Alfredo M. Valencia

All Publications

• Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders. Nature genetics Valencia, A. M., Sankar, A., van der Sluijs, P. J., Satterstrom, F. K., Fu, J., Talkowski, M. E., Vergano, S. A., Santen, G. W., Kadoch, C. 2023

  Abstract

  DNA sequencing-based studies of neurodevelopmental disorders (NDDs) have identified a wide range of genetic determinants. However, a comprehensive analysis of these data, in aggregate, has not to date been performed. Here, we find that genes encoding the mammalian SWI/SNF (mSWI/SNF or BAF) family of ATP-dependent chromatin remodeling protein complexes harbor the greatest number of de novo missense and protein-truncating variants among nuclear protein complexes. Non-truncating NDD-associated protein variants predominantly disrupt the cBAF subcomplex and cluster in four key structural regions associated with high disease severity, including mSWI/SNF-nucleosome interfaces, the ATPase-core ARID-armadillo repeat (ARM) module insertion site, the Arp module and DNA-binding domains. Although over 70% of the residues perturbed in NDDs overlap with those mutated in cancer, ~60% of amino acid changes are NDD-specific. These findings provide a foundation to functionally group variants and link complex aberrancies to phenotypic severity, serving as a resource for the chromatin, clinical genetics and neurodevelopment communities.

  View details for DOI 10.1038/s41588-023-01451-6

  View details for PubMedID 37500730

• Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence. Cancer cell Belk, J. A., Yao, W., Ly, N., Freitas, K. A., Chen, Y. T., Shi, Q., Valencia, A. M., Shifrut, E., Kale, N., Yost, K. E., Duffy, C. V., Daniel, B., Hwee, M. A., Miao, Z., Ashworth, A., Mackall, C. L., Marson, A., Carnevale, J., Vardhana, S. A., Satpathy, A. T. 2022

  Abstract

  T cell exhaustion limits antitumor immunity, but the molecular determinants of this process remain poorly understood. Using a chronic stimulation assay, we performed genome-wide CRISPR-Cas9 screens to systematically discover regulators of T cell exhaustion, which identified an enrichment of epigenetic factors. In vivo CRISPR screens in murine and human tumor models demonstrated that perturbation of the INO80 and BAF chromatin remodeling complexes improved T cell persistence in tumors. In vivo Perturb-seq revealed distinct transcriptional roles of each complex and that depletion of canonical BAF complex members, including Arid1a, resulted in the maintenance of an effector program and downregulation of exhaustion-related genes in tumor-infiltrating T cells. Finally, Arid1a depletion limited the acquisition of exhaustion-associated chromatin accessibility and led to improved antitumor immunity. In summary, we provide an atlas of the genetic regulators of T cell exhaustion and demonstrate that modulation of epigenetic state can improve T cell responses in cancer immunotherapy.

  View details for DOI 10.1016/j.ccell.2022.06.001

  View details for PubMedID 35750052

• Chromatin dynamics in human brain development and disease. Trends in cell biology Valencia, A. M., Pașca, S. P. 2021

  Abstract

  Chromatin-related genes are frequently mutated in neurodevelopmental disorders; yet, the mechanisms by which these perturbations disrupt brain assembly and function are not understood. Here, we describe how recent advances in transcriptional and chromatin profiling in combination with cellular models are beginning to inform our understanding of neurodevelopment and chromatinopathies.

  View details for DOI 10.1016/j.tcb.2021.09.001

  View details for PubMedID 34610892

• Long-term maturation of human cortical organoids matches key early postnatal transitions. Nature neuroscience Gordon, A. n., Yoon, S. J., Tran, S. S., Makinson, C. D., Park, J. Y., Andersen, J. n., Valencia, A. M., Horvath, S. n., Xiao, X. n., Huguenard, J. R., Pașca, S. P., Geschwind, D. H. 2021

