Dr. Dongbo Shi
Dr. Dongbo Shi
Im Neuenheimer Feld 230
Fon 06221 54-5521
dongbo.shi AET cos.uni-heidelberg.de
- Bachelor of Science, Faculty of Science, Kyoto University, Japan, 2009
- Master of Sciece, Graduate school of Biostudies, Kyoto University, 2011 (Supervised by Dr. Tadashi Uemura, and co-supervised by Dr. Toshihiko Fujimori in National Institute of Basic Biology, Japan)
- PhD (life science), Graduate school of Biostudies, Kyoto University, 2014 (Supervised by Dr. Tadashi Uemura, and co-supervised by Dr. Toshihiko Fujimori in National Institute for Basic Biology, Japan)
- 2011-2014 Research Fellowships for Young Scientists (DC1), Japan Society for the Promotion of Science (JSPS)
- 2014-2016 NIBB Research fellow, Division of Embryology, National Institute for Basic Biology, Japan
- 2016-2019 Humboldt Research Fellow (Postdoctral), COS Heidelberg, Heidelberg University
- since 2019 Postdoctoral Researcher, COS Heidelberg, Heidelberg University
- since 2020 JSPS Oversea Research Fellow at COS Heidelberg, Heidelberg University
- since 2020 JST PRESTO Researcher at COS Heidelberg, Heidelberg University
Matsukawa-Usami F, Arata M, Shi D, Oka S, Higuchi Y, Tissir F, Takeichi M, Fujimori T. (2021). Celsr1 and CAMSAP3 differently regulate intercellular and intracellular cilia orientation in oviduct multiciliated cells. the Journal of Cell Science 134: jcs257006
AbstractJournal bioRxiv Pubmed
The molecular mechanisms by which cilia orientation is coordinated within and between multiciliated cells (MCCs) are not fully understood. In the mouse oviduct, MCCs exhibit a characteristic BB orientation and microtubule gradient along the tissue axis. The intracellular polarities were moderately maintained in the cells lacking CELSR1, a planar cell polarity (PCP) factor involved in tissue polarity regulation, although the intercellular coordination of the polarities was disrupted. Whereas CAMSAP3, a microtubule minus-end regulator, is found to be critical for determining the intracellular BB orientation. CAMSAP3 localized to the base of cilia in a polarized manner, and its mutation led to the disruption of intracellular coordination of BB orientation as well as the assembly of microtubules interconnecting BBs without affecting PCP factor localization. Thus, both CELSR1 and CAMSAP3 are responsible for BB orientation but in distinct ways; their cooperation should thus be critical for generating functional multiciliated tissues.
Shi D, Jouannet V, Agusti J, Kaul V, Levitsky V, Sanchez P, Mironova VV, Greb T. (2021). Tissue-specific transcriptome profiling of the Arabidopsis thaliana inflorescence stem reveals local cellular signatures. The Plant Cell doi 10.1093/plcell/koaa019
AbstractJournal bioRxiv Resource web
Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibers, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. By determining overrepresented transcription factor binding regions in the promoters of differentially expressed genes, we identified candidate tissue-specific transcriptional regulators. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrate that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling. Tissue-specific gene expression values can be accessed online at https://arabidopsis-stem.cos.uni-heidelberg.de/.
