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Genetic variations underlying susceptibility to complex autoimmune and allergic diseases are concentrated within noncoding regulatory elements termed enhancers 1 . The functions of a large majority of disease-associated enhancers are unknown, in part owing to their distance from the genes they regulate, a lack of understanding of the cell types in which they operate, and our inability to recapitulate the biology of immune diseases in vitro. Here, using shared synteny to guide loss-of-function analysis of homologues of human enhancers in mice, we show that the prominent autoimmune and allergic disease risk locus at chromosome 11q13.5 2 – 7 contains a distal enhancer that is functional in CD4 + regulatory T (T reg ) cells and required for T reg -mediated suppression of colitis. The enhancer recruits the transcription factors STAT5 and NF-κB to mediate signal-driven expression of Lrrc32 , which encodes the protein glycoprotein A repetitions predominant (GARP). Whereas disruption of the Lrrc32 gene results in early lethality, mice lacking the enhancer are viable but lack GARP expression in Foxp3 + T reg cells, which are unable to control colitis in a cell-transfer model of the disease. In human T reg cells, the enhancer forms conformational interactions with the promoter of LRRC32 and enhancer risk variants are associated with reduced histone acetylation and GARP expression. Finally, functional fine-mapping of 11q13.5 using CRISPR-activation (CRISPRa) identifies a CRISPRa-responsive element in the vicinity of risk variant rs11236797 capable of driving GARP expression. These findings provide a mechanistic basis for association of the 11q13.5 risk locus with immune-mediated diseases and identify GARP as a potential target in their therapy. Shared synteny guides loss-of-function analysis of human enhancer homologues in mice, identifying a distal enhancer at the autoimmune and allergic disease risk locus at chromosome 11q13.5 whose function in regulatory T cells provides a mechanistic basis for its role in disease.

During B cell development, cells that fail to productively rearrange their immunoglobulin VH-DJH gene segments to generate an in-frame junction that codes for a functional pre-B cell receptor are deleted. Markus Müschen and colleagues now report that Bach2 is a key component of this pre-B cell receptor checkpoint that enables the elimination of normal and transformed B cells with nonfunctional V(D)J rearrangements by regulating the expression of p53. The B cell–specific transcription factor BACH2 is required for affinity maturation of B cells. Here we show that Bach2-mediated activation of p53 is required for stringent elimination of pre-B cells that failed to productively rearrange immunoglobulin V H -DJ H gene segments. After productive V H -DJ H gene rearrangement, pre-B cell receptor signaling ends BACH2-mediated negative selection through B cell lymphoma 6 (BCL6)-mediated repression of p53. In patients with pre-B acute lymphoblastic leukemia, the BACH2-mediated checkpoint control is compromised by deletions, rare somatic mutations and loss of its upstream activator, PAX5. Low levels of BACH2 expression in these patients represent a strong independent predictor of poor clinical outcome. In this study, we demonstrate that Bach2 +/+ pre-B cells resist leukemic transformation by Myc through Bach2-dependent upregulation of p53 and do not initiate fatal leukemia in transplant-recipient mice. Chromatin immunoprecipitation sequencing and gene expression analyses carried out by us revealed that BACH2 competes with BCL6 for promoter binding and reverses BCL6-mediated repression of p53 and other cell cycle checkpoint–control genes. These findings identify BACH2 as a crucial mediator of negative selection at the pre-B cell receptor checkpoint and a safeguard against leukemogenesis.

The chemotherapeutic agent CX-5461, or pidnarulex, has been fast-tracked by the United States Food and Drug Administration for early-stage clinical studies of BRCA1- , BRCA2- and PALB2 -mutated cancers. It is under investigation in phase I and II trials. Here, we find that, although CX-5461 exhibits synthetic lethality in BRCA1-/BRCA2 -deficient cells, it also causes extensive, nonselective, collateral mutagenesis in all three cell lines tested, to magnitudes that exceed known environmental carcinogens. The chemotherapeutic agent CX-5461 is shown to be a potent mutagen in hTERT-RPE1, HAP1 and human induced pluripotent stem cells. The compound generates distinct mutational patterns of single- and double-base substitutions, as well as of small insertions and deletions, that were detectable following a single exposure.

Genetic variations underlying susceptibility to complex autoimmune and allergic diseases are concentrated within noncoding regulatory elements termed enhancers . The functions of a large majority of disease-associated enhancers are unknown, in part owing to their distance from the genes they regulate, a lack of understanding of the cell types in which they operate, and our inability to recapitulate the biology of immune diseases in vitro. Here, using shared synteny to guide loss-of-function analysis of homologues of human enhancers in mice, we show that the prominent autoimmune and allergic disease risk locus at chromosome 11q13.5 contains a distal enhancer that is functional in CD4 regulatory T (T ) cells and required for T -mediated suppression of colitis. The enhancer recruits the transcription factors STAT5 and NF-κB to mediate signal-driven expression of Lrrc32, which encodes the protein glycoprotein A repetitions predominant (GARP). Whereas disruption of the Lrrc32 gene results in early lethality, mice lacking the enhancer are viable but lack GARP expression in Foxp3 T cells, which are unable to control colitis in a cell-transfer model of the disease. In human T cells, the enhancer forms conformational interactions with the promoter of LRRC32 and enhancer risk variants are associated with reduced histone acetylation and GARP expression. Finally, functional fine-mapping of 11q13.5 using CRISPR-activation (CRISPRa) identifies a CRISPRa-responsive element in the vicinity of risk variant rs11236797 capable of driving GARP expression. These findings provide a mechanistic basis for association of the 11q13.5 risk locus with immune-mediated diseases and identify GARP as a potential target in their therapy.

T cells coordinate immune functions by differentiating into highly specialised cellular lineages that either promote or suppress immune reactions. Whereas effector T (Teff) cells drive immune activation and promote clearance of infections and cancer, regulatory T (Treg) cells suppress their function to prevent excessive immune reactions that would otherwise result in autoimmune and allergic disease. During cell fate decisions, access to lineage-specific regulatory elements in the genome, which is tightly controlled by chromatin structure, is required to acquire a specific gene expression profile and a new cell identity. The dynamic changes of the chromatin landscape during Treg differentiation are largely unknown. To study this, I measured chromatin accessibility during the activation of naïve CD4 + T cells in the presence of TGF β (iTreg) or no cytokine (Th0) at different time points and integrated them with known gene expression and histone modification datasets to further characterise these changes. This shows that the chromatin landscape in iTreg cells undergoes dynamic remodelling in response to TCR stimulation and cytokine signalling with convergent effects of the two signals at many regulated loci. BACH2 is a transcriptional repressor whose expression is predominantly restricted to lymphocytes. Whether the suppression role of BACH2 is mainly through steric competition with the AP-1 family or involves other mechanisms is currently unclear. To test this, I measured gene-wide accessibility, DNA binding, and gene expression in Bach2-deficient and Bach2-sufficient Treg cells. While BACH2 is a critical regulator of T cell differentiation, its effect on accessible chromatin was minimal supporting a model whereby it functions principally as a steric repressor of AP-1-driven gene expression. Prior to Treg lineage commitment, BACH2 expression is required for induction of Foxp3, but its role after Treg lineage commitment has been unclear. To test this, I examined gene expression and genome-wide chromatin accessibility in natural Treg (nTreg) cells. This shows that BACH2 is repurposed following Treg lineage commitment, and represses the induction of activated Treg genes to promote the quiescence of resting Treg cells.