An N-terminal and ankyrin repeat domain interactome of Shank3 identifies the protein complex with the splicing regulator Nono in mice.

SH3 and ankyrin‐repeat domain containing 3 (Shank3) alternative splicing autism spectrum disorder (ASD) interaction

Journal

Genes to cells : devoted to molecular & cellular mechanisms
ISSN: 1365-2443
Titre abrégé: Genes Cells
Pays: England
ID NLM: 9607379

Informations de publication

Date de publication:
04 Jul 2024
Historique:
revised: 17 06 2024
received: 05 04 2023
accepted: 20 06 2024
medline: 5 7 2024
pubmed: 5 7 2024
entrez: 4 7 2024
Statut: aheadofprint

Résumé

An autism-associated gene Shank3 encodes multiple splicing isoforms, Shank3a-f. We have recently reported that Shank3a/b-knockout mice were more susceptible to kainic acid-induced seizures than wild-type mice at 4 weeks of age. Little is known, however, about how the N-terminal and ankyrin repeat domains (NT-Ank) of Shank3a/b regulate multiple molecular signals in the developing brain. To explore the functional roles of Shank3a/b, we performed a mass spectrometry-based proteomic search for proteins interacting with GFP-tagged NT-Ank. In this study, NT-Ank was predicted to form a variety of complexes with a total of 348 proteins, in which RNA-binding (n = 102), spliceosome (n = 22), and ribosome-associated molecules (n = 9) were significantly enriched. Among them, an X-linked intellectual disability-associated protein, Nono, was identified as a NT-Ank-binding protein. Coimmunoprecipitation assays validated the interaction of Shank3 with Nono in the mouse brain. In agreement with these data, the thalamus of Shank3a/b-knockout mice aberrantly expressed splicing isoforms of autism-associated genes, Nrxn1 and Eif4G1, before and after seizures with kainic acid treatment. These data indicate that Shank3 interacts with multiple RNA-binding proteins in the postnatal brain, thereby regulating the homeostatic expression of splicing isoforms for autism-associated genes after birth.

Identifiants

pubmed: 38964745
doi: 10.1111/gtc.13142
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : Japan Society for the Promotion of Science
ID : JP21K07865
Organisme : Japan Society for the Promotion of Science
ID : JP23K07334
Organisme : Japan Agency for Medical Research and Development
ID : JP20ek0109411
Organisme : Japan Agency for Medical Research and Development
ID : JP20wm0325002h
Organisme : The Ministry of Health, Labour and Welfare of Japan
ID : JP20FC1054
Organisme : The Ministry of Health, Labour and Welfare of Japan
ID : JP21FC1005

Informations de copyright

© 2024 The Author(s). Genes to Cells published by Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Références

