Autism mutations rewire protein interaction networks to drive neurodevelopmental pathology

Nevan J. Krogan · Science

47 min read Original article ↗

Editor’s summary

A large number of genomic and transcriptomic datasets have revealed valuable insights into the biology of autism spectrum disorder (ASD). Wang et al. produced a complementary resource by mapping 100 high-confidence ASD genes and producing a large protein-protein-interaction (PPI) network, identifying more than 1800 interactions, most of which (87%) have never been reported previously. By integrating affinity purification–mass spectrometry data with AlphaFold-based structural predictions and by validating key interactions in human induced pluripotent stem cell–derived organoids and Xenopus embryos, the authors showed that disease-associated variants selectively weakened or strengthened specific PPIs, producing convergent neurodevelopmental phenotypes even when the variants reside in different genes. This study provides a valuable resource for understanding the biology of ASD. —Mattia Maroso

Structured Abstract

INTRODUCTION

Autism spectrum disorder (ASD) is characterized by extreme genetic heterogeneity, with more than 250 high-confidence risk (hcASD) genes identified to date. Defined by rare, large-effect coding variants, these genes show functional and developmental convergence in transcriptomic analyses. However, these approaches have provided only limited mechanistic insight and have not identified specific therapeutic targets beyond the genetic variants themselves. Because proteins are the primary functional units of the cell, mapping the physical ASD interactome—and determining how ASD variants rewire it—is essential to move beyond gene lists and broad pathophysiologic themes toward a deeper causal understanding of neurodevelopmental pathology.

RATIONALE

To augment our molecular understanding of ASD, we used affinity purification–mass spectrometry (AP-MS) to map 100 hcASD proteins and 54 patient-derived missense variants, substantially expanding the known ASD protein interaction landscape. By integrating these datasets with AlphaFold structural modeling and functional studies in Xenopus and human forebrain organoids, we investigated whether genetically distinct risk factors converge onto shared biology and if convergent neurodevelopmental phenotypes arise through the selective rewiring of protein-protein interactions (PPIs) by disease-associated variants.

RESULTS

The resulting ASD-PPI network contains more than 1800 interactions, 87% of which were previously unreported. The network, which is enriched in neural progenitor cells (NPCs) of the excitatory lineage, exhibits a highly interconnected architecture, with risk proteins converging onto shared complexes, including DCAF7. Functional interrogation of selected interactions demonstrated that disruption of the previously uncharacterized DCAF7-DYRK1A-KIAA0232 complex impairs progenitor proliferation and reduces forebrain size in vivo. Furthermore, patient-derived missense mutations frequently induced convergent PPI rewiring. Distinct FOXP1 mutations, for example, weakened its physical interaction with FOXP4, leading to gain-of-function redistribution of FOXP4 to ectopic genomic targets. In human forebrain organoids, this biochemical rewiring drove premature differentiation of cortical neurons and altered neural activity. Genetic deletion of FOXP4 in a FOXP1-mutant background rescued these neurodevelopmental defects; although the exact mechanism requires further determination, this suggests that the rewired interaction underlies the mutant phenotype.

CONCLUSION

Together, these findings define a dual-layered model of molecular convergence in ASD: convergence through shared interaction networks in the wild-type state and convergence through recurrent functional consequences of interaction rewiring in the mutant state. More broadly, this work establishes a scalable framework for systematic interrogation of the autism proteome, enables prioritization of druggable protein interfaces, and provides a rational foundation for precision therapeutic strategies aimed at restoring neurodevelopmental trajectories.

Mapping the ASD interactome reveals molecular convergence.

(A) Protein interactome of 100 hcASD proteins and 54 patient mutations reveals a highly convergent network of protein complexes. (B) Convergent protein complexes were prioritized for functional validation in human neural progenitors and Xenopus. (C) Mutation-driven rewiring, such as FOXP1-FOXP4 interaction disruption, alters brain development, for example, deep-layer neurogenesis in cortical organoids in FOXP1 mutant organoids. R513C, Arg513→Cys; R513H, Arg513→His; L327P, Leu327→Pro; CRISPRi, CRISPR interference; WT, wild type.

Abstract

Systematic mapping of protein-protein interaction (PPI) networks and determining how causal mutations rewire them in autism spectrum disorder (ASD) provide a powerful framework for uncovering disease mechanisms and therapeutic opportunities. Using affinity purification–mass spectrometry, we systematically mapped PPIs for 100 high-confidence ASD genes, uncovering more than 1800 interactions. By assessing the impact of pathogenic missense mutations, leveraging AlphaFold, and validating key findings in human-derived model systems, we identified marked convergence onto shared protein complexes in the wild-type state and convergent PPI rewiring driven by independent mutations. For example, distinct patient-derived variants in FOXP1 disrupt its interactions with FOXP4, leading to changes in cortical neurogenesis and neural activity in brain organoids. Overall, these findings link genetic variation to protein networks and convergent neurodevelopmental dysfunction in ASD.

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References and Notes

1

C. Lord, T. S. Brugha, T. Charman, J. Cusack, G. Dumas, T. Frazier, E. J. H. Jones, R. M. Jones, A. Pickles, M. W. State, J. L. Taylor, J. Veenstra-VanderWeele, Autism spectrum disorder. Nat. Rev. Dis. Primers 6, 5 (2020).

2

B. Tick, P. Bolton, F. Happé, M. Rutter, F. Rijsdijk, Heritability of autism spectrum disorders: A meta-analysis of twin studies. J. Child Psychol. Psychiatry 57, 585–595 (2016).

3

M. J. Maenner, Z. Warren, A. R. Williams, E. Amoakohene, A. V. Bakian, D. A. Bilder, M. S. Durkin, R. T. Fitzgerald, S. M. Furnier, M. M. Hughes, C. M. Ladd-Acosta, D. McArthur, E. T. Pas, A. Salinas, A. Vehorn, S. Williams, A. Esler, A. Grzybowski, J. Hall-Lande, R. H. N. Nguyen, K. Pierce, W. Zahorodny, A. Hudson, L. Hallas, K. C. Mancilla, M. Patrick, J. Shenouda, K. Sidwell, M. DiRienzo, J. Gutierrez, M. H. Spivey, M. Lopez, S. Pettygrove, Y. D. Schwenk, A. Washington, K. A. Shaw, Prevalence and characteristics of autism spectrum disorder among children aged 8 years – Autism and Developmental Disabilities Monitoring Network, 11 sites, United States, 2020. MMWR Surveill. Summ. 72, 1–14 (2023).

4

F. K. Satterstrom, J. A. Kosmicki, J. Wang, M. S. Breen, S. De Rubeis, J.-Y. An, M. Peng, R. Collins, J. Grove, L. Klei, C. Stevens, J. Reichert, M. S. Mulhern, M. Artomov, S. Gerges, B. Sheppard, X. Xu, A. Bhaduri, U. Norman, H. Brand, G. Schwartz, R. Nguyen, E. E. Guerrero, C. Dias, C. Betancur, E. H. Cook, L. Gallagher, M. Gill, J. S. Sutcliffe, A. Thurm, M. E. Zwick, A. D. Børglum, M. W. State, A. E. Cicek, M. E. Talkowski, D. J. Cutler, B. Devlin, S. J. Sanders, K. Roeder, M. J. Daly, J. D. Buxbaum, Autism Sequencing Consortium, iPSYCH-Broad Consortium, Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism. Cell 180, 568–584.e23 (2020).

5

B. Trost, B. Thiruvahindrapuram, A. J. S. Chan, W. Engchuan, E. J. Higginbotham, J. L. Howe, L. O. Loureiro, M. S. Reuter, D. Roshandel, J. Whitney, M. Zarrei, M. Bookman, C. Somerville, R. Shaath, M. Abdi, E. Aliyev, R. V. Patel, T. Nalpathamkalam, G. Pellecchia, O. Hamdan, G. Kaur, Z. Wang, J. R. MacDonald, J. Wei, W. W. L. Sung, S. Lamoureux, N. Hoang, T. Selvanayagam, N. Deflaux, M. Geng, S. Ghaffari, J. Bates, E. J. Young, Q. Ding, C. Shum, L. D’Abate, C. A. Bradley, A. Rutherford, V. Aguda, B. Apresto, N. Chen, S. Desai, X. Du, M. L. Y. Fong, S. Pullenayegum, K. Samler, T. Wang, K. Ho, T. Paton, S. L. Pereira, J.-A. Herbrick, R. F. Wintle, J. Fuerth, J. Noppornpitak, H. Ward, P. Magee, A. Al Baz, U. Kajendirarajah, S. Kapadia, J. Vlasblom, M. Valluri, J. Green, V. Seifer, M. Quirbach, O. Rennie, E. Kelley, N. Masjedi, C. Lord, M. J. Szego, M. H. Zawati, M. Lang, L. J. Strug, C. R. Marshall, G. Costain, K. Calli, A. Iaboni, A. Yusuf, P. Ambrozewicz, L. Gallagher, D. G. Amaral, J. Brian, M. Elsabbagh, S. Georgiades, D. S. Messinger, S. Ozonoff, J. Sebat, C. Sjaarda, I. M. Smith, P. Szatmari, L. Zwaigenbaum, A. Kushki, T. W. Frazier, J. A. S. Vorstman, K. A. Fakhro, B. A. Fernandez, M. E. S. Lewis, R. Weksberg, M. Fiume, R. K. C. Yuen, E. Anagnostou, N. Sondheimer, D. Glazer, D. M. Hartley, S. W. Scherer, Genomic architecture of autism from comprehensive whole-genome sequence annotation. Cell 185, 4409–4427.e18 (2022).

