Abstract
Despite a prominent risk factor for Neurodevelopmental disorders (NDD), it remains unclear how Autism Susceptibility Candidate 2 (AUTS2) controls the neurodevelopmental program. Our studies investigated the role of AUTS2 in neuronal differentiation and discovered that AUTS2, together with WDR68 and SKI, forms a novel protein complex (AWS) specifically in neuronal progenitors and promotes neuronal differentiation through inhibiting BMP signaling. Genomic and biochemical analyses demonstrated that the AWS complex achieves this effect by recruiting the CUL4 E3 ubiquitin ligase complex to mediate poly-ubiquitination and subsequent proteasomal degradation of phosphorylated SMAD1/5/9. Furthermore, using primary cortical neurons, we observed aberrant BMP signaling and dysregulated expression of neuronal genes upon manipulating the AWS complex, indicating that the AWS-CUL4-BMP axis plays a role in regulating neuronal lineage specification in vivo. Thus, our findings uncover a sophisticated cellular signaling network mobilized by a prominent NDD risk factor, presenting multiple potential therapeutic targets for NDD.
Graphical Abstract
Similar content being viewed by others
Data Availability
To review GEO accession GSE178746, use the following link and enter token (evezqiqwhbqldol), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178746.
References
Abbas, T., Sivaprasad, U., Terai, K., Amador, V., Pagano, M., & Dutta, A. (2008). PCNA-dependent regulation of p21 ubiquitylation and degradation via the CRL4Cdt2 ubiquitin ligase complex. Genes & Development, 22, 2496–2506.
Bedogni, F., Hodge, R. D., Nelson, B. R., Frederick, E. A., Shiba, N., Daza, R. A., & Hevner, R. F. (2010). Autism susceptibility candidate 2 (Auts2) encodes a nuclear protein expressed in developing brain regions implicated in autism neuropathology. Gene Expression Patterns, 10, 9–15.
Berk, M., Desai, S. Y., Heyman, H. C., & Colmenares, C. (1997). Mice lacking the ski proto-oncogene have defects in neurulation, craniofacial patterning, and skeletal muscle development. Genes & Development, 11, 2029–2039.
Beunders, G., Voorhoeve, E., Golzio, C., Pardo, L. M., Rosenfeld, J. A., Talkowski, M. E., Simonic, I., Lionel, A. C., Vergult, S., Pyatt, R. E., et al. (2013). Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus. American Journal of Human Genetics, 92, 210–220.
Beunders, G., van de Kamp, J., Vasudevan, P., Morton, J., Smets, K., Kleefstra, T., de Munnik, S. A., Schuurs-Hoeijmakers, J., Ceulemans, B., Zollino, M., et al. (2016). A detailed clinical analysis of 13 patients with AUTS2 syndrome further delineates the phenotypic spectrum and underscores the behavioural phenotype. Journal of Medical Genetics, 53, 523–532.
Bibel, M., Richter, J., Schrenk, K., Tucker, K. L., Staiger, V., Korte, M., Goetz, M., & Barde, Y. A. (2004). Differentiation of mouse embryonic stem cells into a defined neuronal lineage. Nature Neuroscience, 7, 1003–1009.
Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology, 34, 525–527.
Chambers, S. M., Fasano, C. A., Papapetrou, E. P., Tomishima, M., Sadelain, M., & Studer, L. (2009). Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nature Biotechnology, 27, 275–280.
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science (80-. )., 339, 819–823.
Cox, J., & Mann, M. (2008). MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology, 26, 1367–1372.
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003). DAVID: Database for annotation, visualization, and integrated discovery. Genome Biology, 4, 1–11.
Gao, Z., Zhang, J., Bonasio, R., Strino, F., Sawai, A., Parisi, F., Kluger, Y., & Reinberg, D. (2012). PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Molecular Cell, 45, 344–356.
Gao, Z., Lee, P., Stafford, J. M., Schimmelmann, M. V., Schaefer, A., & Reinberg, D. (2014). An AUTS2-Polycomb complex activates gene expression in the CNS. Nature, 516, 349–354.
Graf, D., Malik, Z., Hayano, S., & Mishina, Y. (2016). Common mechanisms in development and disease: BMP signaling in craniofacial development. Cytokine & Growth Factor Reviews, 27, 129–139.
Higa, L. A., Wu, M., Ye, T., Kobayashi, R., Sun, H., & Zhang, H. (2006). CUL4-DDB1 ubiquitin ligase interacts with multiple WD40-repeat proteins and regulates histone methylation. Nature Cell Biology, 8, 1277–1283.
Hori, K., Nagai, T., Shan, W., Sakamoto, A., Taya, S., Hashimoto, R., Hayashi, T., Abe, M., Yamazaki, M., Nakao, K., et al. (2014). Cytoskeletal regulation by AUTS2 in neuronal migration and neuritogenesis. Cell Reports, 9, 2166–2179.
Hori, K., Nagai, T., Shan, W., Sakamoto, A., Abe, M., Yamazaki, M., Sakimura, K., Yamada, K., & Hoshino, M. (2015). Heterozygous disruption of autism susceptibility candidate 2 causes impaired emotional control and cognitive memory. PLoS ONE, 10, e0145979.
Jin, J., Arias, E. E., Chen, J., Harper, J. W., & Walter, J. C. (2006). A family of diverse Cul4-Ddb1-interacting proteins includes Cdt2, which Is required for S phase destruction of the replication factor Cdt1. Molecular Cell, 23, 709–721.
Li, D., & Roberts, R. (2001). WD-repeat proteins: Structure characteristics, biological function, and their involvement in human diseases. Cellular and Molecular Life Sciences, 58, 2085–2097.