Akamine, S., Okuzono, S., Yamamoto, H., Setoyama, D., Sagata, N., Ohgidani, M., Kato, T. A., Ishitani, T., Kato, H., Masuda, K., Matsushita, Y., Ono, H., Ishizaki, Y., Sanefuji, M., Saitsu, H., Matsumoto, N., Kang, D., Kanba, S., Nakabeppu, Y., … Ohga, S. (2020). GNAO1 organizes the cytoskeletal remodeling and firing of developing neurons. The FASEB Journal, 34, 16601–16621.
Barbosa‐Morais, N. L., Irimia, M., Pan, Q., Xiong, H. Y., Gueroussov, S., Lee, L. J., Slobodeniuc, V., Kutter, C., Watt, S., Çolak, R., Kim, T. H., Misquitta‐Ali, C. M., Wilson, M. D., Kim, P. M., Odom, D. T., Frey, B. J., & Blencowe, B. J. (2012). The evolutionary landscape of alternative splicing in vertebrate species. Science, 338, 1587–1593.
Betancur, C., & Buxbaum, J. D. (2013). SHANK3 haploinsufficiency: A "common" but underdiagnosed highly penetrant monogenic cause of autism spectrum disorders. Molecular Autism, 4, 17.
Bidinosti, M., Botta, P., Kruttner, S., Proenca, C. C., Stoehr, N., Bernhard, M., Fruh, I., Mueller, M., Bonenfant, D., Voshol, H., Carbone, W., Neal, S. J., McTighe, S. M., Roma, G., Dolmetsch, R. E., Porter, J. A., Caroni, P., Bouwmeester, T., Luthi, A. & Galimberti, I. (2016). CLK2 inhibition ameliorates autistic features associated with SHANK3 deficiency. Science, 351, 1199–1203.
Bozdagi, O., Sakurai, T., Papapetrou, D., Wang, X., Dickstein, D. L., Takahashi, N., Kajiwara, Y., Yang, M., Katz, A. M., Scattoni, M. L., Harris, M. J., Saxena, R., Silverman, J. L., Crawley, J. N., Zhou, Q., Hof, P. R., & Buxbaum, J. D. (2010). Haploinsufficiency of the autism‐associated Shank3 gene leads to deficits in synaptic function, social interaction, and social communication. Molecular Autism, 1, 15.
Bucher, M., Niebling, S., Han, Y., Molodenskiy, D., Hassani Nia, F., Kreienkamp, H. J., Svergun, D., Kim, E., Kostyukova, A. S., Kreutz, M. R., & Mikhaylova, M. (2021). Autism‐associated SHANK3 missense point mutations impact conformational fluctuations and protein turnover at synapses. eLife, 10, e66165.
Cai, Q., Zeng, M., Wu, X., Wu, H., Zhan, Y., Tian, R., & Zhang, M. (2021). CaMKIIalpha‐driven, phosphatase‐checked postsynaptic plasticity via phase separation. Cell Research, 31, 37–51.
Chau, K. K., Zhang, P., Urresti, J., Amar, M., Pramod, A. B., Chen, J., Thomas, A., Corominas, R., Lin, G. N. & Iakoucheva, L. M. (2021). Full‐length isoform transcriptome of the developing human brain provides further insights into autism. Cell Reports, 36, 109631.
Denkena, J., Zaisser, A., Merz, B., Klinger, B., Kuhl, D., Bluthgen, N. & Hermey, G. (2020). Neuronal activity regulates alternative exon usage. Molecular Brain, 13, 148.
Durand, C. M., Perroy, J., Loll, F., Perrais, D., Fagni, L., Bourgeron, T., Montcouquiol, M., & Sans, N. (2012). SHANK3 Mutations identified in autism lead to modification of dendritic spine morphology via an Actin‐dependent mechanism. Molecular Psychiatry, 17, 71–84.
Engal, E., Baker, M., & Salton, M. (2022). The chromatin roots of abnormal splicing in autism. Trends in Genetics, 38, 892–894.
Engal, E., Zhang, Z., Geminder, O., Jaffe‐Herman, S., Kay, G., Ben‐Hur, A., & Salton, M. (2024). The spectrum of pre‐mRNA splicing in autism. Wiley Interdisciplinary Reviews RNA, 15, e1838.
Feng, P., Li, L., Deng, T., Liu, Y., Ling, N., Qiu, S., Zhang, L., Peng, B., Xiong, W., Cao, L., Zhang, L., & Ye, M. (2020). NONO and tumorigenesis: More than splicing. Journal of Cellular and Molecular Medicine, 24, 4368–4376.
Fisher, E., & Feng, J. (2022). RNA splicing regulators play critical roles in neurogenesis. Wiley Interdisciplinary Reviews RNA, 13, e1728.
Gauthier, J., Champagne, N., Lafreniere, R. G., Xiong, L., Spiegelman, D., Brustein, E., Lapointe, M., Peng, H., Cote, M., Noreau, A., Hamdan, F. F., Addington, A. M., Rapoport, J. L., Delisi, L. E., Krebs, M. O., Joober, R., Fathalli, F., Mouaffak, F., Haghighi, A. P., … Team, S. D. (2010). De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia. Proceedings of the National Academy of Sciences of the United States of America, 107, 7863–7868.
