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She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA. Comparative landscape of genetic dependencies in human and chimpanzee stem cells. Cell 2023; 186:2977-2994.e23. [PMID: 37343560 PMCID: PMC10461406 DOI: 10.1016/j.cell.2023.05.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 08/31/2022] [Revised: 03/14/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether human cells exhibit distinct genetic dependencies. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell-cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells and cerebral organoids, supporting the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells reshaped the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.
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Affiliation(s)
- Richard She
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan K Schaefer
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben A Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
| | - Bryan J Pavlovic
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute Technology, Cambridge, MA 02142, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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Wu J, Yonezawa T, Kishino H. Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection. Genes (Basel) 2022; 13:genes13040708. [PMID: 35456514 PMCID: PMC9031814 DOI: 10.3390/genes13040708] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 12/04/2022] Open
Abstract
It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Moreover, we developed a method to detect fluctuations of species-specific selection on genes based on the deviations of intraspecific genetic diversity predicted from long-term rates. We showed that the evolution of epithelial cells, rather than connective tissue, mainly contributed to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps caused by infectious diseases are the most representative examples of adaptive evolution.
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Affiliation(s)
- Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara 259-1193, Japan
- Correspondence: (J.W.); (H.K.)
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi 243-0034, Japan;
| | - Hirohisa Kishino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo Ward, Tokyo 113-8657, Japan
- The Research Institute of Evolutionary Biology, Tokyo 138-0098, Japan
- AI/Data Science Social Implementation Laboratory, Chuo University, Tokyo 112-8551, Japan
- Correspondence: (J.W.); (H.K.)
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Pollen AA, Bhaduri A, Andrews MG, Nowakowski TJ, Meyerson OS, Mostajo-Radji MA, Di Lullo E, Alvarado B, Bedolli M, Dougherty ML, Fiddes IT, Kronenberg ZN, Shuga J, Leyrat AA, West JA, Bershteyn M, Lowe CB, Pavlovic BJ, Salama SR, Haussler D, Eichler EE, Kriegstein AR. Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution. Cell 2019; 176:743-756.e17. [PMID: 30735633 PMCID: PMC6544371 DOI: 10.1016/j.cell.2019.01.017] [Citation(s) in RCA: 322] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/22/2018] [Accepted: 01/04/2019] [Indexed: 12/22/2022]
Abstract
Direct comparisons of human and non-human primate brains can reveal molecular pathways underlying remarkable specializations of the human brain. However, chimpanzee tissue is inaccessible during neocortical neurogenesis when differences in brain size first appear. To identify human-specific features of cortical development, we leveraged recent innovations that permit generating pluripotent stem cell-derived cerebral organoids from chimpanzee. Despite metabolic differences, organoid models preserve gene regulatory networks related to primary cell types and developmental processes. We further identified 261 differentially expressed genes in human compared to both chimpanzee organoids and macaque cortex, enriched for recent gene duplications, and including multiple regulators of PI3K-AKT-mTOR signaling. We observed increased activation of this pathway in human radial glia, dependent on two receptors upregulated specifically in human: INSR and ITGB8. Our findings establish a platform for systematic analysis of molecular changes contributing to human brain development and evolution.
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Affiliation(s)
- Alex A Pollen
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Madeline G Andrews
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Anatomy, UCSF, San Francisco, CA, USA
| | - Olivia S Meyerson
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Mohammed A Mostajo-Radji
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Elizabeth Di Lullo
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Beatriz Alvarado
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Melanie Bedolli
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ian T Fiddes
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Joe Shuga
- New Technologies, Fluidigm, South San Francisco, CA, USA
| | - Anne A Leyrat
- New Technologies, Fluidigm, South San Francisco, CA, USA
| | - Jay A West
- New Technologies, Fluidigm, South San Francisco, CA, USA
| | - Marina Bershteyn
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Craig B Lowe
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Bryan J Pavlovic
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA
| | - Sofie R Salama
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, USA.
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