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Chung C, Yang X, Hevner RF, Kennedy K, Vong KI, Liu Y, Patel A, Nedunuri R, Barton ST, Noel G, Barrows C, Stanley V, Mittal S, Breuss MW, Schlachetzki JCM, Kingsmore SF, Gleeson JG. Cell-type-resolved mosaicism reveals clonal dynamics of the human forebrain. Nature 2024; 629:384-392. [PMID: 38600385 PMCID: PMC11194162 DOI: 10.1038/s41586-024-07292-5] [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: 10/22/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Debate remains around the anatomical origins of specific brain cell subtypes and lineage relationships within the human forebrain1-7. Thus, direct observation in the mature human brain is critical for a complete understanding of its structural organization and cellular origins. Here we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific mosaic variant barcode analysis. From four hemispheres and two different human neurotypical donors, we identified 287 and 780 mosaic variants, respectively, that were used to deconvolve clonal dynamics. Clonal spread and allele fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted than resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome transcriptome analysis at both a cell-type-specific and a single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1+ inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of mosaic variants across 17 locations within one parietal lobe reveals that restriction of clonal spread in the anterior-posterior axis precedes restriction in the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus, cell-type-resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain.
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Affiliation(s)
- Changuk Chung
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Robert F Hevner
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pathology, UC San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Keng Ioi Vong
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Yang Liu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Rahul Nedunuri
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Scott T Barton
- Division of Medical Education, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Geoffroy Noel
- Division of Anatomy, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Swapnil Mittal
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Johannes C M Schlachetzki
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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Chung C, Yang X, Hevner RF, Kennedy K, Vong KI, Liu Y, Patel A, Nedunuri R, Barton ST, Barrows C, Stanley V, Mittal S, Breuss MW, Schlachetzki JCM, Gleeson JG. Cell-type-resolved somatic mosaicism reveals clonal dynamics of the human forebrain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563814. [PMID: 37961480 PMCID: PMC10634852 DOI: 10.1101/2023.10.24.563814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Debate remains around anatomic origins of specific brain cell subtypes and lineage relationships within the human forebrain. Thus, direct observation in the mature human brain is critical for a complete understanding of the structural organization and cellular origins. Here, we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific Mosaic Variant Barcode Analysis. From four hemispheres from two different human neurotypical donors, we identified 287 and 780 mosaic variants (MVs), respectively that were used to deconvolve clonal dynamics. Clonal spread and allelic fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted compared with resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome-transcriptome analysis at both a cell-type-specific and single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1+ inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of MVs across 17 locations within one parietal lobe reveals restrictions of clonal spread in the anterior-posterior axis precedes that of the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus cell-type resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain.
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Affiliation(s)
- Changuk Chung
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Robert F. Hevner
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
- Department of Pathology, UC San Diego School of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
| | | | - Keng Ioi Vong
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Yang Liu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Rahul Nedunuri
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Scott T. Barton
- Division of Medical Education, School of Medicine, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Swapnil Mittal
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
| | - Martin W. Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Aurora, CO, 80045, USA
| | | | - Joseph G. Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, 92123, USA
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Sinha AA, Gleason DF, Wilson MJ, Wick MR, Reddy PK, Blackard CE. Relationship of prostatic acid phosphatase localization in human prostate by a monoclonal antibody with the Gleason grading system. Prostate 1988; 13:1-15. [PMID: 2458582 DOI: 10.1002/pros.2990130102] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Prostatic acid phosphatase (PAP) was localized in human prostate with a monoclonal antibody prepared against PAP isoenzyme II to determine patterns of its expression in normal, hyperplastic (BPH), and cancerous glands. The monoclonal antibody reacted with both isoenzymes II and IV in immunoblot studies. Formalin-fixed, paraffin-embedded tissue was used from patients who had not been treated with hormones or chemotherapy. In normal glands and BPH, there was marked variation in the intensity of PAP staining in morphologically otherwise similar epithelial cells. There was similar heterogeneity of staining in the adenocarcinomas. Rough quantification of the intensity patterns in the clinical groups indicated a slight shift to more intense staining in BPH and well-differentiated carcinomas but a progressive decline in the PAP staining in the moderately and poorly differentiated tumors. This decrease in intracellular staining with decreasing differentiation is not inconsistent with the clinical observation that serum levels of acid phosphatase generally increase with higher grade and disseminated tumors, since the enzyme is simply more accessible to the circulatory system in those cases. The same decrease may explain the few disseminated tumors that are not associated with elevated serum levels.