Gillentine, M. A., Wang, T., Hoekzema, K., Rosenfeld, J., Liu, P., Guo, H., Kim, C. N., de Vries, B. B. A., Vissers, L. E. L. M., Nordenskjold, M., Kvarnung, M., Lindstrand, A., Nordgren, A., Gecz, J., Iascone, M., Cereda, A., Scatigno, A., Maitz, S., Zanni, G., … Eichler, E. E. (2021). Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders. Genome Medicine, 13, 63.
Gonatopoulos‐Pournatzis, T., Niibori, R., Salter, E. W., Weatheritt, R. J., Tsang, B., Farhangmehr, S., Liang, X., Braunschweig, U., Roth, J., Zhang, S., Henderson, T., Sharma, E., Quesnel‐Vallières, M., Permanyer, J., Maier, S., Georgiou, J., Irimia, M., Sonenberg, N., Forman‐Kay, J. D., … Blencowe, B. J. (2020). Autism‐Misregulated eIF4G microexons control synaptic translation and higher order cognitive functions. Molecular Cell, 77, 1176–1192.e16.
Gotoh, K., Morisaki, T., Setoyama, D., Sasaki, K., Yagi, M., Igami, K., Mizuguchi, S., Uchiumi, T., Fukui, Y., & Kang, D. (2018). Mitochondrial p32/C1qbp is a critical regulator of dendritic cell metabolism and maturation. Cell Reports, 25, 1800–1815.e4.
Han, K., Holder, J. L., Jr., Schaaf, C. P., Lu, H., Chen, H., Kang, H., Tang, J., Wu, Z., Hao, S., Cheung, S. W., Yu, P., Sun, H., Breman, A. M., Patel, A., Lu, H. C. & Zoghbi, H. Y. (2013). SHANK3 overexpression causes manic‐like behaviour with unique pharmacogenetic properties. Nature, 503, 72–77.
Harris, K. P., Akbergenova, Y., Cho, R. W., Baas‐Thomas, M. S., & Littleton, J. T. (2016). Shank modulates postsynaptic Wnt signaling to regulate synaptic development. The Journal of Neuroscience, 36, 5820–5832.
Hassani Nia, F., Woike, D., Kloth, K., Kortum, F., & Kreienkamp, H. J. (2020). Truncating mutations in SHANK3 associated with global developmental delay interfere with nuclear beta‐catenin signaling. Journal of Neurochemistry, 155, 250–263.
Irimia, M., Weatheritt, R. J., Ellis, J. D., Parikshak, N. N., Gonatopoulos‐Pournatzis, T., Babor, M., Quesnel‐Vallières, M., Tapial, J., Raj, B., O'Hanlon, D., Barrios‐Rodiles, M., Sternberg, M. J. E., Cordes, S. P., Roth, F. P., Wrana, J. L., Geschwind, D. H., & Blencowe, B. J. (2014). A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell, 159, 1511–1523.
Itai, T., Sugie, A., Nitta, Y., Maki, R., Suzuki, T., Shinkai, Y., Watanabe, Y., Nakano, Y., Ichikawa, K., Okamoto, N., Utsuno, Y., Koshimizu, E., Fujita, A., Hamanaka, K., Uchiyama, Y., Tsuchida, N., Miyake, N., Misawa, K., Mizuguchi, T., … Matsumoto, N. (2023). A novel NONO variant that causes developmental delay and cardiac phenotypes. Scientific Reports, 13, 975.
Jeong, J., Li, Y., & Roche, K. W. (2021). CaMKII phosphorylation regulates synaptic enrichment of Shank3. eNeuro, 8, ENEURO.0481‐ENEU20.2021.
Knott, G. J., Bond, C. S., & Fox, A. H. (2016). The DBHS proteins SFPQ, NONO and PSPC1: A multipurpose molecular scaffold. Nucleic Acids Research, 44, 3989–4004.
Leung, C. S., Rosenzweig, S., Yoon, B., Marinelli, N. A., Hollingsworth, E. W., Maguire, A. M., Cowen, M. H., Schmidt, M., Imitola, J., Gamsiz Uzun, E. D., & Lizarraga, S. B. (2023). Dysregulation of the chromatin environment leads to differential alternative splicing as a mechanism of disease in a human model of autism spectrum disorder. Human Molecular Genetics, 32, 1634–1646.
Li, D., Wang, Q., Bayat, A., Battig, M. R., Zhou, Y., Bosch, D. G. M., van Haaften, G., Granger, L., Petersen, A. K., Pérez‐Jurado, L. A., Aznar‐Laín, G., Aneja, A., Hancarova, M., Bendova, S., Schwarz, M., Kremlikova Pourova, R., Sedlacek, Z., Keena, B. A., March, M. E., … Hakonarson, H. (2024). Spliceosome malfunction causes neurodevelopmental disorders with overlapping features. The Journal of Clinical Investigation, 134, e171235.
Li, W., Karwacki‐Neisius, V., Ma, C., Tan, L., Shi, Y., Wu, F., & Shi, Y. G. (2020). Nono deficiency compromises TET1 chromatin association and impedes neuronal differentiation of mouse embryonic stem cells. Nucleic Acids Research, 48, 4827–4838.
