde da Universidade do Porto, 4200-319 Porto, Portugal
| | - Luísa Cortez
- Serviço de Endocrinologia, Hospital de Curry Cabral, Centro Hospitalar Universitário Lisboa Central, 1050-099 Lisboa, Portugal
| | - Ana Palha
- Serviço de Endocrinologia, Hospital de Curry Cabral, Centro Hospitalar Universitário Lisboa Central, 1050-099 Lisboa, Portugal
| | - Inês F. Barros
- Serviço de Endocrinologia, Hospital de Braga, 4710-243 Braga, Portugal
| | - Ema Nobre
- Serviço de Endocrinologia, Diabetes e Metabolismo, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-028 Lisboa, Portugal
| | - João S. Duarte
- Serviço de Endocrinologia, Hospital de Egas Moniz, Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal
| | - Cláudia Amaral
- Serviço de Endocrinologia, Hospital de Santo António, Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal
| | - Maria J. Bugalho
- Serviço de Endocrinologia, Diabetes e Metabolismo, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-028 Lisboa, Portugal
| | - Olinda Marques
- Serviço de Endocrinologia, Hospital de Braga, 4710-243 Braga, Portugal
| | - Bernardo D. Pereira
- Serviço de Endocrinologia e Nutrição, Hospital do Divino Espírito Santo de Ponta Delgada, 9500-782 Ponta Delgada, Portugal
| | - Manuel C. Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal
- Correspondence:
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