Wallner ES, Tonn N, Shi D, Jouannet V, Greb T. (2020). SUPPRESSOR OF MAX2 1-LIKE 5 promotes secondary phloem formation during radial stem growth Plant J. 102(5):903-915
As a pre-requisite for constant growth, plants produce vascular tissues at different sites within their post?embryonic body. Interestingly, the formation of vascular tissues during longitudinal and radial expansion of shoot and root axes differs fundamentally with respect to its anatomical configuration. This raises the question to which level regulatory mechanisms of vascular tissue formation are shared throughout plant development. Here, we show that, similar to primary phloem formation during longitudinal growth, the cambium-based formation of secondary phloem depends on the function of SUPPRESSOR OF MAX2 1-LIKE (SMXL) genes. In particular, local SMXL5 deficiency results in the absence of secondary phloem. Moreover, the additional disruption of SMXL4 activity increases tissue production in the cambium region without secondary phloem being formed. Using promoter?reporter lines, we observed that SMXL4 and SMXL5 activities are associated with different stages of secondary phloem formation in the Arabidopsis stem. Based on genome-wide transcriptional profiling and expression analyses of phloem?related markers, we concluded that early steps of phloem formation are impaired in smxl4;smxl5 double mutants and that the additional cambium?derived cells fail to establish phloem-related features. Our results showed that molecular mechanisms determining primary and secondary phloem formation share important properties, but differ slightly with SMXL5 playing a more dominant role in the formation of secondary phloem.
Shi D*, Lebovka I, López-Salmerón V, Sanchez P, Greb T*. (2019). Bifacial cambium stem cells generate xylem and phloem during radial plant growth. Development 146(1):dev171355.
AbstractJournal Interview Highlight Pubmed Press Release *Co-corresponding authors.
A reduced rate of stem cell division is considered a widespread feature which ensures the integrity of genetic information during somatic development of plants and animals. Radial growth of plant shoots and roots is a stem cell-driven process that is fundamental for the mechanical and physiological support of enlarging plant bodies. In most dicotyledonous species, the underlying stem cell niche, the cambium, generates xylem inwards and phloem outwards. Despite the importance and intriguing dynamics of the cambium, the functional characterization of its stem cells is hampered by the lack of experimental tools for accessing distinct cambium sub-domains. Here, we use the hypocotyl of Arabidopsis thaliana to map stem cell activity in the proliferating cambium. Through pulse labeling and genetically encoded lineage tracing, we find that a single bifacial stem cell generates both xylem and phloem cell lineages. This cell is characterized by a specific combination of PXY (TDR), SMXL5 and WOX4 gene activity and a high division rate in comparison with tissue-specific progenitors. Our analysis provides a cellular fate map of radial plant growth, and suggests that stem cell quiescence is not a general prerequisite for life-long tissue production.
Kikuchi K, Nakamura A, Arata M, Shi D, Nakagawa M, Tanaka T, Uemura T, Fujimori T, Kikuchi A, Uezu A, Sakamoto Y, Nakanishi H. (2018). Map7/7D1 and Dvl form a feedback loop that facilitates microtubule remodeling and Wnt5a signaling. EMBO Rep. 19(7). pii: e45471.
The Wnt signaling pathway can be grouped into two classes, the β-catenin-dependent and β-catenin-independent pathways. Wnt5a signaling through a β-catenin-independent pathway promotes microtubule (MT) remodeling during cell-substrate adhesion, cell migration, and planar cell polarity formation. Although Wnt5a signaling and MT remodeling are known to form an interdependent regulatory loop, the underlying mechanism remains unknown. Here we show that in HeLa cells, the paralogous MT-associated proteins Map7 and Map7D1 (Map7/7D1) form an interdependent regulatory loop with Disheveled, the critical signal transducer in Wnt signaling. Map7/7D1 bind to Disheveled, direct its cortical localization, and facilitate the cortical targeting of MT plus-ends in response to Wnt5a signaling. Wnt5a signaling also promotes Map7/7D1 movement toward MT plus-ends, and depletion of the Kinesin-1 member Kif5b abolishes the Map7/7D1 dynamics and Disheveled localization. Furthermore, Disheveled stabilizes Map7/7D1. Intriguingly, Map7/7D1 and its Drosophila ortholog, Ensconsin show planar-polarized distribution in both mouse and fly epithelia, and Ensconsin influences proper localization of Drosophila Disheveled in pupal wing cells. These results suggest that the role of Map7/7D1/Ensconsin in Disheveled localization is evolutionarily conserved.