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Affiliation(s)
- A A Sinha
- Research Service, Veterans Administration Medical Center, Minneapolis, MN 55417
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Aumüller G, Vedder H, Enderle-Schmitt U, Seitz J. Cytochemistry and biochemistry of acid phosphatases VII: Immunohistochemistry of canine prostatic acid phosphatase. Prostate 1987; 11:1-15. [PMID: 3658824 DOI: 10.1002/pros.2990110102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Acid phosphatase (E.C. 3.1.3.2.) has been isolated from canine prostatic gland homogenates by gel permeation chromatography (AcA34 or G150), by affinity chromatography (con A-Sepharose), or by using fluid phase liquid chromatography (FPLC) using Superose 12 and Mono P columns. Acid phosphatase-enriched fractions were submitted to analytical SDS-PAGE or to analytical isoelectric focusing. A protein with a molecular weight of 30 kD (on SDS gels) was used for immunization of rabbits. The antiserum produced was cross-reactive with prostatic acid phosphatase (canine and human) as shown by immunoblotting. When applied to paraffin or plastic sections of normal canine prostate, a positive immunoreaction was found exclusively in the secretory cells. In experimentally altered glands (castration and/or hormone treatment), a varying pattern of immunoreactive cells was found. In canine prostatic carcinomas, intensively reacting cell clusters were found along with nonreactive cells. The antiserum was also slightly cross-reactive with the respective human antigen, but the cross-reactivity of an antiserum prepared against human prostatic secretory acid phosphatase with canine prostatic acid phosphatase was far more pronounced.
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Affiliation(s)
- G Aumüller
- Department of Anatomy and Cell Biology, Philipps-Universität, Marburg, Federal Republic of Germany
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Yeh LC, Lee AJ, Lee NE, Lam KW, Lee JC. Molecular cloning of cDNA for human prostatic acid phosphatase. Gene 1987; 60:191-6. [PMID: 2965059 DOI: 10.1016/0378-1119(87)90227-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A human liver cDNA library in lambda gt11 was screened with polyclonal antiserum to human acid phosphatase isoenzyme 2a/4. About eleven positive clones have been obtained. Two clones, lambda Hap21 and lambda Hap22 were further characterized: clone lambda Hap21 contained a 0.8-kb cDNA insert and clone lambda Hap22 a 1.8-2.0-kb insert. XbaI digestion of lambda Hap22 generated two fragments of 1.0 and 0.9 kb. BglII digestion resulted in a 1.2-kb fragment and several smaller fragments of undetermined size. Clone lambda Hap22 contained all the genes carried by lambda gt11(lac5cI857nin5Sam100) and the 2-kb insert. An Escherichia coli(lambda Hap22) lysogen was generated, and its acid phosphatase activity was approximately ten-fold higher than that in the control nonlysogenic lysate. Western-blot analysis of total proteins present in this E. coli(lambda Hap22) lysate revealed that the non-induced lambda Hap22 prophage directed the synthesis of an approx. 175-kDa protein. This protein was recognized by antibody to the human acid phosphatase isoenzyme 2a/4 and anti-beta-galactosidase and was produced only upon induction with IPTG. These results indicated that lambda Hap22 carried a major portion of the gene coding for the human acid phosphatase isoenzyme 2a and/or 4 and this protein fragment of acid phosphatase was sufficient to manifest enzymatic activity.
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Affiliation(s)
- L C Yeh
- Department of Biochemistry, University of Texas Health Science Center, San Antonio 78284-7760
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