Lilja, J., Zacharchenko, T., Georgiadou, M., Jacquemet, G., de Franceschi, N., Peuhu, E., Hamidi, H., Pouwels, J., Martens, V., Nia, F. H., Beifuss, M., Boeckers, T., Kreienkamp, H. J., Barsukov, I. L., & Ivaska, J. (2017). SHANK proteins limit integrin activation by directly interacting with Rap1 and R‐Ras. Nature Cell Biology, 19, 292–305.
Mircsof, D., Langouet, M., Rio, M., Moutton, S., Siquier‐Pernet, K., Bole‐Feysot, C., Cagnard, N., Nitschke, P., Gaspar, L., Znidaric, M., Alibeu, O., Fritz, A. K., Wolfer, D. P., Schroter, A., Bosshard, G., Rudin, M., Koester, C., Crestani, F., Seebeck, P., … Colleaux, L. (2015). Mutations in NONO lead to syndromic intellectual disability and inhibitory synaptic defects. Nature Neuroscience, 18, 1731–1736.
Monteiro, P., & Feng, G. (2017). SHANK proteins: Roles at the synapse and in autism spectrum disorder. Nature Reviews. Neuroscience, 18, 147–157.
Nguyen, T. M., Schreiner, D., Xiao, L., Traunmuller, L., Bornmann, C. & Scheiffele, P. (2016). An alternative splicing switch shapes neurexin repertoires in principal neurons versus interneurons in the mouse hippocampus. Elife, 5, e22757.
Okuzono, S., Fujii, F., Matsushita, Y., Setoyama, D., Shinmyo, Y., Taira, R., Yonemoto, K., Akamine, S., Motomura, Y., Sanefuji, M., Sakurai, T., Kawasaki, H., Han, K., Kato, T. A., Torisu, H., Kang, D., Nakabeppu, Y., Sakai, Y., & Ohga, S. (2023). Shank3a/b isoforms regulate the susceptibility to seizures and thalamocortical development in the early postnatal period of mice. Neuroscience Research, 193, 13–19.
Peca, J., Feliciano, C., Ting, J. T., Wang, W., Wells, M. F., Venkatraman, T. N., Lascola, C. D., Fu, Z., & Feng, G. (2011). Shank3 mutant mice display autistic‐like behaviours and striatal dysfunction. Nature, 472, 437–442.
Perfitt, T. L., Wang, X., Dickerson, M. T., Stephenson, J. R., Nakagawa, T., Jacobson, D. A., & Colbran, R. J. (2020). Neuronal L‐type Calcium Channel signaling to the nucleus requires a novel CaMKIIalpha‐Shank3 interaction. The Journal of Neuroscience, 40, 2000–2014.
Phelan, K., & McDermid, H. E. (2012). The 22q13.3 deletion syndrome (Phelan‐McDermid syndrome). Molecular Syndromology, 2, 186–201.
Quesnel‐Vallieres, M., Dargaei, Z., Irimia, M., Gonatopoulos‐Pournatzis, T., Ip, J. Y., Wu, M., Sterne‐Weiler, T., Nakagawa, S., Woodin, M. A., Blencowe, B. J., & Cordes, S. P. (2016). Misregulation of an activity‐dependent splicing network as a common mechanism underlying autism Spectrum disorders. Molecular Cell, 64, 1023–1034.
Rogalska, M. E., Vivori, C., & Valcarcel, J. (2023). Regulation of pre‐mRNA splicing: Roles in physiology and disease, and therapeutic prospects. Nature Reviews. Genetics, 24, 251–269.
Ronchetti, D., Traini, V., Silvestris, I., Fabbiano, G., Passamonti, F., Bolli, N., & Taiana, E. (2024). The pleiotropic nature of NONO, a master regulator of essential biological pathways in cancers. Cancer Gene Therapy. https://doi.org/10.1038/s41417‐024‐000763‐x.
Sasaki, K., Gotoh, K., Miake, S., Setoyama, D., Yagi, M., Igami, K., Uchiumi, T., & Kang, D. (2017). p32 is required for appropriate Interleukin‐6 production upon LPS stimulation and protects mice from endotoxin shock. eBioMedicine, 20, 161–172.
Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., & Mann, M. (2006). In‐gel digestion for mass spectrometric characterization of proteins and proteomes. Nature Protocols, 1, 2856–2860.
Stagsted, L. V. W., O'Leary, E. T., Ebbesen, K. K., & Hansen, T. B. (2021). The RNA‐binding protein SFPQ preserves long‐intron splicing and regulates circRNA biogenesis in mammals. eLife, 10, e63088.
Su, C.‐H., Dhananjaya, D., & Tarn, W.‐Y. (2018). Alternative splicing in neurogenesis and brain development. Frontiers in Molecular Biosciences, 5, 12.
