Research in the Yost Lab
Left-Right (LR) Patterning and Cardiovascular Disease in Vertebrates
My lab was one of the earliest to investigate the embryological and cellular mechanisms that govern global LR patterning in vertebrates, starting with a seminal paper in Nature in 1992 that established a critical role for cell-extracellular signals. This began the hunt for the molecular sources for asymmetry in vertebrate embryos. Using a combination of embryological techniques in Xenopus and genetics in zebrafish, we were the first to show the importance of two transient structures in the embryo for the establishment and maintenance of LR asymmetry, that continue to be intensely investigated by many labs. The embryonic midline (notochord and floorplate) separates the two sides of the embryo and prevents asymmetric signals from crossing this barrier. Kupffer’s vesicle was described in the 1860’s by the famous anatomist Karl Wilhelm von Kupffer, but its function was unknown until our lab demonstrated that it has motile cilia that beat in unison to produce an asymmetric flow of extracellular fluid from right to left. We named this structure, which has analogues in mice, amphibians and other vertebrates, the “ciliated organ of asymmetry” and it is responsible LR patterning in the brain, heart and gut. We found the first asymmetrically expressed gene in a vertebrate brain, and we continue to make inroads into the complex LR patterning pathways.
- Yost HJ. Regulation of vertebrate left-right asymmetries by extracellular matrix. Nature. 1992 May 14;357(6374):158-161.
- Hyatt BA, Lohr JL, Yost HJ. Initiation of vertebrate left-right axis formation by maternal Vg1. Nature. 1996 Nov 7;384(6604):62-65.
- Essner JJ, Vogan KJ, Wagner MK, Tabin CJ, Yost HJ, Brueckner M. Conserved function for embryonic nodal cilia. Nature. 2002 Jul 4;418(6893):37-38.
- Bisgrove BW, Su YC, Yost HJ. Maternal Gdf3 is an obligatory cofactor in nodal signaling for embryonic axis formation in zebrafish. eLife. 2017 Nov 15;6. pii: e28534. doi: 10.7554/eLife.28534.
Cardiac Neural Crest in zebrafish
Cardiac neural crest in chick and mice were thought to contribute to the development of the cardiac outflow tract, which then divides and reorganizes LR asymmetrically into the systemic and pulmonary circulation of air-breathing animals. As we first described, the primitive outflow tract in zebrafish is not reorganized in water-living vertebrates, so, from an evolutionary perspective, it was reasonable to hypothesize that cardiac neural crest would not be present in zebrafish. In contrast, we discovered that zebrafish have cardiac neural crest, and importantly, some neural crest fate mapped to ventricular cardiomyocytes. Several prominent labs have substantiated these findings with a variety of fate-mapping techniques. However, as explained in this proposal, the ability to exclusively ablate Neural Crest derived Cardiomyocytes (NC-Cms) and test their functions has been elusive until our recent development of transgenic tools. This proposal builds on our discoveries that NC-Cms and Notch ligand jag2b have critical functions in cardiac development and in adult-onset cardiomyopathy, recently published in Nature Communications.
- Hu N, Yost HJ, Clark EB. Cardiac morphology and blood pressure in the adult zebrafish. Anat Rec. 2001 Sep 1;264(1):1-12. PubMed PMID: 11505366. (featured on journal cover)
- Sato M, Yost HJ. Cardiac neural crest contributes to cardiomyogenesis in zebrafish. Dev Biol. 2003 May 1;257(1):127-39. PubMed PMID: 12710962.
- Sato M, Tsai HJ, Yost HJ. Semaphorin3D regulates invasion of cardiac neural crest cells into the primary heart field. Dev Biol. 2006 Oct 1;298(1):12-21. Epub 2006 Jun 2. PubMed PMID: 16860789.
- Abdul-Wajid S, Demarest B, Yost HJ. Loss of embryonic neural crest cardiomyocytes causes adult hypertrophic cardiomyopathy. Nat Commun. 2018 Nov 2;9(1):4603. doi: 10.1038/s41467-018-07054-8.
My team has created several novel and widely utilized bioinformatics tools for genome analyses in multiple organisms (available on our website). We developed High Resolution Melting Analysis (HRMA) to rapidly genotype mutants in zebrafish, and the Poly Peak Parser algorithm that parses direct sequencing results of heterozygous mutants (small insertions or deletions, such as those created by CRISPR targeted mutagenesis). These tools have been adopted by many other labs for mutation detection in a variety of organisms. By connecting human and zebrafish genetics, we have extensive experience mapping conserved non-coding regions and cardiac-specific differentially methylated regions. To date, our most important bioinformatics contribution is an algorithm called MMAPPR (Mutation Mapping Analysis Pipeline for Pooled RNA-seq) that allows discovery of new mutations in NGS datasets. Initially developed to discover mutations in zebrafish, MMAPPR is species agnostic and is used by over 150 research groups around the world to identify mutations in Ciona, parasitic worms, maize, sorghum and other food crop genetics in India and China, and in wild populations of non-traditional organisms.