6

J. M. Fu, F. K. Satterstrom, M. Peng, H. Brand, R. L. Collins, S. Dong, B. Wamsley, L. Klei, L. Wang, S. P. Hao, C. R. Stevens, C. Cusick, M. Babadi, E. Banks, B. Collins, S. Dodge, S. B. Gabriel, L. Gauthier, S. K. Lee, L. Liang, A. Ljungdahl, B. Mahjani, L. Sloofman, A. N. Smirnov, Autism Sequencing Consortium (ASC)Broad Institute Center for Common Disease Genomics (Broad-CCDG), iPSYCH-BROAD Consortium, Rare coding variation provides insight into the genetic architecture and phenotypic context of autism. Nat. Genet. 54, 1320–1331 (2022).

7

X. Zhou, P. Feliciano, C. Shu, T. Wang, I. Astrovskaya, J. B. Hall, J. U. Obiajulu, J. R. Wright, S. C. Murali, S. X. Xu, L. Brueggeman, T. R. Thomas, O. Marchenko, C. Fleisch, S. D. Barns, L. G. Snyder, B. Han, T. S. Chang, T. N. Turner, W. T. Harvey, A. Nishida, B. J. O’Roak, D. H. Geschwind, J. J. Michaelson, N. Volfovsky, E. E. Eichler, Y. Shen, W. K. Chung, SPARK Consortium, Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nat. Genet. 54, 1305–1319 (2022).

8

C. Lord, T. Charman, A. Havdahl, P. Carbone, E. Anagnostou, B. Boyd, T. Carr, P. J. de Vries, C. Dissanayake, G. Divan, C. M. Freitag, M. M. Gotelli, C. Kasari, M. Knapp, P. Mundy, A. Plank, L. Scahill, C. Servili, P. Shattuck, E. Simonoff, A. T. Singer, V. Slonims, P. P. Wang, M. C. Ysrraelit, R. Jellett, A. Pickles, J. Cusack, P. Howlin, P. Szatmari, A. Holbrook, C. Toolan, J. B. McCauley, The Lancet Commission on the future of care and clinical research in autism. Lancet 399, 271–334 (2022).

9

N. Sestan, M. W. State, Lost in translation: Traversing the complex path from genomics to therapeutics in autism spectrum disorder. Neuron 100, 406–423 (2018).

10

H. R. Willsey, A. J. Willsey, B. Wang, M. W. State, Genomics, convergent neuroscience and progress in understanding autism spectrum disorder. Nat. Rev. Neurosci. 23, 323–341 (2022).

11

J. F. Greenblatt, B. M. Alberts, N. J. Krogan, Discovery and significance of protein-protein interactions in health and disease. Cell 187, 6501–6517 (2024).

12

M. Kim, J. Park, M. Bouhaddou, K. Kim, A. Rojc, M. Modak, M. Soucheray, M. J. McGregor, P. O’Leary, D. Wolf, E. Stevenson, T. K. Foo, D. Mitchell, K. A. Herrington, D. P. Muñoz, B. Tutuncuoglu, K.-H. Chen, F. Zheng, J. F. Kreisberg, M. E. Diolaiti, J. D. Gordan, J.-P. Coppé, D. L. Swaney, B. Xia, L. van ’t Veer, A. Ashworth, T. Ideker, N. J. Krogan, A protein interaction landscape of breast cancer. Science 374, eabf3066 (2021).

13

D. L. Swaney, D. J. Ramms, Z. Wang, J. Park, Y. Goto, M. Soucheray, N. Bhola, K. Kim, F. Zheng, Y. Zeng, M. McGregor, K. A. Herrington, R. O’Keefe, N. Jin, N. K. VanLandingham, H. Foussard, J. Von Dollen, M. Bouhaddou, D. Jimenez-Morales, K. Obernier, J. F. Kreisberg, M. Kim, D. E. Johnson, N. Jura, J. R. Grandis, J. S. Gutkind, T. Ideker, N. J. Krogan, A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science 374, eabf2911 (2021).

14

S. K. Hota, K. S. Rao, A. P. Blair, A. Khalilimeybodi, K. M. Hu, R. Thomas, K. So, V. Kameswaran, J. Xu, B. J. Polacco, R. V. Desai, N. Chatterjee, A. Hsu, J. M. Muncie, A. M. Blotnick, S. A. B. Winchester, L. S. Weinberger, R. Hüttenhain, I. S. Kathiriya, N. J. Krogan, J. J. Saucerman, B. G. Bruneau, Brahma safeguards canalization of cardiac mesoderm differentiation. Nature 602, 129–134 (2022).

15

B. Gonzalez-Teran, M. Pittman, F. Felix, R. Thomas, D. Richmond-Buccola, R. Hüttenhain, K. Choudhary, E. Moroni, M. W. Costa, Y. Huang, A. Padmanabhan, M. Alexanian, C. Y. Lee, B. E. J. Maven, K. Samse-Knapp, S. U. Morton, M. McGregor, C. A. Gifford, J. G. Seidman, C. E. Seidman, B. D. Gelb, G. Colombo, B. R. Conklin, B. L. Black, B. G. Bruneau, N. J. Krogan, K. S. Pollard, D. Srivastava, Transcription factor protein interactomes reveal genetic determinants in heart disease. Cell 185, 794–814.e30 (2022).

16

T. E. Tracy, J. Madero-Pérez, D. L. Swaney, T. S. Chang, M. Moritz, C. Konrad, M. E. Ward, E. Stevenson, R. Hüttenhain, G. Kauwe, M. Mercedes, L. Sweetland-Martin, X. Chen, S.-A. Mok, M. Y. Wong, M. Telpoukhovskaia, S.-W. Min, C. Wang, P. D. Sohn, J. Martin, Y. Zhou, W. Luo, J. Q. Trojanowski, V. M. Y. Lee, S. Gong, G. Manfredi, G. Coppola, N. J. Krogan, D. H. Geschwind, L. Gan, Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration. Cell 185, 712–728.e14 (2022).

17

J. Batra, J. F. Hultquist, D. Liu, O. Shtanko, J. Von Dollen, L. Satkamp, G. M. Jang, P. Luthra, T. M. Schwarz, G. I. Small, E. Arnett, M. Anantpadma, A. Reyes, D. W. Leung, R. Kaake, P. Haas, C. B. Schmidt, L. S. Schlesinger, D. J. LaCount, R. A. Davey, G. K. Amarasinghe, C. F. Basler, N. J. Krogan, Protein interaction mapping identifies RBBP6 as a negative regulator of Ebola virus replication. Cell 175, 1917–1930.e13 (2018).

18

D. E. Gordon, G. M. Jang, M. Bouhaddou, J. Xu, K. Obernier, K. M. White, M. J. O’Meara, V. V. Rezelj, J. Z. Guo, D. L. Swaney, T. A. Tummino, R. Hüttenhain, R. M. Kaake, A. L. Richards, B. Tutuncuoglu, H. Foussard, J. Batra, K. Haas, M. Modak, M. Kim, P. Haas, B. J. Polacco, H. Braberg, J. M. Fabius, M. Eckhardt, M. Soucheray, M. J. Bennett, M. Cakir, M. J. McGregor, Q. Li, B. Meyer, F. Roesch, T. Vallet, A. Mac Kain, L. Miorin, E. Moreno, Z. Z. C. Naing, Y. Zhou, S. Peng, Y. Shi, Z. Zhang, W. Shen, I. T. Kirby, J. E. Melnyk, J. S. Chorba, K. Lou, S. A. Dai, I. Barrio-Hernandez, D. Memon, C. Hernandez-Armenta, J. Lyu, C. J. P. Mathy, T. Perica, K. B. Pilla, S. J. Ganesan, D. J. Saltzberg, R. Rakesh, X. Liu, S. B. Rosenthal, L. Calviello, S. Venkataramanan, J. Liboy-Lugo, Y. Lin, X.-P. Huang, Y. Liu, S. A. Wankowicz, M. Bohn, M. Safari, F. S. Ugur, C. Koh, N. S. Savar, Q. D. Tran, D. Shengjuler, S. J. Fletcher, M. C. O’Neal, Y. Cai, J. C. J. Chang, D. J. Broadhurst, S. Klippsten, P. P. Sharp, N. A. Wenzell, D. Kuzuoglu-Ozturk, H.-Y. Wang, R. Trenker, J. M. Young, D. A. Cavero, J. Hiatt, T. L. Roth, U. Rathore, A. Subramanian, J. Noack, M. Hubert, R. M. Stroud, A. D. Frankel, O. S. Rosenberg, K. A. Verba, D. A. Agard, M. Ott, M. Emerman, N. Jura, M. von Zastrow, E. Verdin, A. Ashworth, O. Schwartz, C. d’Enfert, S. Mukherjee, M. Jacobson, H. S. Malik, D. G. Fujimori, T. Ideker, C. S. Craik, S. N. Floor, J. S. Fraser, J. D. Gross, A. Sali, B. L. Roth, D. Ruggero, J. Taunton, T. Kortemme, P. Beltrao, M. Vignuzzi, A. García-Sastre, K. M. Shokat, B. K. Shoichet, N. J. Krogan, A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459–468 (2020).

