A cellular and spatial map of the choroid plexus across brain ventricles and ages

Neil Dani, Rebecca H. Herbst, Cristin McCabe, Gilad S. Green, Karol Kaiser, Joshua P. Head, Jin Cui, Frederick B. Shipley, Ahram Jang, Danielle Dionne, Lan Nguyen, Christopher Rodman, Samantha J. Riesenfeld, Jan Prochazka, Michaela Prochazkova, Radislav Sedlacek, Feng Zhang, Vitezslav Bryja, Orit Rozenblatt-Rosen, Naomi Habib*Aviv Regev*, Maria K. Lehtinen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

99 Scopus citations

Abstract

The choroid plexus (ChP) in each brain ventricle produces cerebrospinal fluid (CSF) and forms the blood-CSF barrier. Here, we construct a single-cell and spatial atlas of each ChP in the developing, adult, and aged mouse brain. We delineate diverse cell types, subtypes, cell states, and expression programs in epithelial and mesenchymal cells across ages and ventricles. In the developing ChP, we predict a common progenitor pool for epithelial and neuronal cells, validated by lineage tracing. Epithelial and fibroblast cells show regionalized expression by ventricle, starting at embryonic stages and persisting with age, with a dramatic transcriptional shift with maturation, and a smaller shift in each aged cell type. With aging, epithelial cells upregulate host-defense programs, and resident macrophages upregulate interleukin-1β (IL-1β) signaling genes. Our atlas reveals cellular diversity, architecture and signaling across ventricles during development, maturation, and aging of the ChP-brain barrier.

Original languageAmerican English
Pages (from-to)3056-3074.e21
JournalCell
Volume184
Issue number11
DOIs
StatePublished - 27 May 2021

Bibliographical note

Funding Information:
We thank members of the Lehtinen, Regev, Andermann, Fleming, Hla, and Stevens labs and L. Tsai for reagents and helpful discussions; C. Smillie, M. Shannon, H. Zucker, X. Adiconis, M. Kumar, M. Ericsson and the HMS EM Facility, W. Fowle and the Northeastern EM Facility, and the Flow Cytometry facility at the Broad Institute for assistance and advice; and A. Hupalowska and L. Gaffney for illustrations. This work was supported by a Glenn/AFAR postdoctoral fellowship and a Reagan Sloane Shanley research internship (N.D.), a William Randolph Hearst fellowship (N.D. and J.C.), NIH grant T32 HL110852 (J.C.), and NSF graduate research fellowship (F.B.S.). The Czech Science Foundation (grant GX19-28347X to V.B.). The core facility CELLIM is supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), RVO 68378050 from the Czech Academy of Sciences and the LM2018126l CZ.1.05/2.1.00/19.0395, CZ.02.1.01/0.0/0.0/16_013/0001789 grants by MEYS and ERDF, and OP RDI to Czech Centre for Phenogenomics. N.H. was a Howard Hughes Medical Institute fellow of the Helen Hay Whitney Foundation. N.H. is supported by the Israel Science Foundation (ISF) (research grant 1709/19), the Myers Foundation, and Goren-Khazzam. M.K.L. is supported by a Boston Children's Hospital-Broad Institute collaboration grant, the Pediatric Hydrocephalus Foundation, and NIH grant R01 NS088566. This work was also supported by the New York Stem Cell Foundation (M.K.L. and F.Z.), BCH IDDRC grant 1U54HD090255, and the Klarman Cell Observatory. F.Z. and A.R. are investigators of the Howard Hughes Medical Institute. F.Z. and M.K.L. are New York Stem Cell Foundation–Robertson investigators. N.D. R.H.H. N.H. A.R. and M.K.L. designed the study; N.D. J.P.H. and A.J. performed tissue dissections; N.D. and J.P.H. developed whole-tissue explant smFISH and imaging protocols; N.D. D.D. C.M. L.N. and C.R. prepared libraries and performed sequencing with guidance from O.R.-R.; R.H.H. N.H. and G.S.G. performed all computational analysis of scRNA-seq and snRNA-seq data in the lab of A.R. F.Z. and N.H. with help from S.J.R.; J.C. performed electron microscopy studies; K.K. performed confetti and contributed to RNAscope; J.P. M.P. and R.S. generated confetti mice and performed genotyping; N.D. and F.B.S. performed data analysis; and V.B. participated in manuscript discussion and experiment planning. N.D. R.H.H. N.H. A.R. and M.K.L. wrote the manuscript, and all co-authors edited it. A.R. is a co-founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas, and was an SAB member of ThermoFisher Scientific, Syros Pharmaceuticals, Neogene Therapeutics, and Asimov until July 31, 2020. A.R. has been an employee of Genentech since August 1, 2020. O.R.-R. is an employee of Genentech and co-inventor on patent applications filed by the Broad related to single cell genomics. R.H.H. has been an employee of Immunai since August 16, 2020. A.R. R.H.H. N.H. M.K.L. N.D. and A.J. are co-inventors on a provisional patent application filed by the Broad Institute relating to this manuscript.

Funding Information:
We thank members of the Lehtinen, Regev, Andermann, Fleming, Hla, and Stevens labs and L. Tsai for reagents and helpful discussions; C. Smillie, M. Shannon, H. Zucker, X. Adiconis, M. Kumar, M. Ericsson and the HMS EM Facility, W. Fowle and the Northeastern EM Facility, and the Flow Cytometry facility at the Broad Institute for assistance and advice; and A. Hupalowska and L. Gaffney for illustrations. This work was supported by a Glenn/AFAR postdoctoral fellowship and a Reagan Sloane Shanley research internship (N.D.), a William Randolph Hearst fellowship (N.D. and J.C.), NIH grant T32 HL110852 (J.C.), and NSF graduate research fellowship (F.B.S.). The Czech Science Foundation (grant GX19-28347X to V.B.). The core facility CELLIM is supported by the Czech-BioImaging large RI project ( LM2018129 funded by MEYS CR ), RVO 68378050 from the Czech Academy of Sciences and the LM2018126l CZ.1.05/2.1.00/19.0395, CZ.02.1.01/0.0/0.0/16_013/0001789 grants by MEYS and ERDF, and OP RDI to Czech Centre for Phenogenomics. N.H. was a Howard Hughes Medical Institute fellow of the Helen Hay Whitney Foundation. N.H. is supported by the Israel Science Foundation (ISF) (research grant 1709/19 ), the Myers Foundation , and Goren-Khazzam . M.K.L. is supported by a Boston Children’s Hospital-Broad Institute collaboration grant, the Pediatric Hydrocephalus Foundation , and NIH grant R01 NS088566 . This work was also supported by the New York Stem Cell Foundation (M.K.L. and F.Z.), BCH IDDRC grant 1U54HD090255 , and the Klarman Cell Observatory . F.Z. and A.R. are investigators of the Howard Hughes Medical Institute . F.Z. and M.K.L. are New York Stem Cell Foundation –Robertson investigators.

Publisher Copyright:
© 2021 Elsevier Inc.

Keywords

  • aging
  • brain barrier
  • cerebrospinal fluid
  • choroid plexus
  • development
  • single-cell RNA sequencing
  • single-nucleus RNA sequencing

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