  Abstract

  Human stem-cell-derived models provide the promise of accelerating our understanding of brain disorders, but not knowing whether they possess the ability to mature beyond mid- to late-fetal stages potentially limits their utility. We leveraged a directed differentiation protocol to comprehensively assess maturation in vitro. Based on genome-wide analysis of the epigenetic clock and transcriptomics, as well as RNA editing, we observe that three-dimensional human cortical organoids reach postnatal stages between 250 and 300 days, a timeline paralleling in vivo development. We demonstrate the presence of several known developmental milestones, including switches in the histone deacetylase complex and NMDA receptor subunits, which we confirm at the protein and physiological levels. These results suggest that important components of an intrinsic in vivo developmental program persist in vitro. We further map neurodevelopmental and neurodegenerative disease risk genes onto in vitro gene expression trajectories to provide a resource and webtool (Gene Expression in Cortical Organoids, GECO) to guide disease modeling.

  View details for DOI 10.1038/s41593-021-00802-y

  View details for PubMedID 33619405

• Dissecting the molecular basis of human interneuron migration in forebrain assembloids from Timothy syndrome. Cell stem cell Birey, F., Li, M. Y., Gordon, A., Thete, M. V., Valencia, A. M., Revah, O., Paşca, A. M., Geschwind, D. H., Paşca, S. P. 2021

  Abstract

  Defects in interneuron migration can disrupt the assembly of cortical circuits and lead to neuropsychiatric disease. Using forebrain assembloids derived by integration of cortical and ventral forebrain organoids, we have previously discovered a cortical interneuron migration defect in Timothy syndrome (TS), a severe neurodevelopmental disease caused by a mutation in the L-type calcium channel (LTCC) Cav1.2. Here, we find that acute pharmacological modulation of Cav1.2 can regulate the saltation length, but not the frequency, of interneuron migration in TS. Interestingly, the defect in saltation length is related to aberrant actomyosin and myosin light chain (MLC) phosphorylation, while the defect in saltation frequency is driven by enhanced γ-aminobutyric acid (GABA) sensitivity and can be restored by GABA-A receptor antagonism. Finally, we describe hypersynchronous hCS network activity in TS that is exacerbated by interneuron migration. Taken together, these studies reveal a complex role of LTCC function in human cortical interneuron migration and strategies to restore deficits in the context of disease.

  View details for DOI 10.1016/j.stem.2021.11.011

  View details for PubMedID 34990580

• BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms AMERICAN JOURNAL OF HUMAN GENETICS Barish, S., Barakat, T., Michel, B. C., Mashtalir, N., Phillips, J. B., Valencia, A. M., Ugur, B., Wegner, J., Scott, T. M., Bostwick, B., Murdock, D. R., Dai, H., Perenthaler, E., Nikoncuk, A., van Slegtenhorst, M., Brooks, A. S., Keren, B., Nava, C., Mignot, C., Douglas, J., Rodan, L., Nowak, C., Ellard, S., Stals, K., Lynch, S., Faoucher, M., Lesca, G., Edery, P., Engleman, K. L., Zhou, D., Thiffault, I., Herriges, J., Gass, J., Louie, R. J., Stolerman, E., Washington, C., Vetrini, F., Otsubo, A., Pratt, V. M., Conboy, E., Treat, K., Shannon, N., Camacho, J., Wakeling, E., Yuan, B., Chen, C., Rosenfeld, J. A., Westerfield, M., Wangler, M., Yamamoto, S., Kadoch, C., Scott, D. A., Bellen, H. J., Undiagnosed Dis Network 2020; 107 (6): 1096–1112

