Francois Guillemot & Deepak Srivastava

 

Studying the role of the BAF chromatin remodelling complex in intellectual disability using human induced pluripotent stem cells

Joint Crick/King's College London position

Perturbation of brain development and function has a significant impact on families and communities. The most common presentation is intellectual disability (ID), characterised by the impairment of general mental abilities that impact adaptive functioning in conceptual, social and practical domains, affecting up to 3% of individuals in the general population. One third of individuals with ID also have autism spectrum disorder, underlining the important overlap of neurodevelopmental disorders.

It is estimated that approximately 60% of individuals with ID have an identifiable genetic cause. These include chromosomal abnormalities as well as mutations in specific genes. Interestingly, many of the genes mutated in ID regulate the transcription of other genes. Heterozygous de novo mutations (i.e., on one of the 2 copies of the gene in the patient but not in parents) in several genes encoding for components of the BAF complex and related proteins have been described in patients with syndromic and non-syndromic ID (with or without associated recognizable physical features and/or congenital anomalies respectively)1. We recently described a novel disorder (OMIM# 617101) caused by missense and loss of function mutations in BCL11A, a transcription factor associated with the BAF complex2. Overall, mutations in this complex are estimated to account for up to 1% of all cases of de novo mutation in ID1. The BAF or swi/snf complex is involved in chromatin remodelling, a process that regulates how the genome is made accessible to the cellular machinery that controls gene expression3. Determining the mechanisms underlying a common cause of ID will provide insights into human neurodevelopment and cognition. We currently do not understand how components of the BAF complex influence human neurodevelopment and moreover, how perturbations in these processes may contribute to ID.

Recent advances in stem cell biology now allow us to study early neurodevelopment in human neural cell cultures. Induced pluripotent stem cells (iPSCs) are capable of recapitulating early hallmarks of human neurodevelopment4. This cellular system, in combination with genome editing technologies, such as CRISPR/Cas9, have become powerful tools to study cellular mechanisms that are relevant to disease4,5. In this project, we propose to generate and characterise patient-specific iPSCs derived from individuals diagnosed with ID and whom harbour mutations within the BAF complex. In addition, we will utilize a CRISPR/Cas9 genome editing approach to 'correct' disease-causing mutations in specific components of the BAF complex in the patient-specific iPSCs.  Subsequently, we will differentiate iPSCs through the early stages of neurodevelopment using both 2D and 3D culture systems. This approach will allow us to identify aberrant processes during early neural development that might contribute to ID, as well as to perform unbiased transcriptomic approaches to begin to dissect the underlying molecular mechanisms contributing to these abnormal processes. Furthermore, the use of genome-edited patient-specific iPSCs will allow a direct determination of how mutations in different subunits of the BAF complex may contribute to these related phenotypes.

1. Deciphering Developmental Disorders Study (2017)
Prevalence and architecture of de novo mutations in developmental disorders.
Nature  542: 433-438. PubMed abstract

2. Dias, C., Estruch, S. B., Graham, S. A., McRae, J., Sawiak, S. J., Hurst, J. A., Joss, S. K., Holder, S. E., Morton, J. E. V., Turner, C., Thevenon, J., Mellul, K., Sánchez-Andrade, G., Ibarra-Soria, X., Deriziotis, P., Santos, R. F., Lee, S.-C., Faivre, L., Kleefstra, T., Liu, P., Hurles, M. E., DDD Study, Fisher, S. E. and Logan, D. W. (2016)
BCL11A haploinsufficiency causes an intellectual disability syndrome and dysregulates transcription.
American Journal of Human Genetics  99: 253-274. PubMed abstract

3. Kadoch, C. and Crabtree, G. R. (2015)
Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics.
Science advances  1: e1500447. PubMed abstract

4. Deans, P. J. M., Raval, P., Sellers, K. J., Gatford, N. J. F., Halai, S., Duarte, R. R. R., Shum, C., Warre-Cornish, K., Kaplun, V. E., Cocks, G., Hill, M., Bray, N. J., Price, J. and Srivastava, D. P. (2017)
Psychosis risk candidate ZNF804A localizes to synapses and regulates neurite formation and dendritic spine structure.
Biological Psychiatry 82: 49-61. PubMed abstract

5. Dias, C. and Guillemot, F. (2017)
Revealing the inner workings of organoids.
EMBO Journal  36: 1299-1301. PubMed abstract