ZFIN ID: ZDB-LAB-970903-4
Herbomel Lab
PI/Director: Herbomel, Philippe
Co-PI / Senior
Colucci-Guyon, Emma
Contact Person: Herbomel, Philippe
Email: herbomel@pasteur.fr
URL: http://research.pasteur.fr/en/team/mdi/
Address: 'Macrophages & Development of Immunity' Lab Department of Developmental & Stem Cell Biology Institut Pasteur 25 rue du Dr Roux Paris, 75724 cedex 15 France
Country: France
Phone: 33-1-44-38-95-29
Fax: 33-1-40-61-34-40
Line Designation: ip

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In vivo analysis of cell behaviours in embryogenesis; primitive macrophages, granulocytes; developmental hematopoiesis, from stem cell emergence to niches, to tissue leukocytes; microglia; innate immunity; phagocytes-microbes interactions; host responses to viral infection;

Demy, Doris-Lou Post-Doc Hernández-Cerda, Pedro Post-Doc Torcq, Léa Graduate Student
Touret, Anne-Lou Graduate Student Boucontet, Laurent Technical Staff Majello, Sara Technical Staff
Rolin, Yohann Technical Staff Vivier, Catherine Technical Staff Boutout, Laurence Administrative Staff
Laghi, Valerio

Torcq, L., Majello, S., Vivier, C., Schmidt, A.A. (2024) Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells. eLIFE. 12:
Elsaid, R., Mikdache, A., Castillo, K.Q., Salloum, Y., Diabangouaya, P., Gros, G., Feijoo, C.G., Hernández, P.P. (2024) Definitive hematopoiesis is dispensable to sustain erythrocytes and macrophages during zebrafish ontogeny. iScience. 27:108922108922
Viana, F., Boucontet, L., Laghi, V., Schator, D., Ibranosyan, M., Jarraud, S., Colucci-Guyon, E., Buchrieser, C. (2023) Hiding in the yolk: A unique feature of Legionella pneumophila infection of zebrafish. PLoS pathogens. 19:e1011375e1011375
Murayama, E., Vivier, C., Schmidt, A., Herbomel, P. (2023) Alcam-a and Pdgfr-α are essential for the development of sclerotome-derived stromal cells that support hematopoiesis. Nature communications. 14:11711171
Prendergast, A.E., Jim, K.K., Marnas, H., Desban, L., Quan, F.B., Djenoune, L., Laghi, V., Hocquemiller, A., Lunsford, E.T., Roussel, J., Keiser, L., Lejeune, F.X., Dhanasekar, M., Bardet, P.L., Levraud, J.P., van de Beek, D., Vandenbroucke-Grauls, C.M.J.E., Wyart, C. (2023) CSF-contacting neurons respond to Streptococcus pneumoniae and promote host survival during central nervous system infection. Current biology : CB. 33(5):940-956.e10
Touret, A.L., Vivier, C., Schmidt, A., Herbomel, P., Murayama, E. (2022) A dual involvement of Protocadherin-18a in stromal cell development guides the formation of a functional hematopoietic niche. Development (Cambridge, England). 149(19)
Demy, D.L., Touret, A.L., Lancino, M., Tauzin, M., Capuana, L., Pierre, C., Herbomel, P. (2022) Trim33 conditions the lifespan of primitive macrophages and onset of definitive macrophage production. Development (Cambridge, England). 149(18):
Morales, R.A., Rabahi, S., Diaz, O.E., Salloum, Y., Kern, B.C., Westling, M., Luo, X., Parigi, S.M., Monasterio, G., Das, S., Hernández, P.P., Villablanca, E.J. (2022) Interleukin-10 regulates goblet cell numbers through Notch signaling in the developing zebrafish intestine. Mucosal immunology. 15(5):940-951
Leseigneur, C., Boucontet, L., Duchateau, M., Pizarro-Cerda, J., Matondo, M., Colucci-Guyon, E., Dussurget, O. (2022) NAD kinase promotes Staphylococcus aureus pathogenesis by supporting production of virulence factors and protective enzymes. eLIFE. 11