19

S. Jäger, P. Cimermancic, N. Gulbahce, J. R. Johnson, K. E. McGovern, S. C. Clarke, M. Shales, G. Mercenne, L. Pache, K. Li, H. Hernandez, G. M. Jang, S. L. Roth, E. Akiva, J. Marlett, M. Stephens, I. D’Orso, J. Fernandes, M. Fahey, C. Mahon, A. J. O’Donoghue, A. Todorovic, J. H. Morris, D. A. Maltby, T. Alber, G. Cagney, F. D. Bushman, J. A. Young, S. K. Chanda, W. I. Sundquist, T. Kortemme, R. D. Hernandez, C. S. Craik, A. Burlingame, A. Sali, A. D. Frankel, N. J. Krogan, Global landscape of HIV-human protein complexes. Nature 481, 365–370 (2011).

20

H. J. Kang, Y. I. Kawasawa, F. Cheng, Y. Zhu, X. Xu, M. Li, A. M. M. Sousa, M. Pletikos, K. A. Meyer, G. Sedmak, T. Guennel, Y. Shin, M. B. Johnson, Z. Krsnik, S. Mayer, S. Fertuzinhos, S. Umlauf, S. N. Lisgo, A. Vortmeyer, D. R. Weinberger, S. Mane, T. M. Hyde, A. Huttner, M. Reimers, J. E. Kleinman, N. Sestan, Spatio-temporal transcriptome of the human brain. Nature 478, 483–489 (2011).

21

GTEx Consortium, Genetic effects on gene expression across human tissues. Nature 550, 204–213 (2017).

22

A. J. Willsey, S. J. Sanders, M. Li, S. Dong, A. T. Tebbenkamp, R. A. Muhle, S. K. Reilly, L. Lin, S. Fertuzinhos, J. A. Miller, M. T. Murtha, C. Bichsel, W. Niu, J. Cotney, A. G. Ercan-Sencicek, J. Gockley, A. R. Gupta, W. Han, X. He, E. J. Hoffman, L. Klei, J. Lei, W. Liu, L. Liu, C. Lu, X. Xu, Y. Zhu, S. M. Mane, E. S. Lein, L. Wei, J. P. Noonan, K. Roeder, B. Devlin, N. Sestan, M. W. State, Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell 155, 997–1007 (2013).

23

G. Pintacuda, Y.-H. H. Hsu, K. Tsafou, K. W. Li, J. M. Martín, J. Riseman, J. C. Biagini, J. K. T. Ching, D. Mena, M. A. Gonzalez-Lozano, S. B. Egri, J. Jaffe, A. B. Smit, N. Fornelos, K. C. Eggan, K. Lage, Protein interaction studies in human induced neurons indicate convergent biology underlying autism spectrum disorders. Cell Genom. 3, 100250 (2023).

24

N. Murtaza, A. A. Cheng, C. O. Brown, D. P. Meka, S. Hong, J. A. Uy, J. El-Hajjar, N. Pipko, B. K. Unda, B. Schwanke, S. Xing, B. Thiruvahindrapuram, W. Engchuan, B. Trost, E. Deneault, F. Calderon de Anda, B. W. Doble, J. Ellis, E. Anagnostou, G. D. Bader, S. W. Scherer, Y. Lu, K. K. Singh, Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies. Cell Rep. 41, 111678 (2022).

25

Y. Gao, D. Shonai, M. Trn, J. Zhao, E. J. Soderblom, S. A. Garcia-Moreno, C. A. Gersbach, W. C. Wetsel, G. Dawson, D. Velmeshev, Y.-H. Jiang, L. G. Sloofman, J. D. Buxbaum, S. H. Soderling, Proximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions. Nat. Commun. 15, 6801 (2024).

26

T. Singh, T. Poterba, D. Curtis, H. Akil, M. Al Eissa, J. D. Barchas, N. Bass, T. B. Bigdeli, G. Breen, E. J. Bromet, P. F. Buckley, W. E. Bunney, J. Bybjerg-Grauholm, W. F. Byerley, S. B. Chapman, W. J. Chen, C. Churchhouse, N. Craddock, C. M. Cusick, L. DeLisi, S. Dodge, M. A. Escamilla, S. Eskelinen, A. H. Fanous, S. V. Faraone, A. Fiorentino, L. Francioli, S. B. Gabriel, D. Gage, S. A. Gagliano Taliun, A. Ganna, G. Genovese, D. C. Glahn, J. Grove, M.-H. Hall, E. Hämäläinen, H. O. Heyne, M. Holi, D. M. Hougaard, D. P. Howrigan, H. Huang, H.-G. Hwu, R. S. Kahn, H. M. Kang, K. J. Karczewski, G. Kirov, J. A. Knowles, F. S. Lee, D. S. Lehrer, F. Lescai, D. Malaspina, S. R. Marder, S. A. McCarroll, A. M. McIntosh, H. Medeiros, L. Milani, C. P. Morley, D. W. Morris, P. B. Mortensen, R. M. Myers, M. Nordentoft, N. L. O’Brien, A. M. Olivares, D. Ongur, W. H. Ouwehand, D. S. Palmer, T. Paunio, D. Quested, M. H. Rapaport, E. Rees, B. Rollins, F. K. Satterstrom, A. Schatzberg, E. Scolnick, L. J. Scott, S. I. Sharp, P. Sklar, J. W. Smoller, J. L. Sobell, M. Solomonson, E. A. Stahl, C. R. Stevens, J. Suvisaari, G. Tiao, S. J. Watson, N. A. Watts, D. H. Blackwood, A. D. Børglum, B. M. Cohen, A. P. Corvin, T. Esko, N. B. Freimer, S. J. Glatt, C. M. Hultman, A. McQuillin, A. Palotie, C. N. Pato, M. T. Pato, A. E. Pulver, D. St Clair, M. T. Tsuang, M. P. Vawter, J. T. Walters, T. M. Werge, R. A. Ophoff, P. F. Sullivan, M. J. Owen, M. Boehnke, M. C. O’Donovan, B. M. Neale, M. J. Daly, Rare coding variants in ten genes confer substantial risk for schizophrenia. Nature 604, 509–516 (2022).

27

T. J. Nowakowski, A. Bhaduri, A. A. Pollen, B. Alvarado, M. A. Mostajo-Radji, E. Di Lullo, M. Haeussler, C. Sandoval-Espinosa, S. J. Liu, D. Velmeshev, J. R. Ounadjela, J. Shuga, X. Wang, D. A. Lim, J. A. West, A. A. Leyrat, W. J. Kent, A. R. Kriegstein, Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science 358, 1318–1323 (2017).

28

D. Szklarczyk, A. L. Gable, K. C. Nastou, D. Lyon, R. Kirsch, S. Pyysalo, N. T. Doncheva, M. Legeay, T. Fang, P. Bork, L. J. Jensen, C. von Mering, The STRING database in 2021: Customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 49, D605–D612 (2021).

29

S. A. Aleksander, J. Balhoff, S. Carbon, J. M. Cherry, H. J. Drabkin, D. Ebert, M. Feuermann, P. Gaudet, N. L. Harris, D. P. Hill, R. Lee, H. Mi, S. Moxon, C. J. Mungall, A. Muruganugan, T. Mushayahama, P. W. Sternberg, P. D. Thomas, K. Van Auken, J. Ramsey, D. A. Siegele, R. L. Chisholm, P. Fey, M. C. Aspromonte, M. V. Nugnes, F. Quaglia, S. Tosatto, M. Giglio, S. Nadendla, G. Antonazzo, H. Attrill, G. Dos Santos, S. Marygold, V. Strelets, C. J. Tabone, J. Thurmond, P. Zhou, S. H. Ahmed, P. Asanitthong, D. Luna Buitrago, M. N. Erdol, M. C. Gage, M. Ali Kadhum, K. Y. C. Li, M. Long, A. Michalak, A. Pesala, A. Pritazahra, S. C. C. Saverimuttu, R. Su, K. E. Thurlow, R. C. Lovering, C. Logie, S. Oliferenko, J. Blake, K. Christie, L. Corbani, M. E. Dolan, H. J. Drabkin, D. P. Hill, L. Ni, D. Sitnikov, C. Smith, A. Cuzick, J. Seager, L. Cooper, J. Elser, P. Jaiswal, P. Gupta, P. Jaiswal, S. Naithani, M. Lera-Ramirez, K. Rutherford, V. Wood, J. L. De Pons, M. R. Dwinell, G. T. Hayman, M. L. Kaldunski, A. E. Kwitek, S. J. F. Laulederkind, M. A. Tutaj, M. Vedi, S.-J. Wang, P. D’Eustachio, L. Aimo, K. Axelsen, A. Bridge, N. Hyka-Nouspikel, A. Morgat, S. A. Aleksander, J. M. Cherry, S. R. Engel, K. Karra, S. R. Miyasato, R. S. Nash, M. S. Skrzypek, S. Weng, E. D. Wong, E. Bakker, T. Z. Berardini, L. Reiser, A. Auchincloss, K. Axelsen, G. Argoud-Puy, M.-C. Blatter, E. Boutet, L. Breuza, A. Bridge, C. Casals-Casas, E. Coudert, A. Estreicher, M. Livia Famiglietti, M. Feuermann, A. Gos, N. Gruaz-Gumowski, C. Hulo, N. Hyka-Nouspikel, F. Jungo, P. Le Mercier, D. Lieberherr, P. Masson, A. Morgat, I. Pedruzzi, L. Pourcel, S. Poux, C. Rivoire, S. Sundaram, A. Bateman, E. Bowler-Barnett, H. Bye-A-Jee, P. Denny, A. Ignatchenko, R. Ishtiaq, A. Lock, Y. Lussi, M. Magrane, M. J. Martin, S. Orchard, P. Raposo, E. Speretta, N. Tyagi, K. Warner, R. Zaru, A. D. Diehl, R. Lee, J. Chan, S. Diamantakis, D. Raciti, M. Zarowiecki, M. Fisher, C. James-Zorn, V. Ponferrada, A. Zorn, S. Ramachandran, L. Ruzicka, M. Westerfield, Gene Ontology Consortium, The Gene Ontology knowledgebase in 2023. Genetics 224, iyad031 (2023).