- Parant JM, George SA, Pryor R, Wittwer CT, Yost HJ. A rapid and efficient method of genotyping zebrafish mutants. Dev Dyn. 2009 Dec;238(12):3168-3174. PMCID: PMC3888828
- Hill JT, Demarest BL, Bisgrove BW, Gorsi B, Su YC, Yost HJ. MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq. Genome Res. 2013 Apr;23(4):687-697. PMCID: PMC3613585
- Maguire CT, Demarest BL, Hill JT, Palmer JD, Brothman AR, Yost HJ, Condic ML. Genome-wide analysis reveals the unique stem cell identity of human amniocytes. PLoS One. 2013;8(1):e53372. doi: 10.1371/journal.pone.0053372. Epub 2013 Jan 10. PubMed PMID: 23326421; PubMed Central PMCID: PMC3542377.
- Hill JT, Demarest BL, Bisgrove BW, Su YC, Smith M, Yost HJ. Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products. Dev Dyn. 2014 Dec;243(12):1632-1636.
Modeling human diseases in zebrafish
We utilize both forward genetics and reverse genetics approaches in zebrafish, in combination with human genetics, to discover allelic variants, genes and gene regulatory pathways that are implicated in human diseases, including human congenital heart disease, heterotaxy syndrome, ciliopathies, Kabuki Syndrome, Roberts syndrome, and Li-Fraumeni syndrome.
- Parant JM, George SA, Holden JA, Yost HJ. Genetic modeling of Li-Fraumeni syndrome in zebrafish. Dis Model Mech. 2010 Jan-Feb;3(1-2):45-56. PMCID: PMC2806900
- Samson SC, Ferrer T, Jou CJ, Sachse FB, Shankaran SS, Shaw RM, Chi NC, Tristani-Firouzi M, Yost HJ. 3-OST-7 regulates BMP-dependent cardiac contraction. PLoS Biol. 2013 Dec;11(12):e1001727. PMCID: PMC3849020
- Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, Castaldi C, Tikhonoa IR, Bilguvar K, Mane SM, Sanders SJ, Mital S, Russell MW, Gaynor JW, Deanfield J, Giardini A, Porter GA Jr, Srivastava D, Lo CW, Shen Y, Watkins WS, Yandell M, Yost HJ, Tristani-Firouzi M, Newburger JW, Roberts AE, Kim R, Zhao H, Kaltman JR, Goldmuntz E, Chung WK, Seidman JG, Gelb BD, Seidman CE, Lifton RP, Brueckner M. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nature Genet. 2017 Oct 9. doi: 10.1038/ng.3970. PMID: 28991257
- Serrano MA, Demarest BL, Tone-Pah-Hote T, Tristani-Firouzi M, Yost HJ. Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome. bioRxiv 489757; doi: https://doi.org/10.1101/489757
Ciliopathies and Motile Cilia Biology
The field of cilia biology has exploded in the last decade. Building on our discovery that specialized cilia control LR patterning in zebrafish, we extended our studies to understand the cell-cell signals and Gene Regulatory Networks that control the cellular morphogenesis (precursor cell specification, cell migration, epithelialization, lumen formation) of ciliated cells as well as the length, form and function of motile cilia. Our lab has been at the forefront of this field, publishing over 30 research studies that have received over 3100 citations. We invented techniques that allow visualization and quantification of asymmetric fluid flow and knockdown of gene function specifically in ciliated cell lineages, providing first definitive demonstration in any vertebrate for the cell autonomous role of ciliated cells in LR patterning. We are currently studying how asymmetric fluid flow regulates gene expression, discovering novel mechanisms by which major cell-cell signaling pathways (FGF, TGFβ and Wnt) intersect with cilia-dependent cellular pathways. Using genome-wide analyses, we are currently studying the gene regulatory networks that control cilia biology and that convert asymmetric fluid flow to gene function.
- Essner JJ, Amack JD, Nyholm MK, Harris EB, Yost HJ. Kupffer’s vesicle is a ciliated organ of asymmetry in the zebrafish embryo that initiates left-right development of the brain, heart and gut. Development. 2005 Mar;132(6):1247-1260.
- Bisgrove BW, Yost HJ. The roles of cilia in developmental disorders and disease. Development. 2006 Nov;133(21):4131-4143.
- Neugebauer JM, Amack JD, Peterson AG, Bisgrove BW, Yost HJ. FGF signalling during embryo development regulates cilia length in diverse epithelia. Nature. 2009 Apr 2;458(7238):651-654. PMCID: PMC2688717
- Peterson AG, Wang X, Yost HJ. Dvr1 transfers left-right asymmetric signals from Kupffer’s vesicle to lateral plate mesoderm in zebrafish. Dev Biol. 2013 Oct 1;382(1):198-208. PMCID: PMC3888838