Concepts in Multifactorial Etiology of Developmental Disorders: Gene-Gene and Gene-Environment Interactions in Holoprosencephaly

Many common developmental disorders are thought to arise from a complex set of genetic and environmental risk factors. These factors interact with each other to affect the strength and duration of key developmental signaling pathways, thereby increasing the possibility that they fail to achieve the thresholds required for normal embryonic patterning. One such disorder, holoprosencephaly (HPE), serves as a useful model system in understanding various forms of multifactorial etiology. Genomic analysis of HPE cases, epidemiology, and mechanistic studies of animal models have illuminated multiple potential ways that risk factors interact to produce adverse developmental outcomes. Among these are: 1) interactions between driver and modifier genes; 2) oligogenic inheritance, wherein each parent provides predisposing variants in one or multiple distinct loci; 3) interactions between genetic susceptibilities and environmental risk factors that may be insufficient on their own; and 4) interactions of multiple genetic variants with multiple non-genetic risk factors. These studies combine to provide concepts that illuminate HPE and are also applicable to additional disorders with complex etiology, including neural tube defects, congenital heart defects, and oro-facial clefting.

Quantitative Imaging in Whole-mount Zebrafish Embryos Traces Morphogen Gradient Maintenance and Noise Propagation in BMP Signaling

Dorsoventral (DV) embryonic patterning relies on precisely controlled interpretation of morphogen signaling. In all vertebrates, DV axis specification is informed by gradients of bone morphogenetic proteins (BMPs). We developed a 3D single-molecule mRNA quantification method in whole-mount zebrafish to quantify the inputs and outputs in this pathway. In combination with 3D computational modeling of zebrafish embryo development, data from this method revealed that sizzled (Szl), shaped by BMP and Nodal signaling, maintained a consistent inhibition level with chordin (Chd) to maintain the BMP morphogen gradient. Intriguingly, intrinsic BMP morphogen expression is highly noisy at the ventral marginal layer in the early zebrafish gastrula, where the gradient for DV patterning is established, which implies an unexpected role for noise in gradient shaping.

Lyl-1 regulates primitive macrophages and microglia development

During ontogeny, macrophage populations emerge in the Yolk Sac (YS) via two distinct progenitor waves, prior to hematopoietic stem cell development. Macrophage progenitors from the primitive/”early EMP” and transient-definitive/”late EMP” waves both contribute to various resident primitive macrophage populations in the developing embryonic organs. Identifying factors that modulates early stages of macrophage progenitor development may lead to a better understanding of defective function of specific resident macrophage subsets. Here we show that YS primitive macrophage progenitors express Lyl-1, a bHLH transcription factor related to SCL/Tal-1. Transcriptomic analysis of YS macrophage progenitors indicate that primitive macrophage progenitors present at embryonic day 9 are clearly distinct from those present at later stages. Disruption of Lyl-1 basic helix-loop-helix domain leads initially to an increased emergence of primitive macrophage progenitors, and later to their defective differentiation. These defects are associated with a disrupted expression of gene sets related to embryonic patterning and neurodevelopment. Lyl-1-deficiency also induce a reduced production of mature macrophages/microglia in the early brain, as well as a transient reduction of the microglia pool at midgestation and in the newborn. We thus identify Lyl-1 as a critical regulator of primitive macrophages and microglia development, which disruption may impair resident-macrophage function during organogenesis.

A Novel System for Monitoring in vivo Cell Signaling Pathways Involved in Early Embryonic Patterning

<p>Early developmental events, such as the arrangement of the head-tail axis, are fundamentally driven by cell signalling cascades. Such incidents are regulated in a highly complex manner by promoters and inhibitors at many levels of the cascade. This complexity makes it difficult to understand where and when certain signalling occurs, and what effects additional factors have on the signalling system. Nodal signalling, executed by intracellular Smad2/3 signal propagation, is thought to induce the anterior-posterior and head-tail patterning of the early mouse embryo. Target gene outputs of this signalling are fine-tuned by a vast array of modulators; TGBβ co-receptors, extracellular ligand and receptor inhibitors, DNA binding cofactors, and intracellular enhancers and inhibitors. The endogenous target genes of this system cannot be used as a measure of signalling as they themselves feedback on the original system and others, creating diverse signals. In this body of work, we have distilled the Nodal signalling cascade to a single variable by creating a fluorescent genetic reporter to semi-quantitatively measure Smad signalling during early embryonic development. Reporter constructs contain Smad binding elements, a minimal promoter and fluorescent protein elements. Various sensitivity Smad binding elements were created to respond to different thresholds of signalling. Fluorescent microscopy and flow cytometry were used to verify responsiveness of reporter constructs, tested first in a mouse embryonic fibroblast line and subsequently in transgenic embryos. This study will provide an understanding of how extracellular cues dictate gene expression during early embryonic formation. The knowledge acquired from this work may have implications in dairy cattle and human fertility.</p>

A Novel System for Monitoring in vivo Cell Signaling Pathways Involved in Early Embryonic Patterning