30

D. S. Manoli, M. W. State, Autism spectrum disorder genetics and the search for pathological mechanisms. Am. J. Psychiatry 178, 30–38 (2021).

31

K. E. McCluskey, K. M. Stovell, K. Law, E. Kostyanovskaya, J. Schmidt, C. R. T. Exner, J. Dea, E. Brimble, M. W. State, A. J. Willsey, H. R. Willsey, Autism gene variants disrupt enteric neuron migration and cause gastrointestinal dysmotility. Nat. Commun. 16, 2238 (2025).

32

S. Kaushik, F. Haderk, X. Zhao, H.-M. Hu, K. N. Shah, G. M. Jang, V. Olivas, S. Nanjo, J. Jascur, V. B. Masto, D. Ciznadija, I. Sloma, E. Gross, S. L. Weinrich, J. R. Johnson, T. G. Bivona, N. J. Krogan, S. Bandyopadhyay, A tyrosine kinase protein interaction map reveals targetable EGFR network oncogenesis in lung cancer. bioRxiv 2020.07.02.185173 [Preprint] (2020); https://doi.org/10.1101/2020.07.02.185173.

33

D. Halder, C.-H. Lee, J. Y. Hyun, G.-E. Chang, E. Cheong, I. Shin, Suppression of Sin3A activity promotes differentiation of pluripotent cells into functional neurons. Sci. Rep. 7, 44818 (2017).

34

A. Roopra, L. Sharling, I. C. Wood, T. Briggs, U. Bachfischer, A. J. Paquette, N. J. Buckley, Transcriptional repression by neuron-restrictive silencer factor is mediated via the Sin3-histone deacetylase complex. Mol. Cell. Biol. 20, 2147–2157 (2000).

35

M. Quevedo, L. Meert, M. R. Dekker, D. H. W. Dekkers, J. H. Brandsma, D. L. C. van den Berg, Z. Ozgür, W. F. J. van IJcken, J. Demmers, M. Fornerod, R. A. Poot, Mediator complex interaction partners organize the transcriptional network that defines neural stem cells. Nat. Commun. 10, 2669 (2019).

36

N. Ding, H. Zhou, P.-O. Esteve, H. G. Chin, S. Kim, X. Xu, S. M. Joseph, M. J. Friez, C. E. Schwartz, S. Pradhan, T. G. Boyer, Mediator links epigenetic silencing of neuronal gene expression with x-linked mental retardation. Mol. Cell 31, 347–359 (2008).

37

M. J. Jurynec, X. Bai, B. W. Bisgrove, H. Jackson, A. Nechiporuk, R. A. S. Palu, H. A. Grunwald, Y.-C. Su, K. Hoshijima, H. J. Yost, L. I. Zon, D. J. Grunwald, The Paf1 complex and P-TEFb have reciprocal and antagonist roles in maintaining multipotent neural crest progenitors. Development 146, dev180133 (2019).

38

C. Zhang, L. A. Mejia, J. Huang, P. Valnegri, E. J. Bennett, J. Anckar, A. Jahani-Asl, G. Gallardo, Y. Ikeuchi, T. Yamada, M. Rudnicki, J. W. Harper, A. Bonni, The X-linked intellectual disability protein PHF6 associates with the PAF1 complex and regulates neuronal migration in the mammalian brain. Neuron 78, 986–993 (2013).

39

N. J. Krogan, M. Kim, S. H. Ahn, G. Zhong, M. S. Kobor, G. Cagney, A. Emili, A. Shilatifard, S. Buratowski, J. F. Greenblatt, RNA polymerase II elongation factors of Saccharomyces cerevisiae: A targeted proteomics approach. Mol. Cell. Biol. 22, 6979–6992 (2002).

40

E. C. Ung, N. A. Borja, LEO1 haploinsufficiency is associated with developmental delays and autism spectrum disorder. J. Hum. Genet. 71, 109–111 (2026).

41

R. Evans, M. O’Neill, A. Pritzel, N. Antropova, A. Senior, T. Green, A. Žídek, R. Bates, S. Blackwell, J. Yim, O. Ronneberger, S. Bodenstein, M. Zielinski, A. Bridgland, A. Potapenko, A. Cowie, K. Tunyasuvunakool, R. Jain, E. Clancy, P. Kohli, J. Jumper, D. Hassabis, Protein complex prediction with AlphaFold-Multimer. bioRxiv 2021.10.04.463034 [Preprint] (2022); https://doi.org/10.1101/2021.10.04.463034.

42

P. Bryant, G. Pozzati, A. Elofsson, Improved prediction of protein-protein interactions using AlphaFold2. Nat. Commun. 13, 1265 (2022).

43

S. G. Choi, J. Olivet, P. Cassonnet, P.-O. Vidalain, K. Luck, L. Lambourne, K. Spirohn, I. Lemmens, M. Dos Santos, C. Demeret, L. Jones, S. Rangarajan, W. Bian, E. P. Coutant, Y. L. Janin, S. van der Werf, P. Trepte, E. E. Wanker, J. De Las Rivas, J. Tavernier, J.-C. Twizere, T. Hao, D. E. Hill, M. Vidal, M. A. Calderwood, Y. Jacob, Maximizing binary interactome mapping with a minimal number of assays. Nat. Commun. 10, 3907 (2019).

44

Y.-C. Chen, S. V. Rajagopala, T. Stellberger, P. Uetz, Exhaustive benchmarking of the yeast two-hybrid system. Nat. Methods 7, 667–668 (2010).

45

V. J. Heintz, L. Wang, D. J. LaCount, NanoLuc luciferase as a quantitative yeast two-hybrid reporter. FEMS Yeast Res. 21, foab069 (2021).

46

X. Peng, J. Wang, W. Peng, F.-X. Wu, Y. Pan, Protein-protein interactions: Detection, reliability assessment and applications. Brief. Bioinform. 18, 798–819 (2017).

47

P. Braun, M. Tasan, M. Dreze, M. Barrios-Rodiles, I. Lemmens, H. Yu, J. M. Sahalie, R. R. Murray, L. Roncari, A.-S. de Smet, K. Venkatesan, J.-F. Rual, J. Vandenhaute, M. E. Cusick, T. Pawson, D. E. Hill, J. Tavernier, J. L. Wrana, F. P. Roth, M. Vidal, An experimentally derived confidence score for binary protein-protein interactions. Nat. Methods 6, 91–97 (2009).

48

P. Magini, D. J. Smits, L. Vandervore, R. Schot, M. Columbaro, E. Kasteleijn, M. van der Ent, F. Palombo, M. H. Lequin, M. Dremmen, M. C. Y. de Wit, M. Severino, M. T. Divizia, P. Striano, N. Ordonez-Herrera, A. Alhashem, A. Al Fares, M. Al Ghamdi, A. Rolfs, P. Bauer, J. Demmers, F. W. Verheijen, M. Wilke, M. van Slegtenhorst, P. J. van der Spek, M. Seri, A. C. Jansen, R. W. Stottmann, R. B. Hufnagel, R. J. Hopkin, D. Aljeaid, W. Wiszniewski, P. Gawlinski, M. Laure-Kamionowska, F. S. Alkuraya, H. Akleh, V. Stanley, D. Musaev, J. G. Gleeson, M. S. Zaki, N. Brunetti-Pierri, G. Cappuccio, B. Davidov, L. Basel-Salmon, L. Bazak, N. R. Shahar, A. Bertoli-Avella, G. M. Mirzaa, W. B. Dobyns, T. Pippucci, M. Fornerod, G. M. S. Mancini, Loss of SMPD4 causes a developmental disorder characterized by microcephaly and congenital arthrogryposis. Am. J. Hum. Genet. 105, 689–705 (2019).

49

D. Yu, C. Cattoglio, Y. Xue, Q. Zhou, A complex between DYRK1A and DCAF7 phosphorylates the C-terminal domain of RNA polymerase II to promote myogenesis. Nucleic Acids Res. 47, 4462–4475 (2019).

50

F. Glenewinkel, M. J. Cohen, C. R. King, S. Kaspar, S. Bamberg-Lemper, J. S. Mymryk, W. Becker, The adaptor protein DCAF7 mediates the interaction of the adenovirus E1A oncoprotein with the protein kinases DYRK1A and HIPK2. Sci. Rep. 6, 28241 (2016).