Minegishi K, Hashimoto M, Ajima R, Takaoka K, Shinohara K, Ikawa Y, Nishimura H, McMahon AP, Willert K, Okada Y, Sasaki H, Shi D, Fujimori T, Ohtsuka T, Igarashi Y, Yamaguchi TP, Shimono A, Shiratori H, Hamada H. (2017). A Wnt5 Activity Asymmetry and Intercellular Signaling via PCP Proteins Polarize Node Cells for Left-Right Symmetry Breaking. Dev Cell. 40(5):439-452.e4.
Polarization of node cells along the anterior-posterior axis of mouse embryos is responsible for left-right symmetry breaking. How node cells become polarized has remained unknown, however. Wnt5a and Wnt5b are expressed posteriorly relative to the node, whereas genes for Sfrp inhibitors of Wnt signaling are expressed anteriorly. Here we show that polarization of node cells is impaired in Wnt5a-/-Wnt5b-/- and Sfrp mutant embryos, and also in the presence of a uniform distribution of Wnt5a or Sfrp1, suggesting that Wnt5 and Sfrp proteins act as instructive signals in this process. The absence of planar cell polarity (PCP) core proteins Prickle1 and Prickle2 in individual cells or local forced expression of Wnt5a perturbed polarization of neighboring wild-type cells. Our results suggest that opposing gradients of Wnt5a and Wnt5b and of their Sfrp inhibitors, together with intercellular signaling via PCP proteins, polarize node cells along the anterior-posterior axis for breaking of left-right symmetry.
Koyama H, Shi D, Suzuki M, Ueno N, Uemura T, Fujimori T. (2016). Mechanical Regulation of Three-Dimensional Epithelial Fold Pattern Formation in the Mouse Oviduct. Biophys J. 111(3):650-665.
Epithelia exhibit various three-dimensional morphologies linked to organ function in animals. However, the mechanisms of three-dimensional morphogenesis remain elusive. The luminal epithelium of the mouse oviduct forms well-aligned straight folds along the longitudinal direction of the tubes. Disruption of the Celsr1 gene, a planar cell polarity-related gene, causes ectopically branched folds. Here, we evaluated the mechanical contributions of the epithelium to the fold pattern formation. In the mutant oviduct, the epithelium was more intricate along the longitudinal direction than in the wild-type, suggesting a higher ratio of the longitudinal length of the epithelial layer to that of the surrounding smooth muscle (SM) layer (L-Epi/SM ratio). Our mathematical modeling and computational simulations suggested that the L-Epi/SM ratio could explain the differences in fold branching between the two genotypes. Longitudinal epithelial tensions were increased in well-aligned folds compared with those in disorganized folds both in the simulations and in experimental estimations. Artificially increasing the epithelial tensions suppressed the branching in simulations, suggesting that the epithelial tensions can regulate fold patterning. The epithelial tensions could be explained by the combination of line tensions along the epithelial cell-cell boundaries with the polarized cell arrays observed in vivo. These results suggest that the fold pattern is associated with the polarized cell array through the longitudinal epithelial tension. Further simulations indicated that the L-Epi/SM ratio could contribute to fold pattern diversity, suggesting that the L-Epi/SM ratio is a critical parameter in the fold patterning in tubular organs.
Shi D*, Usami F, Komatsu K, Oka S, Abe T, Uemura T, Fujimori T*. (2016). Dynamics of planar cell polarity protein Vangl2 in the mouse oviduct epithelium. Mech Dev. 141:78-89.
AbstractPubmed *Co-corresponding authors.
The planar cell polarity (PCP) pathway regulates morphogenesis in various organs. The polarized localization is a key feature of core PCP factors for orchestrating cell polarity in an epithelial sheet. Several studies using Drosophila melanogaster have investigated the mechanism of the polarized localization. However, to what extent these mechanisms are conserved and how the polarization of core PCP factors is maintained in mature vertebrates are still open questions. Here, we addressed these questions by analyzing the dynamics of Vangl2, a member of core PCP factors, in the mouse oviduct epithelium. Multiple core PCP factors including Vangl2 were expressed in the mouse oviduct in postnatal stages. Vangl1, Vangl2 and Frizzled6 had polarized localization in the oviduct epithelium. Exogenously introduced expression of green fluorescent protein (GFP)-tagged core PCP factors by electroporation revealed that Vangl1, Vangl2 and Prickle2 are localized on the ovarian side of the cell periphery in the oviduct. To visualize the Vangl2 dynamics, we generated the R26-Vangl2-EGFP transgenic mice. In these mice, Vangl2-EGFP was ubiquitously expressed and showed polarized localization in multiple organs including the oviduct, the trachea, the lateral ventricle and the uterus. Fluorescence recovery after photobleaching (FRAP) analysis in the mature oviduct revealed that Vangl2 in the enriched subdomain of cell periphery (cellular edge) was more stable than Vangl2 in the less-enriched cellular edge. Furthermore, when a subregion of a Vangl2-enriched cellular edge was bleached, the Vangl2-enriched subregion neighboring the bleached region in the same cellular edge tended to decrease more intensities than the neighboring sub-region in the next Vangl2-enriched cellular edge. Finally, the polarization of Vangl2 was observed in nocodazole treated mouse viduct, suggesting the maintenance of Vangl2 asymmetry is independent of microtubule formation. Taken together, we revealed the characteristics of Vangl2 dynamics in the oviduct epithelium, and found that Vangl2 forms stable complex at the enriched cellular edge and forms compartments. Our data collectively suggest that the mechanism for maintenance of Vangl2 asymmetry in mature mouse oviduct is different from the microtubule dependent polarized transport model, which has been proposed for the reinforcement of the asymmetry of two core PCP proteins, Flamingo and Dishevelled, in the developing fly.
Shi D, Komatsu K, Hirao M, Toyooka Y, Koyama H, Tissir F, Goffinet AM, Uemura T, Fujimori T. (2014). Celsr1 is required for the generation of polarity at multiple levels of the mouse oviduct. Development. 141(23):4558-68.
The oviduct is an important organ in reproduction where fertilization occurs, and through which the fertilized eggs are carried to the uterus in mammals. This organ is highly polarized, where the epithelium forms longitudinal folds along the ovary-uterus axis, and the epithelial multicilia beat towards the uterus to transport the ovulated ova. Here, we analyzed the postnatal development of mouse oviduct and report that multilevel polarities of the oviduct are regulated by a planar cell polarity (PCP) gene, Celsr1. In the epithelium, Celsr1 is concentrated in the specific cellular boundaries perpendicular to the ovary-uterus axis from postnatal day 2. We found a new feature of cellular polarity in the oviduct - the apical surface of epithelial cells is elongated along the ovary-uterus axis. In Celsr1-deficient mice, the ciliary motion is not orchestrated along the ovary-uterus axis and the transport ability of beating cilia is impaired. Epithelial cells show less elongation and randomized orientation, and epithelial folds show randomized directionality and ectopic branches in the mutant. Our mosaic analysis suggests that the geometry of epithelial cells is primarily regulated by Celsr1 and as a consequence the epithelial folds are aligned. Taken together, we reveal the characteristics of the multilevel polarity formation processes in the mouse oviduct epithelium and suggest a novel function of the PCP pathway for proper tissue morphogenesis.
Imuta Y, Koyama H, Shi D, Eiraku M, Fujimori T, Sasaki H. (2014). Mechanical control of notochord morphogenesis by extra-embryonic tissues in mouse embryos. Mech Dev. 132:44-58.
Mammalian embryos develop in coordination with extraembryonic tissues, which support embryonic development by implanting embryos into the uterus, supplying nutrition, providing a confined niche, and also providing patterning signals to embryos. Here, we show that in mouse embryos, the expansion of the amniotic cavity (AC), which is formed between embryonic and extraembryonic tissues, provides the mechanical forces required for a type of morphogenetic movement of the notochord known as convergent extension (CE) in which the cells converge to the midline and the tissue elongates along the antero-posterior (AP) axis. The notochord is stretched along the AP axis, and the expansion of the AC is required for CE. Both mathematical modeling and physical simulation showed that a rectangular morphology of the early notochord caused the application of anisotropic force along the AP axis to the notochord through the isotropic expansion of the AC. AC expansion acts upstream of planar cell polarity (PCP) signaling, which regulates CE movement. Our results highlight the importance of extraembryonic tissues as a source of the forces that control the morphogenesis of embryos.
Mouri K, Nishino Y, Arata M, Shi D, Horiuchi SY, Uemura T. (2014). A novel planar polarity gene pepsinogen-like regulates wingless expression in a posttranscriptional manner. Dev Dyn. 243(6):791-9.
BACKGROUND: Planar cell polarity (PCP) originally referred to the coordination of global organ axes and individual cell polarity within the plane of the epithelium. More recently, it has been accepted that pertinent PCP regulators play essential roles not only in epithelial sheets, but also in various rearranging cells. RESULTS: We identified pepsinogen-like (pcl) as a new planar polarity gene, using Drosophila wing epidermis as a model. Pcl protein is predicted to belong to a family of aspartic proteases. When pcl mutant clones were observed in pupal wings, PCP was disturbed in both mutant and wild-type cells that were juxtaposed to the clone border. We examined levels of known PCP proteins in wing imaginal discs. The amount of the seven-pass transmembrane cadherin Flamingo (Fmi), one of the PCP "core group" members, was significantly decreased in mutant clones, whereas neither the amount of nor the polarized localization of Dachsous (Ds) at cell boundaries was affected. In addition to the PCP phenotype, the pcl mutation caused loss of wing margins. Intriguingly, this was most likely due to a dramatic decrease in the level of Wingless (Wg) protein, but not due to a decrease in the level of wg transcripts. CONCLUSIONS: Our results raise the possibility that Pcl regulates Wg expression post-transcriptionally, and PCP, by proteolytic cleavages.
Shi D, Komatsu K, Uemura T, Fujimori T. (2011). Analysis of ciliary beat frequency and ovum transport ability in the mouse oviduct. Genes Cells. 16(3):282-90.
The oviduct is important in reproduction where fertilization occurs, and the fertilized eggs are conveyed to the uterus. Multi-ciliated cells of the oviductal epithelium and muscle contractions are believed to generate this unidirectional flow. Although there are many studies in human oviducts, there are few reports on mouse oviductal ciliary movements where we can dissect underlying genetic programs. To study ciliary movements in the mouse oviduct, we exposed the ovary-side of the oviduct (infundibulum) longitudinally and recorded the ciliary beatings in a hanging drop preparation. We calculated the ciliary beat frequency (CBF) by automated image analysis and found that the average CBF was 10.9 ± 3.3 and 8.5 ± 2.5 Hz (±standard deviation) during the diestrus and estrus stages, respectively. Mapping of the CBF to multiple locations in the epithelium showed that the cilia beat regularly at a local level, but have a range of frequencies within the entire plane. We also observed ova with cumulus cells were transported to the uterus side by the opened oviduct at the diestrus and estrus stages. These results suggest that the ciliated cells of the infundibulum can generate unidirectional flows and are able to deliver ova by their ciliary activities despite their discordance in beating periodicity.
Tissir F, Qu Y, Montcouquiol M, Zhou L, Komatsu K, Shi D, Fujimori T, Labeau J, Tyteca D, Courtoy P, Poumay Y, Uemura T, Goffinet AM. (2010). Lack of cadherins Celsr2 and Celsr3 impairs ependymal ciliogenesis, leading to fatal hydrocephalus. Nat Neurosci. 13(6):700-7.
Comment in Nat Neurosci. 2010 Jun;13(6):654-5.
Review and other articles
Koyama H, Shi D, Fujimori T. (2019). Biophysics in oviduct: Planar cell polarity, cilia, epithelial fold and tube morphogenesis, egg dynamics. Biophysics and Physicobiology 16:89-107.
