A Mouse Model of Zhu-Tokita-Takenouchi-Kim Syndrome Reveals Indispensable Son Functions in Myeloid-Lymphoid Lineage Balance and Terminal Differentiation

Abstract

SON is a DNA- and RNA-binding protein mainly localized in nuclear speckles. Compromised SON function leads to aberrant and alternative RNA splicing, particularly for transcripts bearing weak splice sites. SON also binds to DNA and suppresses H3K4me3 modifications at transcription start sites by inhibiting the MLL1/2 methyltransferase complex. More recent studies suggest that SON serves as the core of nuclear speckles, and SON is required for the association between nuclear speckles and p53 target genes to boost RNA expression. Therefore, SON governs the expression of a myriad of target genes by regulating transcription and RNA splicing as well as nuclear speckle assembly, yet exerts its effects on specific sets of genes. However, the role of SON in organ development and hematopoiesis remains poorly understood. Recently, we identified that heterozygous loss-of-function (LoF) mutations in the SON gene cause a neurodevelopmental disorder with multi-organ anomalies in human patients. This syndrome has been designated as a novel rare disease named Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome. The ZTTK SON-Shine Foundation, a family-initiated non-profit organization, was launched, and through this foundation, we work with families to characterize clinical symptoms associated with SON LoF. Among the clinical symptoms observed in individuals with ZTTK syndrome, a noticeable feature is a wide range of hematological abnormalities, including bone marrow failure, high mean corpuscular volume (MCV), polycythemia, severe anemia, and thrombosis. Furthermore, immunoglobulin deficiency, poor responses to vaccines, and frequent infections were reported, implicating SON LoF in various hematopoietic abnormalities. To study how heterozygous LoF of SON affects organ development and causes clinical features associated with ZTTK syndrome, we created a mouse model of Son haploinsufficiency ( Son +/-). While complete knockout of Son ( Son -/-) led to embryonic lethality, Son +/- mice were viable and recapitulated many clinical features of human ZTTK syndrome patients. The Son +/- mice showed severe growth retardation, signs of cognitive impairment, skeletal abnormalities, kidney agenesis/hypoplasia, and, importantly, hematopoietic abnormalities, such as high MCV, low lymphocyte counts, and immunoglobulin deficiency. To examine the hematopoietic features found in ZTTK syndrome patients are due to SON LoF, we further examined hematopoiesis of our Son +/- mice. We found that Son +/- fetal liver as well as adult mouse bone marrow contain a reduced size of the early-stage hematopoietic stem and progenitor cell (HSPC) pool (marked as Lin-Sca1+cKit+: LSK). Analysis of LSK subpopulations revealed that Son +/- mice have myeloid-lymphoid lineage imbalance at the stage of multipotent progenitor (MPP), with increased megakaryocyte/erythroid lineage-biased MPPs (MPP2) while lymphoid lineage-biased MPPs (MPP4) are decreased. In addition, erythroid terminal differentiation and B cell maturation were impaired in Son +/- mice. Single-cell RNA-sequencing of mouse bone marrow Lin-cKit+ cells and transcriptome-based clustering also revealed that Son haploinsufficiency leads to a reduction in lymphoid lineage-committed progenitor cells and decreased expression of lymphoid lineage/B cell development genes, while erythroid lineage-promoting genes were aberrantly activated in myeloid lineage progenitors. Deep bulk RNA-sequencing and alternative splicing analysis identified that that Son haploinsufficiency caused alternative splicing of chromatin modifiers genes and epigenetic regulator genes. Furthermore, from our ATAC-sequencing analysis, we found that Son haploinsufficiency causes decreased chromatin accessibility in the gene loci critical for lymphoid lineage specification. Taken together, our Son +/- mouse model revealed that the normal level of Son is required to achieve the sufficient expression levels of the genes directing lymphoid lineage specification, B cell lineage development, and erythroid terminal differentiation. Our study demonstrates the indispensable roles of SON in multiple stages of hematopoiesis and provides valuable insight into the clinical significance of abnormal SON levels in hematopoietic diseases.