51

Y. Miyata, E. Nishida, Identification of FAM53C as a cytosolic-anchoring inhibitory binding protein of the kinase DYRK1A. Life Sci. Alliance 6, e202302129 (2023).

52

D. Polioudakis, L. de la Torre-Ubieta, J. Langerman, A. G. Elkins, X. Shi, J. L. Stein, C. K. Vuong, S. Nichterwitz, M. Gevorgian, C. K. Opland, D. Lu, W. Connell, E. K. Ruzzo, J. K. Lowe, T. Hadzic, F. I. Hinz, S. Sabri, W. E. Lowry, M. B. Gerstein, K. Plath, D. H. Geschwind, A single-cell transcriptomic atlas of human neocortical development during mid-gestation. Neuron 103, 785–801.e8 (2019).

53

A. Bhaduri, C. Sandoval-Espinosa, M. Otero-Garcia, I. Oh, R. Yin, U. C. Eze, T. J. Nowakowski, A. R. Kriegstein, An atlas of cortical arealization identifies dynamic molecular signatures. Nature 598, 200–204 (2021).

54

R. Oughtred, J. Rust, C. Chang, B.-J. Breitkreutz, C. Stark, A. Willems, L. Boucher, G. Leung, N. Kolas, F. Zhang, S. Dolma, J. Coulombe-Huntington, A. Chatr-Aryamontri, K. Dolinski, M. Tyers, The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. 30, 187–200 (2021).

55

J. Xiang, S. Yang, N. Xin, M. A. Gaertig, R. H. Reeves, S. Li, X.-J. Li, DYRK1A regulates Hap1-Dcaf7/WDR68 binding with implication for delayed growth in Down syndrome. Proc. Natl. Acad. Sci. U.S.A. 114, E1224–E1233 (2017).

56

Q. Wang, Z. Geng, Y. Gong, K. Warren, H. Zheng, Y. Imamura, Z. Gao, WDR68 is essential for the transcriptional activation of the PRC1-AUTS2 complex and neuronal differentiation of mouse embryonic stem cells. Stem Cell Res. 33, 206–214 (2018).

57

M. Lasser, N. Sun, Y. Xu, S. Wang, S. Drake, K. Law, S. Gonzalez, B. Wang, V. Drury, O. Castillo, Y. Zaltsman, J. Dea, E. Bader, K. E. McCluskey, M. W. State, A. J. Willsey, H. R. Willsey, Pleiotropy of autism-associated chromatin regulators. Development 150, dev201515 (2023).

58

H. R. Willsey, Y. Xu, A. Everitt, J. Dea, C. R. T. Exner, A. J. Willsey, M. W. State, R. M. Harland, The neurodevelopmental disorder risk gene DYRK1A is required for ciliogenesis and control of brain size in Xenopus embryos. Development 147, dev189290 (2020).

59

A. Jourdon, F. Wu, J. Mariani, D. Capauto, S. Norton, L. Tomasini, A. Amiri, M. Suvakov, J. D. Schreiner, Y. Jang, A. Panda, C. K. Nguyen, E. M. Cummings, G. Han, K. Powell, A. Szekely, J. C. McPartland, K. Pelphrey, K. Chawarska, P. Ventola, A. Abyzov, F. M. Vaccarino, Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis. Nat. Neurosci. 26, 1505–1515 (2023).

60

S. Frendo-Cumbo, T. Li, D. A. Ammendolia, E. Coyaud, E. M. N. Laurent, Y. Liu, P. J. Bilan, G. Polevoy, B. Raught, J. A. Brill, A. Klip, J. H. Brumell, DCAF7 regulates cell proliferation through IRS1-FOXO1 signaling. iScience 25, 105188 (2022).

61

S. Najas, J. Arranz, P. A. Lochhead, A. L. Ashford, D. Oxley, J. M. Delabar, S. J. Cook, M. J. Barallobre, M. L. Arbonés, DYRK1A-mediated cyclin D1 degradation in neural stem cells contributes to the neurogenic cortical defects in Down syndrome. EBioMedicine 2, 120–134 (2015).

62

A. Recasens, S. J. Humphrey, M. Ellis, M. Hoque, R. H. Abbassi, B. Chen, M. Longworth, E. J. Needham, D. E. James, T. G. Johns, B. W. Day, M. Kassiou, P. Yang, L. Munoz, Global phosphoproteomics reveals DYRK1A regulates CDK1 activity in glioblastoma cells. Cell Death Discov. 7, 81 (2021).

63

V. Graham, J. Khudyakov, P. Ellis, L. Pevny, SOX2 functions to maintain neural progenitor identity. Neuron 39, 749–765 (2003).

64

N. C. Hettige, H. Peng, H. Wu, X. Zhang, V. Yerko, Y. Zhang, M. Jefri, V. Soubannier, G. Maussion, S. Alsuwaidi, A. Ni, C. Rocha, J. Krishnan, V. McCarty, L. Antonyan, A. Schuppert, G. Turecki, E. A. Fon, T. M. Durcan, C. Ernst, FOXG1 dose tunes cell proliferation dynamics in human forebrain progenitor cells. Stem Cell Reports 17, 475–488 (2022).

65

S. F. Bellmaine, D. A. Ovchinnikov, D. T. Manallack, C. E. Cuddy, A. G. Elefanty, E. G. Stanley, E. J. Wolvetang, S. J. Williams, M. Pera, Inhibition of DYRK1A disrupts neural lineage specificationin human pluripotent stem cells. eLife 6, e24502 (2017).

66

K. E. Samocha, J. A. Kosmicki, K. J. Karczewski, A. H. O’Donnell-Luria, E. Pierce-Hoffman, D. G. MacArthur, B. M. Neale, M. J. Daly, Regional missense constraint improves variant deleteriousness prediction. bioRxiv 148353 [Preprint] (2017); https://doi.org/10.1101/148353.

67

E. L. Huttlin, L. Ting, R. J. Bruckner, F. Gebreab, M. P. Gygi, J. Szpyt, S. Tam, G. Zarraga, G. Colby, K. Baltier, R. Dong, V. Guarani, L. P. Vaites, A. Ordureau, R. Rad, B. K. Erickson, M. Wühr, J. Chick, B. Zhai, D. Kolippakkam, J. Mintseris, R. A. Obar, T. Harris, S. Artavanis-Tsakonas, M. E. Sowa, P. De Camilli, J. A. Paulo, J. W. Harper, S. P. Gygi, The BioPlex Network: A systematic exploration of the human interactome. Cell 162, 425–440 (2015).

68

M. Y. Hein, N. C. Hubner, I. Poser, J. Cox, N. Nagaraj, Y. Toyoda, I. A. Gak, I. Weisswange, J. Mansfeld, F. Buchholz, A. A. Hyman, M. Mann, A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 163, 712–723 (2015).

69

A. Calderone, L. Castagnoli, G. Cesareni, mentha: A resource for browsing integrated protein-interaction networks. Nat. Methods 10, 690–691 (2013).

70

K. Luck, D.-K. Kim, L. Lambourne, K. Spirohn, B. E. Begg, W. Bian, R. Brignall, T. Cafarelli, F. J. Campos-Laborie, B. Charloteaux, D. Choi, A. G. Coté, M. Daley, S. Deimling, A. Desbuleux, A. Dricot, M. Gebbia, M. F. Hardy, N. Kishore, J. J. Knapp, I. A. Kovács, I. Lemmens, M. W. Mee, J. C. Mellor, C. Pollis, C. Pons, A. D. Richardson, S. Schlabach, B. Teeking, A. Yadav, M. Babor, D. Balcha, O. Basha, C. Bowman-Colin, S.-F. Chin, S. G. Choi, C. Colabella, G. Coppin, C. D’Amata, D. De Ridder, S. De Rouck, M. Duran-Frigola, H. Ennajdaoui, F. Goebels, L. Goehring, A. Gopal, G. Haddad, E. Hatchi, M. Helmy, Y. Jacob, Y. Kassa, S. Landini, R. Li, N. van Lieshout, A. MacWilliams, D. Markey, J. N. Paulson, S. Rangarajan, J. Rasla, A. Rayhan, T. Rolland, A. San-Miguel, Y. Shen, D. Sheykhkarimli, G. M. Sheynkman, E. Simonovsky, M. Taşan, A. Tejeda, V. Tropepe, J.-C. Twizere, Y. Wang, R. J. Weatheritt, J. Weile, Y. Xia, X. Yang, E. Yeger-Lotem, Q. Zhong, P. Aloy, G. D. Bader, J. De Las Rivas, S. Gaudet, T. Hao, J. Rak, J. Tavernier, D. E. Hill, M. Vidal, F. P. Roth, M. A. Calderwood, A reference map of the human binary protein interactome. Nature 580, 402–408 (2020).

71

G. G. Tall, A. M. Krumins, A. G. Gilman, Mammalian Ric-8A (synembryn) is a heterotrimeric Gα protein guanine nucleotide exchange factor. J. Biol. Chem. 278, 8356–8362 (2003).

72

C. A. Pearson, D. M. Moore, H. O. Tucker, J. D. Dekker, H. Hu, A. Miquelajáuregui, B. G. Novitch, Foxp1 regulates neural stem cell self-renewal and bias toward deep layer cortical fates. Cell Rep. 30, 1964–1981.e3 (2020).