  Abstract

  SWI/SNF-related intellectual disability disorders (SSRIDDs) are rare neurodevelopmental disorders characterized by developmental disability, coarse facial features, and fifth digit/nail hypoplasia that are caused by pathogenic variants in genes that encode for members of the SWI/SNF (or BAF) family of chromatin remodeling complexes. We have identified 12 individuals with rare variants (10 loss-of-function, 2 missense) in the BICRA (BRD4 interacting chromatin remodeling complex-associated protein) gene, also known as GLTSCR1, which encodes a subunit of the non-canonical BAF (ncBAF) complex. These individuals exhibited neurodevelopmental phenotypes that include developmental delay, intellectual disability, autism spectrum disorder, and behavioral abnormalities as well as dysmorphic features. Notably, the majority of individuals lack the fifth digit/nail hypoplasia phenotype, a hallmark of most SSRIDDs. To confirm the role of BICRA in the development of these phenotypes, we performed functional characterization of the zebrafish and Drosophila orthologs of BICRA. In zebrafish, a mutation of bicra that mimics one of the loss-of-function variants leads to craniofacial defects possibly akin to the dysmorphic facial features seen in individuals harboring putatively pathogenic BICRA variants. We further show that Bicra physically binds to other non-canonical ncBAF complex members, including the BRD9/7 ortholog, CG7154, and is the defining member of the ncBAF complex in flies. Like other SWI/SNF complex members, loss of Bicra function in flies acts as a dominant enhancer of position effect variegation but in a more context-specific manner. We conclude that haploinsufficiency of BICRA leads to a unique SSRIDD in humans whose phenotypes overlap with those previously reported.

  View details for DOI 10.1016/j.ajhg.2020.11.003

  View details for Web of Science ID 000596042000006

  View details for PubMedID 33232675

  View details for PubMedCentralID PMC7820627

• A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms CELL Mashtalir, N., Suzuki, H., Farrell, D. P., Sankar, A., Luo, J., Filipovski, M., D'Avino, A. R., St Pierre, R., Valencia, A. M., Onikubo, T., Roeder, R. G., Han, Y., He, Y., Ranish, J. A., DiMaio, F., Walz, T., Kadoch, C. 2020; 183 (3): 802-+

  Abstract

  Mammalian SWI/SNF complexes are ATP-dependent chromatin remodeling complexes that regulate genomic architecture. Here, we present a structural model of the endogenously purified human canonical BAF complex bound to the nucleosome, generated using cryoelectron microscopy (cryo-EM), cross-linking mass spectrometry, and homology modeling. BAF complexes bilaterally engage the nucleosome H2A/H2B acidic patch regions through the SMARCB1 C-terminal α-helix and the SMARCA4/2 C-terminal SnAc/post-SnAc regions, with disease-associated mutations in either causing attenuated chromatin remodeling activities. Further, we define changes in BAF complex architecture upon nucleosome engagement and compare the structural model of endogenous BAF to those of related SWI/SNF-family complexes. Finally, we assign and experimentally interrogate cancer-associated hot-spot mutations localizing within the endogenous human BAF complex, identifying those that disrupt BAF subunit-subunit and subunit-nucleosome interfaces in the nucleosome-bound conformation. Taken together, this integrative structural approach provides important biophysical foundations for understanding the mechanisms of BAF complex function in normal and disease states.

  View details for DOI 10.1016/j.cell.2020.09.051

  View details for Web of Science ID 000583031600027

  View details for PubMedID 33053319

  View details for PubMedCentralID PMC7717177

• The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma. Nature structural & molecular biology McBride, M. J., Mashtalir, N., Winter, E. B., Dao, H. T., Filipovski, M., D'Avino, A. R., Seo, H. S., Umbreit, N. T., St Pierre, R., Valencia, A. M., Qian, K., Zullow, H. J., Jaffe, J. D., Dhe-Paganon, S., Muir, T. W., Kadoch, C. 2020; 27 (9): 836-845

  Abstract

  Interactions between chromatin-associated proteins and the histone landscape play major roles in dictating genome topology and gene expression. Cancer-specific fusion oncoproteins, which display unique chromatin localization patterns, often lack classical DNA-binding domains, presenting challenges in identifying mechanisms governing their site-specific chromatin targeting and function. Here we identify a minimal region of the human SS18-SSX fusion oncoprotein (the hallmark driver of synovial sarcoma) that mediates a direct interaction between the mSWI/SNF complex and the nucleosome acidic patch. This binding results in altered mSWI/SNF composition and nucleosome engagement, driving cancer-specific mSWI/SNF complex targeting and gene expression. Furthermore, the C-terminal region of SSX confers preferential affinity to repressed, H2AK119Ub-marked nucleosomes, underlying the selective targeting to polycomb-marked genomic regions and synovial sarcoma-specific dependency on PRC1 function. Together, our results describe a functional interplay between a key nucleosome binding hub and a histone modification that underlies the disease-specific recruitment of a major chromatin remodeling complex.