Laghi, V., Rezelj, V., Boucontet, L., Frétaud, M., Da Costa, B., Boudinot, P., Salinas, I., Lutfalla, G., Vignuzzi, M., Levraud, J.P. (2022) Exploring Zebrafish Larvae as a COVID-19 Model: Probable Abortive SARS-CoV-2 Replication in the Swim Bladder. Frontiers in cellular and infection microbiology. 12:790851
Blokzijl-Franke, S., Ponsioen, B., Schulte-Merker, S., Herbomel, P., Kissa, K., Choorapoikayil, S., den Hertog, J. (2021) Phosphatidylinositol-3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells. Oncogene. 40(15):2741-2755
Colucci-Guyon, E., Rifflet, A., Saint-Auret, S., da Costa, A., Boucontet, L., Laval, T., Prehaud, C., Blanchard, N., Levraud, J.P., Boneca, I.G., Demangel, C., Guenin-Macé, L. (2020) Spatiotemporal analysis of mycolactone distribution in vivo reveals partial diffusion in the central nervous system. PLoS neglected tropical diseases. 14:e0008878
Demy, D.L., Carrère, M., Noche, R., Tauzin, M., Le Bris, M., Baek, C., Leshchiner, I., Goessling, W., Herbomel, P. (2020) The cationic amino acid exporter Slc7a7 is induced and vital in tissue macrophages with sustained efferocytic activity. Journal of Cell Science. 133(20):
Demy, D.L., Campanari, M.L., Munoz-Ruiz, R., Durham, H.D., Gentil, B.J., Kabashi, E. (2020) Functional Characterization of Neurofilament Light Splicing and Misbalance in Zebrafish. Cells. 9(5):
Bowes, C., Redd, M., Yousfi, M., Tauzin, M., Murayama, E., Herbomel, P. (2019) Coronin 1A depletion restores the nuclear stability and viability of Aip1/Wdr1-deficient neutrophils. The Journal of cell biology. 218(10):3258-3271
Levraud, J.P., Herbomel, P. (2019) Resident Macrophage Lookalikes of Unexpected Origin. Developmental Cell. 49:501-502
Lavalou, P., Eckert, H., Damy, L., Constanty, F., Majello, S., Bitetti, A., Graindorge, A., Shkumatava, A. (2019) Strategies for Genetic Inactivation of Long Noncoding RNAs in Zebrafish. RNA (New York, N.Y.). 25(8):897-904
Colucci-Guyon, E., Batista, A.S., Oliveira, S.D.S., Blaud, M., Bellettini, I.C., Marteyn, B.S., Leblanc, K., Herbomel, P., Duval, R. (2019) Ultraspecific live imaging of the dynamics of zebrafish neutrophil granules by a histopermeable fluorogenic benzochalcone probe. Chemical science. 10:3654-3670
Verweij, F.J., Revenu, C., Arras, G., Dingli, F., Loew, D., Pegtel, M.D., Follain, G., Allio, G., Goetz, J.G., Zimmermann, P., Herbomel, P., Del Bene, F., Raposo, G., van Niel, G. (2019) Live Tracking of Inter-organ Communication by Endogenous Exosomes In Vivo. Developmental Cell. 48(4):573-589.e4
Lancino, M., Majello, S., Herbert, S., De Chaumont, F., Tinevez, J.Y., Olivo-Marin, J.C., Herbomel, P., Schmidt, A. (2018) Anisotropic organization of circumferential actomyosin characterizes hematopoietic stem cells emergence in the zebrafish. eLIFE. 7:
Boucontet, L., Passoni, G., Thiry, V., Maggi, L., Herbomel, P., Levraud, J.P., Colucci-Guyon, E. (2018) A Model of Superinfection of Virus-Infected Zebrafish Larvae: Increased Susceptibility to Bacteria Associated With Neutrophil Death. Frontiers in immunology. 9:1084
Demy, D.L., Tauzin, M., Lancino, M., le Cabec, V., Redd, M., Murayama, E., Maridonneau-Parini, I., Trede, N., Herbomel, P. (2017) Trim33 / Tif1-γ is essential for macrophage and neutrophil mobilisation to developmental or inflammatory cues. Journal of Cell Science. 130(17):2797-2807