73

C. Bacon, M. Schneider, C. Le Magueresse, H. Froehlich, C. Sticht, C. Gluch, H. Monyer, G. A. Rappold, Brain-specific Foxp1 deletion impairs neuronal development and causes autistic-like behaviour. Mol. Psychiatry 20, 632–639 (2015).

74

X. Li, J. Xiao, H. Fröhlich, X. Tu, L. Li, Y. Xu, H. Cao, J. Qu, G. A. Rappold, J.-G. Chen, Foxp1 regulates cortical radial migration and neuronal morphogenesis in developing cerebral cortex. PLOS ONE 10, e0127671 (2015).

75

A. Ortiz, F. Ayhan, N. Khandelwal, E. Outland, M. Jankovic, M. Harper, G. Konopka, Cell type-specific roles of FOXP1 in the excitatory neuronal lineage during early neocortical murine development. Cell Rep. 44, 115384 (2025).

76

T. Kadoshima, H. Sakaguchi, T. Nakano, M. Soen, S. Ando, M. Eiraku, Y. Sasai, Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell-derived neocortex. Proc. Natl. Acad. Sci. U.S.A. 110, 20284–20289 (2013).

77

B. Paulsen, S. Velasco, A. J. Kedaigle, M. Pigoni, G. Quadrato, A. J. Deo, X. Adiconis, A. Uzquiano, R. Sartore, S. M. Yang, S. K. Simmons, P. Symvoulidis, K. Kim, K. Tsafou, A. Podury, C. Abbate, A. Tucewicz, S. N. Smith, A. Albanese, L. Barrett, N. E. Sanjana, X. Shi, K. Chung, K. Lage, E. S. Boyden, A. Regev, J. Z. Levin, P. Arlotta, Autism genes converge on asynchronous development of shared neuron classes. Nature 602, 268–273 (2022).

78

H. R. Willsey, C. R. T. Exner, Y. Xu, A. Everitt, N. Sun, B. Wang, J. Dea, G. Schmunk, Y. Zaltsman, N. Teerikorpi, A. Kim, A. S. Anderson, D. Shin, M. Seyler, T. J. Nowakowski, R. M. Harland, A. J. Willsey, M. W. State, Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron 109, 788–804.e8 (2021).

79

H. S. Kaya-Okur, S. J. Wu, C. A. Codomo, E. S. Pledger, T. D. Bryson, J. G. Henikoff, K. Ahmad, S. Henikoff, CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).

80

D. Trudler, S. Ghatak, M. Bula, J. Parker, M. Talantova, M. Luevanos, S. Labra, T. Grabauskas, S. M. Noveral, M. Teranaka, E. Schahrer, N. Dolatabadi, C. Bakker, K. Lopez, A. Sultan, P. Patel, A. Chan, Y. Choi, R. Kawaguchi, P. Stankiewicz, I. Garcia-Bassets, P. Kozbial, M. G. Rosenfeld, N. Nakanishi, D. H. Geschwind, S. F. Chan, W. Lin, N. J. Schork, R. Ambasudhan, S. A. Lipton, Dysregulation of miRNA expression and excitation in MEF2C autism patient hiPSC-neurons and cerebral organoids. Mol. Psychiatry 30, 1479–1496 (2025).

81

F. P. McCready, K. S. Pradeepan, M. Khaki, W. Wei, M. Guevara-Ferrer, N. Matusiak, B. Feng, A. Piekna, J. Martinez-Trujillo, J. Ellis, Hypersynchronous iPSC-derived SHANK2 neuronal networks are rescued by mGluR5 agonism. Stem Cell Reports 20, 102718 (2025).

82

C. Loveday, K. Tatton-Brown, M. Clarke, I. Westwood, A. Renwick, E. Ramsay, A. Nemeth, J. Campbell, S. Joss, M. Gardner, A. Zachariou, A. Elliott, E. Ruark, R. van Montfort, N. Rahman, Childhood Overgrowth Collaboration, Mutations in the PP2A regulatory subunit B family genes PPP2R5B, PPP2R5C and PPP2R5D cause human overgrowth. Hum. Mol. Genet. 24, 4775–4779 (2015).

83

A. J. Willsey, M. T. Morris, S. Wang, H. R. Willsey, N. Sun, N. Teerikorpi, T. B. Baum, G. Cagney, K. J. Bender, T. A. Desai, D. Srivastava, G. W. Davis, J. Doudna, E. Chang, V. Sohal, D. H. Lowenstein, H. Li, D. Agard, M. J. Keiser, B. Shoichet, M. von Zastrow, L. Mucke, S. Finkbeiner, L. Gan, N. Sestan, M. E. Ward, R. Huttenhain, T. J. Nowakowski, H. J. Bellen, L. M. Frank, M. K. Khokha, R. P. Lifton, M. Kampmann, T. Ideker, M. W. State, N. J. Krogan, The Psychiatric Cell Map Initiative: A convergent systems biological approach to illuminating key molecular pathways in neuropsychiatric disorders. Cell 174, 505–520 (2018).

84

I. Iossifov, B. J. O’Roak, S. J. Sanders, M. Ronemus, N. Krumm, D. Levy, H. A. Stessman, K. T. Witherspoon, L. Vives, K. E. Patterson, J. D. Smith, B. Paeper, D. A. Nickerson, J. Dea, S. Dong, L. E. Gonzalez, J. D. Mandell, S. M. Mane, M. T. Murtha, C. A. Sullivan, M. F. Walker, Z. Waqar, L. Wei, A. J. Willsey, B. Yamrom, Y.-H. Lee, E. Grabowska, E. Dalkic, Z. Wang, S. Marks, P. Andrews, A. Leotta, J. Kendall, I. Hakker, J. Rosenbaum, B. Ma, L. Rodgers, J. Troge, G. Narzisi, S. Yoon, M. C. Schatz, K. Ye, W. R. McCombie, J. Shendure, E. E. Eichler, M. W. State, M. Wigler, The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014).

85

S. J. Sanders, X. He, A. J. Willsey, A. G. Ercan-Sencicek, K. E. Samocha, A. E. Cicek, M. T. Murtha, V. H. Bal, S. L. Bishop, S. Dong, A. P. Goldberg, C. Jinlu, J. F. Keaney III, L. Klei, J. D. Mandell, D. Moreno-De-Luca, C. S. Poultney, E. B. Robinson, L. Smith, T. Solli-Nowlan, M. Y. Su, N. A. Teran, M. F. Walker, D. M. Werling, A. L. Beaudet, R. M. Cantor, E. Fombonne, D. H. Geschwind, D. E. Grice, C. Lord, J. K. Lowe, S. M. Mane, D. M. Martin, E. M. Morrow, M. E. Talkowski, J. S. Sutcliffe, C. A. Walsh, T. W. Yu, D. H. Ledbetter, C. L. Martin, E. H. Cook, J. D. Buxbaum, M. J. Daly, B. Devlin, K. Roeder, M. W. State, Autism Sequencing Consortium, Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron 87, 1215–1233 (2015).

86

S. V. Precious, C. M. Kelly, A. E. Reddington, N. N. Vinh, R. C. Stickland, V. Pekarik, C. Scherf, R. Jeyasingham, J. Glasbey, M. Holeiter, L. Jones, M. V. Taylor, A. E. Rosser, FoxP1 marks medium spiny neurons from precursors to maturity and is required for their differentiation. Exp. Neurol. 282, 9–18 (2016).

87

N. I. Ahmed, N. Khandelwal, A. G. Anderson, E. Oh, R. M. Vollmer, A. Kulkarni, J. R. Gibson, G. Konopka, Compensation between FOXP transcription factors maintains proper striatal function. Cell Rep. 43, 114257 (2024).

88

T. Avino, J. J. Hutsler, Supernumerary neurons within the cerebral cortical subplate in autism spectrum disorders. Brain Res. 1760, 147350 (2021).

89

T. Li, R. Wernersson, R. B. Hansen, H. Horn, J. Mercer, G. Slodkowicz, C. T. Workman, O. Rigina, K. Rapacki, H. H. Stærfeldt, S. Brunak, T. S. Jensen, K. Lage, A scored human protein-protein interaction network to catalyze genomic interpretation. Nat. Methods 14, 61–64 (2017).

90

M. Giurgiu, J. Reinhard, B. Brauner, I. Dunger-Kaltenbach, G. Fobo, G. Frishman, C. Montrone, A. Ruepp, CORUM: The comprehensive resource of mammalian protein complexes-2019. Nucleic Acids Res. 47, D559–D563 (2019).

91

J. Cox, M. Mann, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

92

G. Teo, G. Liu, J. Zhang, A. I. Nesvizhskii, A.-C. Gingras, H. Choi, SAINTexpress: Improvements and additional features in Significance Analysis of INTeractome software. J. Proteomics 100, 37–43 (2014).

93

M. E. Sowa, E. J. Bennett, S. P. Gygi, J. W. Harper, Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389–403 (2009).

95

M. Choi, C.-Y. Chang, T. Clough, D. Broudy, T. Killeen, B. MacLean, O. Vitek, MSstats: An R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 30, 2524–2526 (2014).

96

J. D. Storey, R. Tibshirani, Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U.S.A. 100, 9440–9445 (2003).

97

M. Krzywinski, N. Altman, Comparing samples—Part II. Nat. Methods 11, 355–356 (2014).

98

D. B. Bekker-Jensen, C. D. Kelstrup, T. S. Batth, S. C. Larsen, C. Haldrup, J. B. Bramsen, K. D. Sørensen, S. Høyer, T. F. Ørntoft, C. L. Andersen, M. L. Nielsen, J. V. Olsen, An optimized shotgun strategy for the rapid generation of comprehensive human proteomes. Cell Syst. 4, 587–599.e4 (2017).

99

J. Lonsdale, J. Thomas, M. Salvatore, R. Phillips, E. Lo, S. Shad, R. Hasz, G. Walters, F. Garcia, N. Young, B. Foster, M. Moser, E. Karasik, B. Gillard, K. Ramsey, S. Sullivan, J. Bridge, H. Magazine, J. Syron, J. Fleming, L. Siminoff, H. Traino, M. Mosavel, L. Barker, S. Jewell, D. Rohrer, D. Maxim, D. Filkins, P. Harbach, E. Cortadillo, B. Berghuis, L. Turner, E. Hudson, K. Feenstra, L. Sobin, J. Robb, P. Branton, G. Korzeniewski, C. Shive, D. Tabor, L. Qi, K. Groch, S. Nampally, S. Buia, A. Zimmerman, A. Smith, R. Burges, K. Robinson, K. Valentino, D. Bradbury, M. Cosentino, N. Diaz-Mayoral, M. Kennedy, T. Engel, P. Williams, K. Erickson, K. Ardlie, W. Winckler, G. Getz, D. DeLuca, D. MacArthur, M. Kellis, A. Thomson, T. Young, E. Gelfand, M. Donovan, Y. Meng, G. Grant, D. Mash, Y. Marcus, M. Basile, J. Liu, J. Zhu, Z. Tu, N. J. Cox, D. L. Nicolae, E. R. Gamazon, H. K. Im, A. Konkashbaev, J. Pritchard, M. Stevens, T. Flutre, X. Wen, E. T. Dermitzakis, T. Lappalainen, R. Guigo, J. Monlong, M. Sammeth, D. Koller, A. Battle, S. Mostafavi, M. McCarthy, M. Rivas, J. Maller, I. Rusyn, A. Nobel, F. Wright, A. Shabalin, M. Feolo, N. Sharopova, A. Sturcke, J. Paschal, J. M. Anderson, E. L. Wilder, L. K. Derr, E. D. Green, J. P. Struewing, G. Temple, S. Volpi, J. T. Boyer, E. J. Thomson, M. S. Guyer, C. Ng, A. Abdallah, D. Colantuoni, T. R. Insel, S. E. Koester, A. R. Little, P. K. Bender, T. Lehner, Y. Yao, C. C. Compton, J. B. Vaught, S. Sawyer, N. C. Lockhart, J. Demchok, H. F. Moore, The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580–585 (2013).

100

N. N. Parikshak, R. Luo, A. Zhang, H. Won, J. K. Lowe, V. Chandran, S. Horvath, D. H. Geschwind, Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 155, 1008–1021 (2013).

101

M. Lek, K. J. Karczewski, E. V. Minikel, K. E. Samocha, E. Banks, T. Fennell, A. H. O’Donnell-Luria, J. S. Ware, A. J. Hill, B. B. Cummings, T. Tukiainen, D. P. Birnbaum, J. A. Kosmicki, L. E. Duncan, K. Estrada, F. Zhao, J. Zou, E. Pierce-Hoffman, J. Berghout, D. N. Cooper, N. Deflaux, M. DePristo, R. Do, J. Flannick, M. Fromer, L. Gauthier, J. Goldstein, N. Gupta, D. Howrigan, A. Kiezun, M. I. Kurki, A. L. Moonshine, P. Natarajan, L. Orozco, G. M. Peloso, R. Poplin, M. A. Rivas, V. Ruano-Rubio, S. A. Rose, D. M. Ruderfer, K. Shakir, P. D. Stenson, C. Stevens, B. P. Thomas, G. Tiao, M. T. Tusie-Luna, B. Weisburd, H.-H. Won, D. Yu, D. M. Altshuler, D. Ardissino, M. Boehnke, J. Danesh, S. Donnelly, R. Elosua, J. C. Florez, S. B. Gabriel, G. Getz, S. J. Glatt, C. M. Hultman, S. Kathiresan, M. Laakso, S. McCarroll, M. I. McCarthy, D. McGovern, R. McPherson, B. M. Neale, A. Palotie, S. M. Purcell, D. Saleheen, J. M. Scharf, P. Sklar, P. F. Sullivan, J. Tuomilehto, M. T. Tsuang, H. C. Watkins, J. G. Wilson, M. J. Daly, D. G. MacArthur, Exome Aggregation Consortium, Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016).

102

C. A. Cassa, D. Weghorn, D. J. Balick, D. M. Jordan, D. Nusinow, K. E. Samocha, A. O’Donnell-Luria, D. G. MacArthur, M. J. Daly, D. R. Beier, S. R. Sunyaev, Estimating the selective effects of heterozygous protein-truncating variants from human exome data. Nat. Genet. 49, 806–810 (2017).

103

B. S. Abrahams, D. E. Arking, D. B. Campbell, H. C. Mefford, E. M. Morrow, L. A. Weiss, I. Menashe, T. Wadkins, S. Banerjee-Basu, A. Packer, SFARI Gene 2.0: A community-driven knowledgebase for the autism spectrum disorders (ASDs). Mol. Autism 4, 36 (2013).

104

J. Kaplanis, K. E. Samocha, L. Wiel, Z. Zhang, K. J. Arvai, R. Y. Eberhardt, G. Gallone, S. H. Lelieveld, H. C. Martin, J. F. McRae, P. J. Short, R. I. Torene, E. de Boer, P. Danecek, E. J. Gardner, N. Huang, J. Lord, I. Martincorena, R. Pfundt, M. R. F. Reijnders, A. Yeung, H. G. Yntema, L. E. L. M. Vissers, J. Juusola, C. F. Wright, H. G. Brunner, H. V. Firth, D. R. FitzPatrick, J. C. Barrett, M. E. Hurles, C. Gilissen, K. Retterer, Deciphering Developmental Disorders Study, Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 586, 757–762 (2020).

105

J. Grove, S. Ripke, T. D. Als, M. Mattheisen, R. K. Walters, H. Won, J. Pallesen, E. Agerbo, O. A. Andreassen, R. Anney, S. Awashti, R. Belliveau, F. Bettella, J. D. Buxbaum, J. Bybjerg-Grauholm, M. Bækvad-Hansen, F. Cerrato, K. Chambert, J. H. Christensen, C. Churchhouse, K. Dellenvall, D. Demontis, S. De Rubeis, B. Devlin, S. Djurovic, A. L. Dumont, J. I. Goldstein, C. S. Hansen, M. E. Hauberg, M. V. Hollegaard, S. Hope, D. P. Howrigan, H. Huang, C. M. Hultman, L. Klei, J. Maller, J. Martin, A. R. Martin, J. L. Moran, M. Nyegaard, T. Nærland, D. S. Palmer, A. Palotie, C. B. Pedersen, M. G. Pedersen, T. dPoterba, J. B. Poulsen, B. S. Pourcain, P. Qvist, K. Rehnström, A. Reichenberg, J. Reichert, E. B. Robinson, K. Roeder, P. Roussos, E. Saemundsen, S. Sandin, F. K. Satterstrom, G. Davey Smith, H. Stefansson, S. Steinberg, C. R. Stevens, P. F. Sullivan, P. Turley, G. B. Walters, X. Xu, K. Stefansson, D. H. Geschwind, M. Nordentoft, D. M. Hougaard, T. Werge, O. Mors, P. B. Mortensen, B. M. Neale, M. J. Daly, A. D. Børglum, Autism Spectrum Disorder Working Group of the Psychiatric Genomics Consortium, BUPGEN, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, 23andMe Research Team, Identification of common genetic risk variants for autism spectrum disorder. Nat. Genet. 51, 431–444 (2019).

106

C. A. de Leeuw, J. M. Mooij, T. Heskes, D. Posthuma, MAGMA: Generalized gene-set analysis of GWAS data. PLOS Comput. Biol. 11, e1004219 (2015).

107

M. Mirdita, K. Schütze, Y. Moriwaki, L. Heo, S. Ovchinnikov, M. Steinegger, ColabFold: Making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).

