Eaf1 and Eaf2 mediate zebrafish dorsal-ventral axis patterning via suppressing Wnt/β-Catenin activity

A mode of action protein based approach that characterizes the relationships among most major diseases

Disease classification is important for understanding disease commonalities on both the phenotypical and molecular levels. Based on predicted disease mode of action (MOA) proteins, our algorithm PICMOA (Pan-disease Classification in Mode of Action Protein Space) classifies 3526 diseases across 20 clinically classified classifications (ICD10-CM major classifications). At the top level, all diseases can be classified into "infectious" and "non-infectious" diseases. Non-infectious diseases are classified into 9 classes. To demonstrate the validity of the classifications, for common pathways predicted based on MOA proteins, 77% of the top 10 most frequent pathways have literature evidence of association to their respective disease classes/subclasses. These results indicate that PICMOA will be useful for understanding common disease mechanisms and facilitating the development of drugs for a class of diseases, rather than a single disease. The MOA proteins, molecular functions, pathways for classes, and individual diseases are available at https://sites.gatech.edu/cssb/PICMOA/ .

The temporal control and activity of maternal zsquildlike-A/hnrnpaba during zebrafish embryogenesis indicate a role in early pattern formation

During embryogenesis in Danio rerio (zebrafish), the earliest morphological patterning events are dependent on the precise temporal translation and/or localization of specific maternal mRNAs/proteins. Dorsoventral patterning in particular requires the translocation of maternal factors that are present in the Balbiani Body from the vegetal region of the unfertilized egg to the future dorsal side of the embryo (Fuentes et al., 2020), leading to the localized activation of the β-catenin pathway in the cells in that region. Since zebrafish are chordates, this dorsoventral patterning then leads to the formation of neural tissue on the dorsal side of the embryo. What is not yet clear is the identity of all maternal and zygotic factors that first establish dorsoventral patterning, and which factors lead to the establishment of neural versus non-neural tissue. Taking an evolutionary approach to this question, we investigated a gene in zebrafish, zsquidlike-A (hnrnpaba), that is homologous to a key dorsoventral patterning gene in fruit flies (Drosophila melanogaster) called squid (Kelley, 1993). While dorsoventral patterning in flies and fish looks quite different both morphologically and at the molecular level, we demonstrate that not only has a key dorsoventral patterning gene in flies been conserved in fish, maternal fish zsquidlike-A protein is synthesized precisely as dorsoventral patterning is unfolding in fish embryos, and in its absence, dorsoventral patterning is severely disrupted.

Zebrafish ELL-associated factors Eaf1/2 modulate erythropoiesis via regulating gata1a expression and WNT signaling to facilitate hypoxia tolerance

EAF1 and EAF2, the eleven-nineteen lysine-rich leukemia (ELL)-associated factors which can assemble to the super elongation complex (AFF1/4, AF9/ENL, ELL, and P-TEFb), are reported to participate in RNA polymerase II to actively regulate a variety of biological processes, including leukemia and embryogenesis, but whether and how EAF1/2 function in hematopoietic system related hypoxia tolerance during embryogenesis remains unclear. Here, we unveiled that deletion of EAF1/2 (eaf1^-/- and eaf2^-/-) caused reduction in hypoxia tolerance in zebrafish, leading to reduced erythropoiesis during hematopoietic processes. Meanwhile, eaf1^-/- and eaf2^-/- mutants showed significant reduction in the expression of key transcriptional regulators scl, lmo2, and gata1a in erythropoiesis at both 24 h post fertilization (hpf) and 72 hpf, with gata1a downregulated while scl and lmo2 upregulated at 14 hpf. Mechanistically, eaf1^-/- and eaf2^-/- mutants exhibited significant changes in the expression of epigenetic modified histones, with a significant increase in the binding enrichment of modified histone H3K27me3 in gata1a promoter rather than scl and lmo2 promoters. Additionally, eaf1^-/- and eaf2^-/- mutants exhibited a dynamic expression of canonical WNT/β-catenin signaling during erythropoiesis, with significant reduction in p-β-Catenin level and in the binding enrichment of both scl and lmo2 promoters with the WNT transcriptional factor TCF4 at 24 hpf. These findings demonstrate an important role of Eaf1/2 in erythropoiesis in zebrafish and may have shed some light on regeneration medicine for anemia and related diseases and on molecular basis for fish economic or productive traits, such as growth, disease resistance, hypoxia tolerance, and so on.

The maternal coordinate system: Molecular-genetics of embryonic axis formation and patterning in the zebrafish

Axis specification of the zebrafish embryo begins during oogenesis and relies on proper formation of well-defined cytoplasmic domains within the oocyte. Upon fertilization, maternally-regulated cytoplasmic flow and repositioning of dorsal determinants establish the coordinate system that will build the structure and developmental body plan of the embryo. Failure of specific genes that regulate the embryonic coordinate system leads to catastrophic loss of body structures. Here, we review the genetic principles of axis formation and discuss how maternal factors orchestrate axis patterning during zebrafish early embryogenesis. We focus on the molecular identity and functional contribution of genes controlling critical aspects of oogenesis, egg activation, blastula, and gastrula stages. We examine how polarized cytoplasmic domains form in the oocyte, which set off downstream events such as animal-vegetal polarity and germ line development. After gametes interact and form the zygote, cytoplasmic segregation drives the animal-directed reorganization of maternal determinants through calcium- and cell cycle-dependent signals. We also summarize how maternal genes control dorsoventral, anterior-posterior, mesendodermal, and left-right cell fate specification and how signaling pathways pattern these axes and tissues during early development to instruct the three-dimensional body plan. Advances in reverse genetics and phenotyping approaches in the zebrafish model are revealing positional patterning signatures at the single-cell level, thus enhancing our understanding of genotype-phenotype interactions in axis formation. Our emphasis is on the genetic interrogation of novel and specific maternal regulatory mechanisms of axis specification in the zebrafish.

Conditional Deletion of Eaf1 Induces Murine Prostatic Intraepithelial Neoplasia in Mice

ELL-associated factor 1 is a transcription elongation factor that shares significant homology and functional similarity to the androgen-responsive prostate tumor suppressor ELL-associated factor 2. EAF2 is frequently down-regulated in advanced prostate cancer and Eaf2 deletion in the mouse induced the development of murine prostatic intraepithelial neoplasia. Here we show that similar to EAF2, EAF1 is frequently down-regulated in advanced prostate cancer. Co-downregulation of EAF1 and EAF2 occurred in 40% of clinical specimens with Gleason score >7. We developed and characterized a murine model of prostate-epithelial specific deletion of Eaf1 in the prostate and crossed it with our previously generated mouse with conventional deletion of Eaf2. The prostates of Eaf1 deletion mice displayed murine prostatic intraepithelial neoplasia lesions with increased proliferation and inflammation. Combined deletion of Eaf1 and Eaf2 in the murine model induced an increased incidence in mPIN lesions characterized by increased proliferation and CD3+ T cells and CD19+ B cells infiltration compared to individual deletion of either Eaf1 or Eaf2 in the murine prostate. These results suggest that EAF1 may play a tumor suppressive role in the prostate. Cooperation between EAF1 and EAF2 may be important for prostate maintaining prostate epithelial homeostasis, and concurrent loss of these two tumor suppressors may promote prostate tumorigenesis and progression.