  View details for DOI 10.1038/s41594-020-0466-9

  View details for PubMedID 32747783

• Recurrent SMARCB1 Mutations Reveal a Nucleosome Acidic Patch Interaction Site That Potentiates mSWI/SNF Complex Chromatin Remodeling. Cell Valencia, A. M., Collings, C. K., Dao, H. T., St Pierre, R., Cheng, Y. C., Huang, J., Sun, Z. Y., Seo, H. S., Mashtalir, N., Comstock, D. E., Bolonduro, O., Vangos, N. E., Yeoh, Z. C., Dornon, M. K., Hermawan, C., Barrett, L., Dhe-Paganon, S., Woolf, C. J., Muir, T. W., Kadoch, C. 2019; 179 (6): 1342-1356.e23

  Abstract

  Mammalian switch/sucrose non-fermentable (mSWI/SNF) complexes are multi-component machines that remodel chromatin architecture. Dissection of the subunit- and domain-specific contributions to complex activities is needed to advance mechanistic understanding. Here, we examine the molecular, structural, and genome-wide regulatory consequences of recurrent, single-residue mutations in the putative coiled-coil C-terminal domain (CTD) of the SMARCB1 (BAF47) subunit, which cause the intellectual disability disorder Coffin-Siris syndrome (CSS), and are recurrently found in cancers. We find that the SMARCB1 CTD contains a basic α helix that binds directly to the nucleosome acidic patch and that all CSS-associated mutations disrupt this binding. Furthermore, these mutations abrogate mSWI/SNF-mediated nucleosome remodeling activity and enhancer DNA accessibility without changes in genome-wide complex localization. Finally, heterozygous CSS-associated SMARCB1 mutations result in dominant gene regulatory and morphologic changes during iPSC-neuronal differentiation. These studies unmask an evolutionarily conserved structural role for the SMARCB1 CTD that is perturbed in human disease.

  View details for DOI 10.1016/j.cell.2019.10.044

  View details for PubMedID 31759698

  View details for PubMedCentralID PMC7175411

• Chromatin regulatory mechanisms and therapeutic opportunities in cancer. Nature cell biology Valencia, A. M., Kadoch, C. 2019; 21 (2): 152-161

  Abstract

  Research over the past several decades has unmasked a major contribution of disrupted chromatin regulatory processes to human disease, particularly cancer. Advances in genome-wide technologies have highlighted frequent mutations in genes encoding chromatin-associated proteins, identified unexpected synthetic lethal opportunities and enabled increasingly comprehensive structural and functional dissection. Here, we review recent progress in our understanding of oncogenic mechanisms at each level of chromatin organization and regulation, and discuss new strategies towards therapeutic intervention.

  View details for DOI 10.1038/s41556-018-0258-1

  View details for PubMedID 30602726

  View details for PubMedCentralID PMC6755910

• A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation NATURE CELL BIOLOGY Michel, B. C., D'Avino, A. R., Cassel, S. H., Mashtalir, N., McKenzie, Z. M., McBride, M. J., Valencia, A. M., Zhou, Q., Bocker, M., Soares, L. M., Pan, J., Remillard, D. I., Lareau, C. A., Zullow, H. J., Fortoul, N., Gray, N. S., Bradner, J. E., Chan, H., Kadoch, C. 2018; 20 (12): 1410-+

  Abstract

  Mammalian SWI/SNF chromatin remodelling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF and a newly characterized non-canonical complex (ncBAF). However, their complex-specific targeting on chromatin, functions and roles in disease remain largely undefined. Here, we comprehensively mapped complex assemblies on chromatin and found that ncBAF complexes uniquely localize to CTCF sites and promoters. We identified ncBAF subunits as synthetic lethal targets specific to synovial sarcoma and malignant rhabdoid tumours, which both exhibit cBAF complex (SMARCB1 subunit) perturbation. Chemical and biological depletion of the ncBAF subunit, BRD9, rapidly attenuates synovial sarcoma and malignant rhabdoid tumour cell proliferation. Importantly, in cBAF-perturbed cancers, ncBAF complexes maintain gene expression at retained CTCF-promoter sites and function in a manner distinct from fusion oncoprotein-bound complexes. Together, these findings unmask the unique targeting and functional roles of ncBAF complexes and present new cancer-specific therapeutic targets.

  View details for DOI 10.1038/s41556-018-0221-1

  View details for Web of Science ID 000451328500013

  View details for PubMedID 30397315

  View details for PubMedCentralID PMC6698386

• Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes. Cell Mashtalir, N., D'Avino, A. R., Michel, B. C., Luo, J., Pan, J., Otto, J. E., Zullow, H. J., McKenzie, Z. M., Kubiak, R. L., St Pierre, R., Valencia, A. M., Poynter, S. J., Cassel, S. H., Ranish, J. A., Kadoch, C. 2018; 175 (5): 1272-1288.e20

  Abstract

  Mammalian SWI/SNF (mSWI/SNF) ATP-dependent chromatin remodeling complexes are multi-subunit molecular machines that play vital roles in regulating genomic architecture and are frequently disrupted in human cancer and developmental disorders. To date, the modular organization and pathways of assembly of these chromatin regulators remain unknown, presenting a major barrier to structural and functional determination. Here, we elucidate the architecture and assembly pathway across three classes of mSWI/SNF complexes-canonical BRG1/BRM-associated factor (BAF), polybromo-associated BAF (PBAF), and newly defined ncBAF complexes-and define the requirement of each subunit for complex formation and stability. Using affinity purification of endogenous complexes from mammalian and Drosophila cells coupled with cross-linking mass spectrometry (CX-MS) and mutagenesis, we uncover three distinct and evolutionarily conserved modules, their organization, and the temporal incorporation of these modules into each complete mSWI/SNF complex class. Finally, we map human disease-associated mutations within subunits and modules, defining specific topological regions that are affected upon subunit perturbation.

  View details for DOI 10.1016/j.cell.2018.09.032

  View details for PubMedID 30343899

  View details for PubMedCentralID PMC6791824

• SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nature genetics Nakayama, R. T., Pulice, J. L., Valencia, A. M., McBride, M. J., McKenzie, Z. M., Gillespie, M. A., Ku, W. L., Teng, M., Cui, K., Williams, R. T., Cassel, S. H., Qing, H., Widmer, C. J., Demetri, G. D., Irizarry, R. A., Zhao, K., Ranish, J. A., Kadoch, C. 2017; 49 (11): 1613-1623

  Abstract

  Perturbations to mammalian SWI/SNF (mSWI/SNF or BAF) complexes contribute to more than 20% of human cancers, with driving roles first identified in malignant rhabdoid tumor, an aggressive pediatric cancer characterized by biallelic inactivation of the core BAF complex subunit SMARCB1 (BAF47). However, the mechanism by which this alteration contributes to tumorigenesis remains poorly understood. We find that BAF47 loss destabilizes BAF complexes on chromatin, absent significant changes in complex assembly or integrity. Rescue of BAF47 in BAF47-deficient sarcoma cell lines results in increased genome-wide BAF complex occupancy, facilitating widespread enhancer activation and opposition of Polycomb-mediated repression at bivalent promoters. We demonstrate differential regulation by two distinct mSWI/SNF assemblies, BAF and PBAF complexes, enhancers and promoters, respectively, suggesting that each complex has distinct functions that are perturbed upon BAF47 loss. Our results demonstrate collaborative mechanisms of mSWI/SNF-mediated gene activation, identifying functions that are co-opted or abated to drive human cancers and developmental disorders.

  View details for DOI 10.1038/ng.3958

  View details for PubMedID 28945250

  View details for PubMedCentralID PMC5803080