108

J. Jumper, R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, K. Tunyasuvunakool, R. Bates, A. Žídek, A. Potapenko, A. Bridgland, C. Meyer, S. A. A. Kohl, A. J. Ballard, A. Cowie, B. Romera-Paredes, S. Nikolov, R. Jain, J. Adler, T. Back, S. Petersen, D. Reiman, E. Clancy, M. Zielinski, M. Steinegger, M. Pacholska, T. Berghammer, S. Bodenstein, D. Silver, O. Vinyals, A. W. Senior, K. Kavukcuoglu, P. Kohli, D. Hassabis, Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

109

C. B. Pantazis, A. Yang, E. Lara, J. A. McDonough, C. Blauwendraat, L. Peng, H. Oguro, J. Kanaujiya, J. Zou, D. Sebesta, G. Pratt, E. Cross, J. Blockwick, P. Buxton, L. Kinner-Bibeau, C. Medura, C. Tompkins, S. Hughes, M. Santiana, F. Faghri, M. A. Nalls, D. Vitale, S. Ballard, Y. A. Qi, D. M. Ramos, K. M. Anderson, J. Stadler, P. Narayan, J. Papademetriou, L. Reilly, M. P. Nelson, S. Aggarwal, L. U. Rosen, P. Kirwan, V. Pisupati, S. L. Coon, S. W. Scholz, T. Priebe, M. Öttl, J. Dong, M. Meijer, L. J. M. Janssen, V. S. Lourenco, R. van der Kant, D. Crusius, D. Paquet, A.-C. Raulin, G. Bu, A. Held, B. J. Wainger, R. M. C. Gabriele, J. M. Casey, S. Wray, D. Abu-Bonsrah, C. L. Parish, M. S. Beccari, D. W. Cleveland, E. Li, I. V. L. Rose, M. Kampmann, C. Calatayud Aristoy, P. Verstreken, L. Heinrich, M. Y. Chen, B. Schüle, D. Dou, E. L. F. Holzbaur, M. C. Zanellati, R. Basundra, M. Deshmukh, S. Cohen, R. Khanna, M. Raman, Z. S. Nevin, M. Matia, J. Van Lent, V. Timmerman, B. R. Conklin, K. Johnson Chase, K. Zhang, S. Funes, D. A. Bosco, L. Erlebach, M. Welzer, D. Kronenberg-Versteeg, G. Lyu, E. Arenas, E. Coccia, L. Sarrafha, T. Ahfeldt, J. C. Marioni, W. C. Skarnes, M. R. Cookson, M. E. Ward, F. T. Merkle, A reference human induced pluripotent stem cell line for large-scale collaborative studies. Cell Stem Cell 29, 1685–1702.e22 (2022).

110

S. Jäger, N. Gulbahce, P. Cimermancic, J. Kane, N. He, S. Chou, I. D’Orso, J. Fernandes, G. Jang, A. D. Frankel, T. Alber, Q. Zhou, N. J. Krogan, Purification and characterization of HIV-human protein complexes. Methods 53, 13–19 (2011).

111

L. Gheiratmand, E. Coyaud, G. D. Gupta, E. M. Laurent, M. Hasegan, S. L. Prosser, J. Gonçalves, B. Raught, L. Pelletier, Spatial and proteomic profiling reveals centrosome-independent features of centriolar satellites. EMBO J. 38, e101109 (2019).

112

A. C. O’Neill, F. Uzbas, G. Antognolli, F. Merino, K. Draganova, A. Jäck, S. Zhang, G. Pedini, J. P. Schessner, K. Cramer, A. Schepers, F. Metzger, M. Esgleas, P. Smialowski, R. Guerrini, S. Falk, R. Feederle, S. Freytag, Z. Wang, M. Bahlo, R. Jungmann, C. Bagni, G. H. H. Borner, S. P. Robertson, S. M. Hauck, M. Götz, Spatial centrosome proteome of human neural cells uncovers disease-relevant heterogeneity. Science 376, eabf9088 (2022).

113

H. L. Sive, R. M. Grainger, R. M. Harland, Early Development of Xenopus Laevis: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 2000).

114

P. D. Nieuwkoop, Normal Table of Xenopus Laevis (Daudin): A Systematical and Chronological Survey of the Development from the Fertilized Egg Till the End of Metamorphosis (Garland Science, 1994).

115

Y. Qi, X.-J. Zhang, N. Renier, Z. Wu, T. Atkin, Z. Sun, M. Z. Ozair, J. Tchieu, B. Zimmer, F. Fattahi, Y. Ganat, R. Azevedo, N. Zeltner, A. H. Brivanlou, M. Karayiorgou, J. Gogos, M. Tomishima, M. Tessier-Lavigne, S.-H. Shi, L. Studer, Combined small-molecule inhibition accelerates the derivation of functional cortical neurons from human pluripotent stem cells. Nat. Biotechnol. 35, 154–163 (2017).

116

J. W. Linsley, K. Shah, N. Castello, M. Chan, D. Haddad, Z. Doric, S. Wang, W. Leks, J. Mancini, V. Oza, A. Javaherian, K. Nakamura, D. Kokel, S. Finkbeiner, Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration. Nat. Commun. 12, 5284 (2021).

117

M. K. Keaveney, H.-A. Tseng, T. L. Ta, H. J. Gritton, H.-Y. Man, X. Han, A MicroRNA-based gene-targeting tool for virally labeling interneurons in the rodent cortex. Cell Rep. 24, 294–303 (2018).

118

H. Zhang, N. Lu, C. Feng, S. W. Thurston, Y. Xia, L. Zhu, X. M. Tu, On fitting generalized linear mixed-effects models for binary responses using different statistical packages. Stat. Med. 30, 2562–2572 (2011).

119

D. R. Stirling, M. J. Swain-Bowden, A. M. Lucas, A. E. Carpenter, B. A. Cimini, A. Goodman, CellProfiler 4: Improvements in speed, utility and usability. BMC Bioinformatics 22, 433 (2021).

120

M.-G. Shin, N. Amirani, S. Lam, N. Al Bistami, E. Vertudes, K. Raja, J. A. Kaye, R. Thomas, S. Finkbeiner, RMeDPower2 for Biology: guiding design, experimental structure and analyses of repeated measures data for biological studies. bioRxiv 2022.07.18.500490 [Preprint] (2022); https://doi.org/10.1101/2022.07.18.500490.

121

N. Sun, N. Teyssier, B. Wang, S. Drake, M. Seyler, Y. Zaltsman, A. Everitt, N. Teerikorpi, H. R. Willsey, H. Goodarzi, R. Tian, M. Kampmann, A. J. Willsey, Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis. bioRxiv 2023.12.22.573108 [Preprint] (2024); https://doi.org/10.1101/2023.12.22.573108.

122

D. T. Forster, S. C. Li, Y. Yashiroda, M. Yoshimura, Z. Li, L. A. V. Isuhuaylas, K. Itto-Nakama, D. Yamanaka, Y. Ohya, H. Osada, B. Wang, G. D. Bader, C. Boone, BIONIC: Biological network integration using convolutions. Nat. Methods 19, 1250–1261 (2022).

123

F. Zheng, S. Zhang, C. Churas, D. Pratt, I. Bahar, T. Ideker, HiDeF: Identifying persistent structures in multiscale ’omics data. Genome Biol. 22, 21 (2021).

124

J. Dutkowski, M. Kramer, M. A. Surma, R. Balakrishnan, J. M. Cherry, N. J. Krogan, T. Ideker, A gene ontology inferred from molecular networks. Nat. Biotechnol. 31, 38–45 (2013).

125

M. Hu, S. Alkhairy, I. Lee, R. T. Pillich, D. Fong, K. Smith, R. Bachelder, T. Ideker, D. Pratt, Evaluation of large language models for discovery of gene set function. Nat. Methods 22, 82–91 (2025).

126

G. Tesei, T. K. Schulze, R. Crehuet, K. Lindorff-Larsen, Accurate model of liquid-liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties. Proc. Natl. Acad. Sci. U.S.A. 118, e2111696118 (2021).

127

J. Frazer, P. Notin, M. Dias, A. Gomez, J. K. Min, K. Brock, Y. Gal, D. S. Marks, Disease variant prediction with deep generative models of evolutionary data. Nature 599, 91–95 (2021).

128

Y. Matsumoto, Y. Hayashi, C. R. Schlieve, M. Ikeya, H. Kim, T. D. Nguyen, S. Sami, S. Baba, E. Barruet, A. Nasu, I. Asaka, T. Otsuka, S. Yamanaka, B. R. Conklin, J. Toguchida, E. C. Hsiao, Induced pluripotent stem cells from patients with human fibrodysplasia ossificans progressiva show increased mineralization and cartilage formation. Orphanet J. Rare Dis. 8, 190 (2013).

129

Y. Chen, C. A. Tristan, L. Chen, V. M. Jovanovic, C. Malley, P.-H. Chu, S. Ryu, T. Deng, P. Ormanoglu, D. Tao, Y. Fang, J. Slamecka, H. Hong, C. A. LeClair, S. Michael, C. P. Austin, A. Simeonov, I. Singeç, A versatile polypharmacology platform promotes cytoprotection and viability of human pluripotent and differentiated cells. Nat. Methods 18, 528–541 (2021).

130

J. G. Doench, N. Fusi, M. Sullender, M. Hegde, E. W. Vaimberg, K. F. Donovan, I. Smith, Z. Tothova, C. Wilen, R. Orchard, H. W. Virgin, J. Listgarten, D. E. Root, Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).

131

I. C. Clark, K. M. Fontanez, R. H. Meltzer, Y. Xue, C. Hayford, A. May-Zhang, C. D’Amato, A. Osman, J. Q. Zhang, P. Hettige, J. S. A. Ishibashi, C. L. Delley, D. W. Weisgerber, J. M. Replogle, M. Jost, K. T. Phong, V. E. Kennedy, C. A. C. Peretz, E. A. Kim, S. Song, W. Karlon, J. S. Weissman, C. C. Smith, Z. J. Gartner, A. R. Abate, Microfluidics-free single-cell genomics with templated emulsification. Nat. Biotechnol. 41, 1557–1566 (2023).

132

C. S. Cutts, S. J. Eglen, Detecting pairwise correlations in spike trains: An objective comparison of methods and application to the study of retinal waves. J. Neurosci. 34, 14288–14303 (2014).