Passoni, G., Langevin, C., Palha, N., Mounce, B.C., Briolat, V., Affaticati, P., De Job, E., Joly, J.S., Vignuzzi, M., Saleh, M.C., Herbomel, P., Boudinot, P., Levraud, J.P. (2017) Imaging of viral neuroinvasion in the zebrafish reveals that Sindbis and chikungunya viruses favour different entry routes. Disease models & mechanisms. 10(7):847-857
Mazon-Moya, M.J., Willis, A.R., Torraca, V., Boucontet, L., Shenoy, A.R., Colucci-Guyon, E., Mostowy, S. (2017) Septins restrict inflammation and protect zebrafish larvae from Shigella infection. PLoS pathogens. 13:e1006467
Delmaghani, S., Aghaie, A., Bouyacoub, Y., El Hachmi, H., Bonnet, C., Riahi, Z., Chardenoux, S., Perfettini, I., Hardelin, J.P., Houmeida, A., Herbomel, P., Petit, C. (2016) Mutations in CDC14A, Encoding a Protein Phosphatase Involved in Hair Cell Ciliogenesis, Cause Autosomal-Recessive Severe to Profound Deafness. American journal of human genetics. 98:1266-1270
Murayama, E., Sarris, M., Redd, M., Le Guyader, D., Vivier, C., Horsley, W., Trede, N., Herbomel, P. (2015) NACA deficiency reveals the crucial role of somite-derived stromal cells in haematopoietic niche formation. Nature communications. 6:8375
Mazon Moya, M.J., Colucci-Guyon, E., Mostowy, S. (2014) Use of Shigella flexneri to Study Autophagy-Cytoskeleton Interactions. Journal of visualized experiments : JoVE. (91):e51601
Briolat, V., Jouneau, L., Carvalho, R., Palha, N., Langevin, C., Herbomel, P., Schwartz, O., Spaink, H.P., Levraud, J.P., Boudinot, P. (2014) Contrasted Innate Responses to Two Viruses in Zebrafish: Insights into the Ancestral Repertoire of Vertebrate IFN-Stimulated Genes. Journal of immunology (Baltimore, Md. : 1950). 192:4328-41
Choorapoikayil, S., Kers, R., Herbomel, P., Kissa, K., and den Hertog, J. (2014) Pivotal role of Pten in the balance between proliferation and differentiation of hematopoietic stem cells in zebrafish. Blood.
Recher, G., Jouralet, J., Brombin, A., Heuzé, A., Mugniery, E., Hermel, J.M., Desnoulez, S., Savy, T., Herbomel, P., Bourrat, F., Peyriéras, N., Jamen, F., and Joly, J.S. (2013) Zebrafish midbrain slow-amplifying progenitors exhibit high levels of transcripts for nucleotide and ribosome biogenesis. Development (Cambridge, England). 140(24):4860-9
Deng, Q., Sarris, M., Bennin, D.A., Green, J.M., Herbomel, P., and Huttenlocher, A. (2013) Localized bacterial infection induces systemic activation of neutrophils through Cxcr2 signaling in zebrafish. Journal of Leukocyte Biology. 93(5):761-9
Demy, D.L., Ranta, Z., Giorgi, J.M., Gonzalez, M., Herbomel, P., and Kissa, K. (2013) Generating parabiotic zebrafish embryos for cell migration and homing studies. Nature Methods. 10(3):256-258
Mostowy, S., Boucontet, L., Mazon Moya, M.J., Sirianni, A., Boudinot, P., Hollinshead, M., Cossart, P., Herbomel, P., Levraud, J.P., and Colucci-Guyon, E. (2013) The Zebrafish as a New Model for the In Vivo Study of Shigella flexneri Interaction with Phagocytes and Bacterial Autophagy. PLoS pathogens. 9(9):e1003588
Palha, N., Guivel-Benhassine, F., Briolat, V., Lutfalla, G., Sourisseau, M., Ellett, F., Wang, C.H., Lieschke, G.J., Herbomel, P., Schwartz, O., and Levraud, J.P. (2013) Real-time whole-body visualization of chikungunya virus infection and host interferon response in zebrafish. PLoS pathogens. 9(9):e1003619
Prudent, J., Popgeorgiev, N., Bonneau, B., Thibaut, J., Gadet, R., Lopez, J., Gonzalo, P., Rimokh, R., Manon, S., Houart, C., Herbomel, P., Aouacheria, A., and Gillet, G. (2013) Bcl-wav and the mitochondrial calcium uniporter drive gastrula morphogenesis in zebrafish. Nature communications. 4:2330
Sarris, M., Masson, J.B., Maurin, D., Van der Aa, L.M., Boudinot, P., Lortat-Jacob, H., and Herbomel, P. (2012) Inflammatory Chemokines Direct and Restrict Leukocyte Migration within Live Tissues as Glycan-Bound Gradients. Current biology : CB. 22(24):2375-2382
Herbomel, P. (2012) Infection-induced hematopoiesis: a zebrafish perspective. Cell Stem Cell. 10(2):105-106
Rendueles, O., Ferrières, L., Frétaud, M., Bégaud, E., Herbomel, P., Levraud, J.P., and Ghigo, J.M. (2012) A new zebrafish model of Oro-intestinal pathogen colonization reveals a key role for adhesion in protection by probiotic bacteria. PLoS pathogens. 8(7):e1002815
Renaud, O., Herbomel, P., and Kissa, K. (2011) Studying cell behavior in whole zebrafish embryos by confocal live imaging: application to hematopoietic stem cells. Nature Protocols. 6(12):1897-1904
Colucci-Guyon, E., Tinevez, J.Y., Renshaw, S.A., and Herbomel, P. (2011) Strategies of professional phagocytes in vivo: unlike macrophages, neutrophils engulf only surface-associated microbes. Journal of Cell Science. 124(Pt 18):3053-9
Ludwig, M., Palha, N., Torhy, C., Briolat, V., Colucci-Guyon, E., Brémont, M., Herbomel, P., Boudinot, P., and Levraud, J.P. (2011) Whole-Body Analysis of a Viral Infection: Vascular Endothelium is a Primary Target of Infectious Hematopoietic Necrosis Virus in Zebrafish Larvae. PLoS pathogens. 7(2):e1001269
Aggad, D., Stein, C., Sieger, D., Mazel, M., Boudinot, P., Herbomel, P., Levraud, J.P., Lutfalla, G., and Leptin, M. (2010) In Vivo Analysis of Ifn-γ1 and Ifn-γ2 Signaling in Zebrafish. Journal of immunology (Baltimore, Md. : 1950). 185(11):6774-6782
Kissa, K., and Herbomel, P. (2010) Blood stem cells emerge from aortic endothelium by a novel type of cell transition. Nature. 464(7285):112-115
Aggad, D., Mazel, M., Boudinot, P., Mogensen, K.E., Hamming, O.J., Hartmann, R., Kotenko, S., Herbomel, P., Lutfalla, G., and Levraud, J.P. (2009) The two groups of zebrafish virus-induced interferons signal via distinct receptors with specific and shared chains. Journal of immunology (Baltimore, Md. : 1950). 183(6):3924-3931
Levraud, J.P., Disson, O., Kissa, K., Bonne, I., Cossart, P., Herbomel, P., and Lecuit, M. (2009) Real-time observation of Listeria-phagocyte interactions in the living zebrafish larva. Infection and Immunity. 77(9):3651-3660
van der Aa, L.M., Levraud, J.P., Yahmi, M., Lauret, E., Briolat, V., Herbomel, P., Benmansour, A., and Boudinot, P. (2009) A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish. BMC Biology. 7:7
Olivari, F.A., Hernández, P.P., and Allende, M.L. (2008) Acute copper exposure induces oxidative stress and cell death in lateral line hair cells of zebrafish larvae. Brain research. 1244:1-12
Hernández, P.P., and Allende, M.L. (2008) Zebrafish (Danio rerio) as a model for studying the genetic basis of copper toxicity, deficiency, and metabolism. The American journal of clinical nutrition. 88(3):835S-839S