<p>Early developmental events, such as the arrangement of the head-tail axis, are fundamentally driven by cell signalling cascades. Such incidents are regulated in a highly complex manner by promoters and inhibitors at many levels of the cascade. This complexity makes it difficult to understand where and when certain signalling occurs, and what effects additional factors have on the signalling system. Nodal signalling, executed by intracellular Smad2/3 signal propagation, is thought to induce the anterior-posterior and head-tail patterning of the early mouse embryo. Target gene outputs of this signalling are fine-tuned by a vast array of modulators; TGBβ co-receptors, extracellular ligand and receptor inhibitors, DNA binding cofactors, and intracellular enhancers and inhibitors. The endogenous target genes of this system cannot be used as a measure of signalling as they themselves feedback on the original system and others, creating diverse signals. In this body of work, we have distilled the Nodal signalling cascade to a single variable by creating a fluorescent genetic reporter to semi-quantitatively measure Smad signalling during early embryonic development. Reporter constructs contain Smad binding elements, a minimal promoter and fluorescent protein elements. Various sensitivity Smad binding elements were created to respond to different thresholds of signalling. Fluorescent microscopy and flow cytometry were used to verify responsiveness of reporter constructs, tested first in a mouse embryonic fibroblast line and subsequently in transgenic embryos. This study will provide an understanding of how extracellular cues dictate gene expression during early embryonic formation. The knowledge acquired from this work may have implications in dairy cattle and human fertility.</p>

Quantitative imaging in whole-mount zebrafish embryos traces morphogen gradient maintenance and noise propagation in BMP signaling

Dorsoventral (DV) embryonic patterning relies on precisely controlled interpretation of morphogen signaling. In all vertebrates, DV axis specification is informed by gradients of Bone Morphogenetic Proteins (BMPs). We developed a 3D single-molecule mRNA quantification method in whole-mount zebrafish to quantify the inputs and outputs in this pathway. In combination with 3D computational modeling of zebrafish embryo development, data from this method revealed that Sizzled (Szl), shaped by BMP and Nodal signaling, kept a consistent inhibition level with Chordin (Chd) to maintain the BMP morphogen gradient. Intriguingly, BMP morphogen intrinsic expression is highly noisy at the ventral marginal layer in early zebrafish gastrula, where the gradient for DV patterning is established, which implies an unexpected role for noise in gradient shaping.

The histone lysine acetyltransferase HBO1 (KAT7) regulates hematopoietic stem cell quiescence and self-renewal

The histone acetyltransferase HBO1 (MYST2, KAT7) is indispensable for postgastrulation development, histone H3 lysine 14 acetylation (H3K14Ac) and the expression of embryonic patterning genes. In this study, we report the role of HBO1 in regulating hematopoietic stem cell function in adult hematopoiesis. We used two complementary cre-recombinase transgenes to conditionally delete Hbo1 (Mx1-Cre and Rosa26-CreERT2). Hbo1 null mice became moribund due to hematopoietic failure with pancytopenia in the blood and bone marrow two to six weeks after Hbo1 deletion. Hbo1 deleted bone marrow cells failed to repopulate hemoablated recipients in competitive transplantation experiments. Hbo1 deletion caused a rapid loss of hematopoietic progenitors (HPCs). The numbers of lineage-restricted progenitors for the erythroid, myeloid, B-and T-cell lineages were reduced. Loss of HBO1 resulted in an abnormally high rate of recruitment of quiescent hematopoietic stem cells (HSCs) into the cell cycle. Cycling HSCs produced progenitors at the expense of self-renewal, which led to the exhaustion of the HSC pool. Mechanistically, genes important for HSC functions were downregulated in HSC-enriched cell populations after Hbo1 deletion, including genes essential for HSC quiescence and self-renewal, such as Mpl, Tek(Tie-2), Gfi1b, Egr1, Tal1(Scl), Gata2, Erg, Pbx1, Meis1 and Hox9, as well as genes important for multipotent progenitor cells and lineage-specific progenitor cells, such as Gata1. HBO1 was required for H3K14Ac through the genome and particularly at gene loci required for HSC quiescence and self-renewal. Our data indicate that HBO1 promotes the expression of a transcription factor network essential for HSC maintenance and self-renewal in adult hematopoiesis.

L-bodies are RNA-protein condensates driving RNA localization in Xenopus oocytes

RNP granules are membrane-less compartments within cells, formed by phase separation, that function as regulatory hubs for diverse biological processes. However, the mechanisms by which RNAs and proteins interact to promote RNP granule structure and function in vivo remain unclear. In Xenopus laevis oocytes, maternal mRNAs are localized as large RNPs to the vegetal hemisphere of the developing oocyte, where local translation is critical for proper embryonic patterning. Here, we demonstrate that RNPs containing vegetally localized RNAs represent a new class of cytoplasmic RNP granule, termed Localization-bodies (L-bodies). We show that L-bodies contain a dynamic protein-containing phase surrounding a non-dynamic RNA-containing phase. Our results support a role for RNA as a critical component within these RNP granules and suggest that cis-elements within localized mRNAs may drive subcellular RNA localization through control over phase behavior.

Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish

Adenosine deaminases (ADARs) catalyze the deamination of adenosine to inosine, also known as A-to-I editing, in RNA. Although A-to-I editing occurs widely across animals, and is well studied, new biological roles are still being discovered. Here, we study the role of A-to-I editing in early zebrafish development. We demonstrate that Adar, the zebrafish orthologue of mammalian ADAR1, is essential for establishing the antero-posterior and dorso-ventral axes and patterning. Genome-wide editing discovery revealed pervasive editing in maternal and the earliest zygotic transcripts, the majority of which occurred in the 3-UTR. Interestingly, transcripts implicated in gastrulation as well as dorso-ventral and antero-posterior patterning were found to contain multiple editing sites. Adar knockdown or overexpression affected gene expression and global editing patterns at 12 hpf, but not earlier. Our study established that RNA editing by Adar is necessary for the earliest steps of embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes.