Bio


Paul Bump is an explorer of the small and squishy. His research in strange, enigmatic, marine invertebrates hopes to unlock secrets around basic biological processes and provide novel perspectives to advance fundamental cell biology research. He currently studies how an organism can build two wildly different bodies during its life while having access to the same genetic information. While puzzling, the process of indirect development, with distinct larval and adult body plans, is the most common developmental strategy in many animals. His research involves studying the metamorphosis of Schizocardium californicum, an indirect developing hemichordate worm, which transforms from a small swimming planktonic balloon into a burrowing, muscular worm in a 24-48 hour time period.

All Publications


  • Programmed cell removal by calreticulin in tissue homeostasis and cancer. Nature communications Feng, M., Marjon, K. D., Zhu, F., Weissman-Tsukamoto, R., Levett, A., Sullivan, K., Kao, K. S., Markovic, M., Bump, P. A., Jackson, H. M., Choi, T. S., Chen, J., Banuelos, A. M., Liu, J., Gip, P., Cheng, L., Wang, D., Weissman, I. L. 2018; 9 (1): 3194

    Abstract

    Macrophage-mediated programmed cell removal (PrCR) is a process essential for the clearance of unwanted (damaged, dysfunctional, aged, or harmful) cells. The detection and recognition of appropriate target cells by macrophages is a critical step for successful PrCR, but its molecular mechanisms have not been delineated. Here using the models of tissue turnover, cancer immunosurveillance, and hematopoietic stem cells, we show that unwanted cells such as aging neutrophils and living cancer cells are susceptible to "labeling" by secreted calreticulin (CRT) from macrophages, enabling their clearance through PrCR. Importantly, we identified asialoglycans on the target cells to which CRT binds to regulate PrCR, and the availability of such CRT-binding sites on cancer cells correlated with the prognosis of patients in various malignancies. Our study reveals a general mechanism of target cell recognition by macrophages, which is the key for the removal of unwanted cells by PrCR in physiological and pathophysiological processes.

    View details for PubMedID 30097573

  • Genome-wide analysis of facial skeletal regionalization in zebrafish. Development (Cambridge, England) Askary, A., Xu, P., Barske, L., Bay, M., Bump, P., Balczerski, B., Bonaguidi, M. A., Crump, J. G. 2017

    Abstract

    Patterning of the facial skeleton involves the precise deployment of thousands of genes in distinct regions of the pharyngeal arches. Despite the significance for craniofacial development, how genetic programs drive this regionalization remains incompletely understood. Here we use combinatorial labeling of zebrafish cranial neural crest-derived cells (CNCCs) to define global gene expression along the dorsoventral axis of the developing arches. Intersection of region-specific transcriptomes with expression changes in response to signaling perturbations demonstrates complex roles for Endothelin1 (Edn1) signaling in the intermediate joint-forming region, yet a surprisingly minor role in ventral-most regions. Analysis of co-variance across multiple sequencing experiments further reveals clusters of co-regulated genes, with in situ hybridization confirming the domain-specific expression of novel genes. We then created loss-of-function alleles for 12 genes and uncovered antagonistic functions of two new Edn1 targets, follistatin a (fsta) and emx2, in regulating cartilaginous joints in the hyoid arch. Our unbiased discovery and functional analysis of genes with regional expression in zebrafish arch CNCCs reveals complex regulation by Edn1 and points to novel candidates for craniofacial disorders.

    View details for DOI 10.1242/dev.151712

    View details for PubMedID 28705894

  • Competition between Jagged-Notch and Endothelin1 Signaling Selectively Restricts Cartilage Formation in the Zebrafish Upper Face PLOS GENETICS Barske, L., Askary, A., Zuniga, E., Balczerski, B., Bump, P., Nichols, J. T., Crump, J. G. 2016; 12 (4)

    Abstract

    The intricate shaping of the facial skeleton is essential for function of the vertebrate jaw and middle ear. While much has been learned about the signaling pathways and transcription factors that control facial patterning, the downstream cellular mechanisms dictating skeletal shapes have remained unclear. Here we present genetic evidence in zebrafish that three major signaling pathways - Jagged-Notch, Endothelin1 (Edn1), and Bmp - regulate the pattern of facial cartilage and bone formation by controlling the timing of cartilage differentiation along the dorsoventral axis of the pharyngeal arches. A genomic analysis of purified facial skeletal precursors in mutant and overexpression embryos revealed a core set of differentiation genes that were commonly repressed by Jagged-Notch and induced by Edn1. Further analysis of the pre-cartilage condensation gene barx1, as well as in vivo imaging of cartilage differentiation, revealed that cartilage forms first in regions of high Edn1 and low Jagged-Notch activity. Consistent with a role of Jagged-Notch signaling in restricting cartilage differentiation, loss of Notch pathway components resulted in expanded barx1 expression in the dorsal arches, with mutation of barx1 rescuing some aspects of dorsal skeletal patterning in jag1b mutants. We also identified prrx1a and prrx1b as negative Edn1 and positive Bmp targets that function in parallel to Jagged-Notch signaling to restrict the formation of dorsal barx1+ pre-cartilage condensations. Simultaneous loss of jag1b and prrx1a/b better rescued lower facial defects of edn1 mutants than loss of either pathway alone, showing that combined overactivation of Jagged-Notch and Bmp/Prrx1 pathways contribute to the absence of cartilage differentiation in the edn1 mutant lower face. These findings support a model in which Notch-mediated restriction of cartilage differentiation, particularly in the second pharyngeal arch, helps to establish a distinct skeletal pattern in the upper face.

    View details for DOI 10.1371/journal.pgen.1005967

    View details for Web of Science ID 000375231900019

    View details for PubMedID 27058748

    View details for PubMedCentralID PMC4825933