Kissa, K., Murayama, E., Zapata, A., Cortes, A., Perret, E., Machu, C., and Herbomel, P. (2008) Live imaging of emerging hematopoietic stem cells and early thymus colonization. Blood. 111(3):1147-1156
Le Guyader, D., Redd, M.J., Colucci-Guyon, E., Murayama, E., Kissa, K., Briolat, V., Mordelet, E., Zapata, A., Shinomiya, H., and Herbomel, P. (2008) Origins and unconventional behavior of neutrophils in developing zebrafish. Blood. 111(1):132-141
Levraud, J.P., Colucci-Guyon, E., Redd, M.J., Lutfalla, G., and Herbomel, P. (2008) In Vivo Analysis of Zebrafish Innate Immunity. Methods in molecular biology (Clifton, N.J.). 415:337-363
Lepiller, S., Laurens, V., Bouchot, A., Herbomel, P., Solary, E., and Chluba, J. (2007) Imaging of nitric oxide in a living vertebrate using a diaminofluorescein probe. Free radical biology & medicine. 43(4):619-627
Kissa, K., Murayama, E., and Herbomel, P. (2007) The zebrafish reveals the odyssey of hematopoietic precursors in developing vertebrate embryos. Medecine sciences : M/S. 23(8-9):698-700
Levraud, J.P., Boudinot, P., Colin, I., Benmansour, A., Peyriéras, N., Herbomel, P., and Lutfalla, G. (2007) Identification of the Zebrafish IFN Receptor: Implications for the Origin of the Vertebrate IFN System. Journal of immunology (Baltimore, Md. : 1950). 178(7):4385-4394
Murayama, E., Kissa, K., Zapata, A., Mordelet, E., Briolat, V., Lin, H.F., Handin, R.I., and Herbomel, P. (2006) Tracing Hematopoietic Precursor Migration to Successive Hematopoietic Organs during Zebrafish Development. Immunity. 25(6):963-975
Murayama, E., Herbomel, P., Kawakami, A., Takeda, H., and Nagasawa H. (2005) Otolith matrix proteins OMP-1 and Otolin-1 are necessary for normal otolith growth and their correct anchoring onto the sensory maculae. Mechanisms of Development. 122(6):791-803
Herbomel, P., and Levraud, J.P. (2005) Imaging Early Macrophage Differentiation, Migration, and Behaviors in Live Zebrafish Embryos. Methods in molecular medicine. 105:199-214
Mathieu, J., Griffin, K., Herbomel, P., Dickmeis, T., Strähle, U., Kimelman, D., Rosa, F.M., and Peyriéras, N. (2004) Nodal and Fgf pathways interact through a positive regulatory loop and synergize to maintain mesodermal cell populations. Development (Cambridge, England). 131(3):629-641
Traver, D., Herbomel, P., Patton, E.E., Murphey, R.D., Yoder, J.A., Litman, G.W., Catic, A., Amemiya, C.T., Zon, L.I., and Trede, N.S. (2003) The zebrafish as a model organism to study development of the immune system. Advances in immunology. 81:253-330
Davis, J.M., Clay, H., Lewis, J.L., Ghori, N., Herbomel, P., and Ramakrishnan, L. (2002) Real-time visualization of mycobacterium-macrophage interactions leading to initiation of granuloma formation in zebrafish embryos. Immunity. 17(6):693-702
Herbomel, P., Thisse, B., and Thisse, C. (2001) Zebrafish early macrophages colonize cephalic mesenchyme and developing brain, retina, and epidermis through a M-CSF receptor-dependent invasive process. Developmental Biology. 238(2):274-288
Herbomel, P. (1999) Spinning nuclei in the brain of the zebrafish embryo. Current biology : CB. 9(17):R627-R628
Herbomel, P., Thisse, B., and Thisse, C. (1999) Ontogeny and behaviour of early macrophages in the zebrafish embryo. Development (Cambridge, England). 126(17):3735-3745