DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders

Lessel, I; Baresic, A; Chinn, IK; May, J; Goenka, A; Chandler, KE; Posey, JE; Afenjar, A; Averdunk, L; Bedeschi, MF; Besnard, T; Brager, R; Brick, L; Brugger, M; Brunet, T; Byrne, S; de la Calle-Martín, O; Capra, V; Cardenas, P; Chappé, C; Chong, HJ; Cogne, B; Conboy, E; Cope, H; Courtin, T; Deb, W; Dilena, R; Dubourg, C; Elgizouli, M; Fernandes, E; Fitzgerald, KK; Gangi, S; George-Abraham, JK; Gucsavas-Calikoglu, M; Haack, TB; Hadonou, M; Hanker, B; Hüning, I; Iascone, M; Isidor, B; Järvelä, I; Jin, JJ; Jorge, AAL; Josifova, D; Kalinauskiene, R; Kamsteeg, EJ; Keren, B; Kessler, E; Kölbel, H; Kozenko, M; Kubisch, C; Kuechler, A; Leal, SM; Leppälä, J; Luu, SM; Lyon, GJ; Madan-Khetarpal, S; Mancardi, M; Marchi, E; Mehta, L; Menendez, B; Morel, CF; Harasink, SM; Nevay, DL; Nigro, V; Odent, S; Oegema, R; Pappas, J; Pastore, MT; Perilla-Young, Y; Platzer, K; Powell-Hamilton, N; Rabin, R; Rekab, A; Rezende, RC; Robert, L; Romano, F; Scala, M; Poths, K; Schrauwen, I; Sebastian, J; Short, J; Sidlow, R; Sullivan, J; Szakszon, K; Tan, QKG; Wagner, M; Wieczorek, D; Yuan, B; Maeding, N; Strunk, D; Begtrup, A; Banka, S; Lupski, JR; Tolosa, E; Lessel, D (2025) DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders. The American Journal of Human Genetics, 112 (2). pp. 394-413. ISSN 00029297

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Abstract

BCL11B is a Cys2-His2 zinc-finger (C2H2-ZnF) domain-containing, DNA-binding, transcription factor with established roles in the development of various organs and tissues, primarily the immune and nervous systems. BCL11B germline variants have been associated with a variety of developmental syndromes. However, genotype-phenotype correlations along with pathophysiologic mechanisms of selected variants mostly remain elusive. To dissect these, we performed genotype-phenotype correlations of 92 affected individuals harboring a pathogenic or likely pathogenic BCL11B variant, followed by immune phenotyping, analysis of chromatin immunoprecipitation DNA-sequencing data, dual-luciferase reporter assays, and molecular modeling. These integrative analyses enabled us to define three clinical subtypes of BCL11B-related disorders. It is likely that gene-disruptive BCL11B variants and missense variants affecting zincbinding cysteine and histidine residues cause mild to moderate neurodevelopmental delay with increased propensity for behavioral and dental anomalies, allergies and asthma, and reduced type 2 innate lymphoid cells. Missense variants within C2H2-ZnF DNA-contacting a helices cause highly variable clinical presentations ranging from multisystem anomalies with demise in the first years of life to lateonset, hyperkinetic movement disorder with poor fine motor skills. Those not in direct DNA contact cause a milder phenotype through reduced, target-specific transcriptional activity. However, missense variants affecting C2H2-ZnFs, DNA binding, and ''specificity residues'' impair BCL11B transcriptional activity in a target-specific, dominant-negative manner along with aberrant regulation of alternative DNA targets, resulting in more severe and unpredictable clinical outcomes. Taken together, we suggest that the phenotypic severity and variability is largely dependent on the DNA-binding affinity and specificity of altered BCL11B proteins.

Item Type:	Article
Uncontrolled Keywords:	BCL11B; C2H2-type zinc finger protein; recognition code; genotype-phenotype correlation; type 2 innate lymphoid cells
Subjects:	BIOMEDICINE AND HEALTHCARE > Basic Medical Sciences
Divisions:	Division of Electronics
Depositing User:	Ema Buhin Šaler
Date Deposited:	25 Mar 2026 07:28
URI:	http://fulir.irb.hr/id/eprint/11454
DOI:	10.1016/j.ajhg.2024.12.012

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