Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients

Abstract

The pioneer transcription factor (TF) PU.1 controls hematopoietic cell fate by decompacting stem cell heterochromatin and allowing nonpioneer TFs to enter otherwise inaccessible genomic sites. PU.1 deficiency fatally arrests lymphopoiesis and myelopoiesis in mice, but human congenital PU.1 disorders have not previously been described. We studied six unrelated agammaglobulinemic patients, each harboring a heterozygous mutation (four de novo, two unphased) of SPI1, the gene encoding PU.1. Affected patients lacked circulating B cells and possessed few conventional dendritic cells. Introducing disease-similar SPI1 mutations into human hematopoietic stem and progenitor cells impaired early in vitro B cell and myeloid cell differentiation. Patient SPI1 mutations encoded destabilized PU.1 proteins unable to nuclear localize or bind target DNA. In PU.1-haploinsufficient pro–B cell lines, euchromatin was less accessible to nonpioneer TFs critical for B cell development, and gene expression patterns associated with the pro– to pre–B cell transition were undermined. Our findings molecularly describe a novel form of agammaglobulinemia and underscore PU.1’s critical, dose-dependent role as a hematopoietic euchromatin gatekeeper.

I SPI1 something needed for B cells

“…Pioneer TFs are characterized by having the unique property of enabling the opening of previously closed chromatin sites that then enable activation of specific cellular programs (Mayran et al, 2019). The findings by Le Coz et al (2021) further underscore the key role of PU.1 as a pioneer TF (Iwafuchi-Doi and Zaret, 2014;Minderjahn et al, 2020). The authors report a novel monogenic cause of a congenital blood disorder involving a master TF, thereby providing important phenotypic and molecular insight into the physiological roles of the SPI1 gene in human hematopoiesis and extending the range of hematopoietic master TFs that are altered in disease.…”

“…The activation of lineage-specific transcriptional programs is tightly governed by master hematopoietic TFs. Here, by using exome sequencing, Le Coz et al (2021) examine a series of patients with agammaglobulinemia—a condition characterized by a paucity of B lymphocytes and therefore defective humoral immunity—and identify six unrelated patients with heterozygous germline mutations in the SPI1 gene, which encodes the hematopoietic master TF PU.1.…”

“… Le Coz et al (2021) define the clinical and molecular phenotype of this novel inherited PU.1 haploinsufficiency syndrome, which they term PU.1-mutated agammaglobulinemia (PU.MA). PU.1 is a key transcriptional regulator required in the development of multiple hematopoietic lineages ( Scott et al, 1994 ).…”

“…PU.1 has been shown to have multifaceted roles in hematopoiesis, with reduced PU.1 levels causing B cell developmental arrest, but other specific PU.1 perturbations can favor B cell over myeloid lineage development ( DeKoter et al, 2007 ; Heinz et al, 2013 ; Houston et al, 2007 ). By providing comprehensive phenotypic data, Le Coz et al (2021) help clarify some of the prior observations on the dosage-dependent role of PU.1 in hematopoietic lineage specification. The authors perform detailed immune phenotyping and transcriptional profiling of blood and bone marrow cells from PU.MA patients and observe a significant reduction of circulating B cells and dendritic cells, as well as a B cell maturation arrest.…”

“…Using these SPI1 -edited hematopoietic stem and progenitor cells as a model system for human hematopoiesis in the setting of PU.MA, the authors demonstrate that biallelic PU.1 expression is critical for B cell and myeloid cell development. Examining patient bone marrow cells by cellular indexing of transcriptomes and epitope sequencing, Le Coz et al (2021) identify the B cell developmental defect in the pro– to pre–B cell transition. On a molecular level, mutant heterozygous SPI1 alleles were confirmed to result in destabilized, transcriptionally inert PU.1 proteins that do not appear to exert dominant negative effects.…”