Organs and tissues in multi-cellular organisms exhibit various morphologies. Tubular organs have multi-scale morphological features which are closely related to their functions. Here we discuss morphogenesis and the mechanical functions of the vertebrate oviduct in the female reproductive tract, also known as the fallopian tube. The oviduct functions to convey eggs from the ovary to the uterus. In the luminal side of the oviduct, the epithelium forms multiple folds (or ridges) well-aligned along the longitudinal direction of the tube. In the epithelial cells, cilia are formed orienting toward the downstream of the oviduct. The cilia and the folds are supposed to be involved in egg transportation. Planar cell polarity (PCP) is developed in the epithelium, and the disruption of the Celsr1 gene, a PCP related-gene, causes randomization of both cilia and fold orientations, discontinuity of the tube, inefficient egg transportation, and infertility. In this review article, we briefly introduce various biophysical and biomechanical issues in the oviduct, including physical mechanisms of formation of PCP and organized cilia orientation, epithelial cell shape regulation, fold pattern formation generated by mechanical buckling, tubulogenesis, and egg transportation regulated by fluid flow. We also mention about possible roles of the oviducts in egg shape formation and embryogenesis, sinuous patterns of tubes, and fold and tube patterns observed in other tubular organs such as the gut, airways, etc.
Shi D, Tavhelidse T, Thumberger T, Wittbrodt J, Greb T. (2017). Bifacial stem cell niches in fish and plants. Curr Opin Genet Dev. 45:28-33.
Embryonic development is key for determining the architecture and shape of multicellular bodies. However, most cells are produced postembryonically in, at least partly, differentiated organs. In this regard, organismal growth faces common challenges in coordinating expansion and function of body structures. Here we compare two examples for postembryonic growth processes from two different kingdoms of life to reveal common regulatory principles: lateral growth of plants and the enlargement of the fish retina. In both cases, growth is based on stem cell systems mediating radial growth by a bifacial mode of tissue production. Surprisingly, although being evolutionary distinct, we find similar patterns in regulatory circuits suggesting the existence of preferable solutions to a common developmental problem.
Shi D, Arata M, Usui T, Fujimori T, Uemura T. (2016). Seven-Pass Transmembrane Cadherin CELSRs, and Fat4 and Dchs1 Cadherins: From Planar Cell Polarity to Three-Dimensional Organ Architecture. The Cadherin Superfamily. Chapter 10. Springer
In this chapter, two subfamilies of atypical cadherins are described: thesubfamily of seven-pass transmembrane cadherins (7-TM cadherins) and Fat andDachsous cadherins. Pioneering genetic studies in Drosophila have defined both subfamilies and dissected their roles in animal development. It is now clear that the founding members in Drosophila and their respective vertebrate homologues make critical and essential contributions to a variety of dynamic behaviors of cell populations, and that malfunctions of those atypical cadherins cause anomalies in embryonic development, resulting in postnatal organ malformation or embryonic demise. Here we discuss how the atypical cadherins control cell behaviors with the emphasis on one particular orchestration of cells along the axes of tissues, organs, or bodies, inclusively designated as planar cell polarity (PCP). Nowadays the purview of PCP ranges from the unidirectional orientation of subcellular structures, such as wing hairs of Drosophila and vertebrate motile cilia, to three-dimensional dynamics of multicellular units, such as tilting hair follicles, neural tube closure, epithelial folding in the oviduct, and collective cell migration. The PCP field is at an extraordinarily exciting juncture, bursting with questions about functions of 7-TM cadherins and Fat and Dachsous cadherins at the cellular and molecular level.
Shi D, Fujimori T, Uemura T. (2013). Atypical cadherin negotiates a turn. Dev Cell. 26(1):1-2.
Planar cell polarity (PCP) signaling is involved in many polarized cell behaviors. In this issue of Developmental Cell, Tatin et al. (2013) show that the atypical cadherin Celsr1 is transiently localized to cellular protrusions in lymphatic endothelial cells and acts to orient valve-forming cells perpendicular to the vessel axis.