Li, Z., & Chen, Y. G. (2013). Functions of BMP signaling in embryonic stem cell fate determination. Experimental Cell Research, 319, 113–119.
Liu, S., Aldinger, K. A., Cheng, C. V., Kiyama, T., Dave, M., McNamara, H. K., Zhao, W., Stafford, J. M., Descostes, N., Lee, P., et al. (2021). NRF1 association with AUTS2-Polycomb mediates specific gene activation in the brain. Molecular Cell, 81, 4663–4676.e8.
Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 1–21.
Luo, K., Stroschein, S. L., Wang, W., Chen, D., Martens, E., Zhou, S., & Zhou, Q. (1999). The Ski oncoprotein interacts with the Smad proteins to repress TGF̄ signaling. Genes & Development, 13, 2196–2206.
Massagué, J. (2012). TGFβ signalling in context. Nature Reviews Molecular Cell Biology, 13, 616–630.
Miyata, Y., Shibata, T., Aoshima, M., Tsubata, T., & Nishida, E. (2014). The molecular chaperone TRiC/CCT binds to the Trp-Asp 40 (WD40) repeat protein WDR68 and promotes its folding, protein kinase DYRK1A binding, and nuclear accumulation. Journal of Biological Chemistry, 289, 33320–33332.
Monderer-Rothkoff, G., Tal, N., Risman, M., Shani, O., Nissim-Rafinia, M., Malki-Feldman, L., Medvedeva, V., Groszer, M., Meshorer, E., & Shifman, S. (2021). AUTS2 isoforms control neuronal differentiation. Molecular Psychiatry, 26, 666–681.
Morikawa, M., Koinuma, D., Tsutsumi, S., Vasilaki, E., Kanki, Y., Heldin, C. H., Aburatani, H., & Miyazono, K. (2011). ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif. Nucleic Acids Research, 39, 8712–8727.
Oksenberg, N., & Ahituv, N. (2013). The role of AUTS2 in neurodevelopment and human evolution. Trends in Genetics, 29, 600–608.
Oksenberg, N., Stevison, L., Wall, J. D., & Ahituv, N. (2013). Function and Regulation of AUTS2, a gene implicated in autism and human evolution. PLoS Genetics, 9, e1003221.
Russo, D., Della Ragione, F., Rizzo, R., Sugiyama, E., Scalabrì, F., Hori, K., Capasso, S., Sticco, L., Fioriniello, S., De Gregorio, R., et al. (2018). Glycosphingolipid metabolic reprogramming drives neural differentiation. The EMBO Journal, 37, e97674.
Stirnimann, C., Petsalaki, E., Russell, R., & Muller, C. (2010). WD40 protiens propel cellular networks. Trends in Biochemical Sciences, 35, 531–538.
Stroschein, S. L., Wang, W., Zhou, S., Zhou, Q., & Luo, K. (1999). Negative feedback regulation of TGF-β signaling by the SnoN oncoprotein. Science, 286, 771–774.
Sun, Y., Liu, X., Eaton, E. N., Lane, W. S., Lodish, H. F., & Weinberg, R. A. (1999). Interaction of the Ski oncoprotein with Smad3 regulates TGF-β signaling. Molecular Cell, 4, 499–509.
Talkowski, M. E., Rosenfeld, J. A., Blumenthal, I., Pillalamarri, V., Chiang, C., Heilbut, A., Ernst, C., Hanscom, C., Rossin, E., Lindgren, A. M., et al. (2012). Sequencing chromosomal abnormalities reveals neurodevelopmental Loci that confer risk across diagnostic boundaries. Cell, 149, 525–537.
Wang, Q., Geng, Z., Gong, Y., Warren, K., Zheng, H., Imamura, Y., & Gao, Z. (2018). WDR68 is essential for the transcriptional activation of the PRC1-AUTS2 complex and neuronal differentiation of mouse embryonic stem cells. Stem Cell Research, 33, 206–214.
Watabe, T., & Miyazono, K. (2009). Roles of TGF-β family signaling in stem cell renewal and differentiation. Cell Research, 19, 103–115.
Yao, M., Zhou, X., Zhou, J., Gong, S., Hu, G., Li, J., Huang, K., Lai, P., Shi, G., Hutchins, A. P., et al. (2018). PCGF5 is required for neural differentiation of embryonic stem cells. Nature Communications, 9, 1–12.
Acknowledgements
We would like to thank Dr. Kathleen Mulder for the discussion of the experiments. We thank Dr. Abraham Thomas and the Microscopy Imaging Core for assistance in imaging and Dr. Yuka Imamura and the Genome Sciences Facility for assistance in deep sequencing. The Auts2 mouse strain is a gift from Dr. Danny Reinberg. This work was supported by the following NIH grants: R35GM133496 to Z. Gao; R00AA024837 to J. Stafford; R35ES031707 to Y. Wang. Z. Geng, Q.W., W.M., T.W., J.C., and E.G. conducted the experiments; R.H. and D.D. provided guidance and help on the immunofluorescence analysis; Z. Gao, J.S., and Y.W. designed the experiments; Z.Geng and Z.Gao wrote the paper. All authors contributed to the discussion of the manuscript.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Geng, Z., Wang, Q., Miao, W. et al. AUTS2 Controls Neuronal Lineage Choice Through a Novel PRC1-Independent Complex and BMP Inhibition. Stem Cell Rev and Rep 19, 531–549 (2023). https://doi.org/10.1007/s12015-022-10459-0
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12015-022-10459-0