Takeiwa, T., Ikeda, K., Horie, K., & Inoue, S. (2024). Role of RNA binding proteins of the drosophila behavior and human splicing (DBHS) family in health and cancer. RNA Biology, 21, 1–17.
Tiek, D. M., Khatib, S. A., Trepicchio, C. J., Heckler, M. M., Divekar, S. D., Sarkaria, J. N., Glasgow, E., & Riggins, R. B. (2019). Estrogen‐related receptor beta activation and isoform shifting by cdc2‐like kinase inhibition restricts migration and intracranial tumor growth in glioblastoma. The FASEB Journal, 33, 13476–13491.
Wang, X., Han, M., Wang, S., Sun, Y., Zhao, W., Xue, Z., Liang, X., Huang, B., Li, G., Chen, A., Li, X., & Wang, J. (2022). Targeting the splicing factor NONO inhibits GBM progression through GPX1 intron retention. Theranostics, 12, 5451–5469.
Wang, X., Xu, Q., Bey, A. L., Lee, Y., & Jiang, Y. H. (2014). Transcriptional and functional complexity of Shank3 provides a molecular framework to understand the phenotypic heterogeneity of SHANK3 causing autism and Shank3 mutant mice. Molecular Autism, 5, 30.
Woike, D., Wang, E., Tibbe, D., Hassani Nia, F., Failla, A. V., Kibaek, M., Overgard, T. M., Larsen, M. J., Fagerberg, C. R., Barsukov, I., & Kreienkamp, H. J. (2022). Mutations affecting the N‐terminal domains of SHANK3 point to different pathomechanisms in neurodevelopmental disorders. Scientific Reports, 12, 902.
Yang, R., Feng, X., Arias‐Cavieres, A., Mitchell, R. M., Polo, A., Hu, K., Zhong, R., Qi, C., Zhang, R. S., Westneat, N., Portillo, C. A., Nobrega, M. A., Hansel, C., Garcia Iii, A. J., & Zhang, X. (2023). Upregulation of SYNGAP1 expression in mice and human neurons by redirecting alternative splicing. Neuron, 111, 1637–1650.e5.
Yu, D., Huang, C. J., & Tucker, H. O. (2024). Established and evolving roles of the multifunctional non‐POU domain‐containing octamer‐binding protein (NonO) and splicing factor proline‐ and glutamine‐rich (SFPQ). Journal of Developmental Biology, 12, 3.
Zhang, S., Cooper, J. A., Chong, Y. S., Naveed, A., Mayoh, C., Jayatilleke, N., Liu, T., Amos, S., Kobelke, S., Marshall, A. C., Meers, O., Choi, Y. S., Bond, C. S., & Fox, A. H. (2023). NONO enhances mRNA processing of super‐enhancer‐associated GATA2 and HAND2 genes in neuroblastoma. EMBO Reports, 24, e54977.

Auteurs

Sayaka Okuzono (S)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
Section of Pediatrics, Department of Medicine, Fukuoka Dental College, Fukuoka, Japan.

Fumihiko Fujii (F)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Daiki Setoyama (D)

Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Ryoji Taira (R)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Yohei Shinmyo (Y)

Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.

Hiroki Kato (H)

Department of Molecular Cell Biology and Oral Anatomy, Graduate School of Dental Science, Kyushu University, Fukuoka, Japan.

Keiji Masuda (K)

Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan.

Kousuke Yonemoto (K)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Satoshi Akamine (S)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Yuki Matsushita (Y)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Yoshitomo Motomura (Y)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Takeshi Sakurai (T)

Medical Innovation Center, Kyoto University Graduate School of Medicine, Kyoto, Japan.

Hiroshi Kawasaki (H)

Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.

Kihoon Han (K)

Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea.

Takahiro A Kato (TA)

Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Hiroyuki Torisu (H)

Section of Pediatrics, Department of Medicine, Fukuoka Dental College, Fukuoka, Japan.

Dongchon Kang (D)

Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Yusaku Nakabeppu (Y)

Division of Neurofunctional Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.

Shouichi Ohga (S)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Yasunari Sakai (Y)

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.

Classifications MeSH