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Developmental Biology/Physiology Dr. Thomas Thumberger

Thomas Thumberger is a developmental biologist researching medaka fish development under the aspect of abberant glycosylation.

Im Neuenheimer Feld 230
69120 Heidelberg
Fon +49 6221 54-6254
Fax +49 6221 54-5639
thomas.thumberger@cos.uni-heidelberg.de

published advances in targeted genome editing

guide RNA design for targeted genome editing

Efficient and comprehensive prediction and selection of guide RNAs for targeted genome editing and evaluation of potential off-targets in genomes with CCTOP

guide RNA design for base editing
base editing pipeline with up to 100% efficiency in the injected generation, design of codon changes and predicition of off-targets available through our tool ACEofBASEs

limitations of the genome editing space
boosting Cas9 efficiency

tagging endonucleases with the “hei-tag” (a myc-flexible-linker-oNLS; optimized nuclear localization signal) dramatically boosts Cas9 efficiency by simultaneously reducing allelic variance boosting efficiency of Cas9 editing by applying the “hei-tag” to endonucleases

hei-tag-Cas9 = heiCas9 with increased genome targeting efficiency
facilitate single-copy integration via homology directed repair

Any donor sequence introduced into a cell will inevietably concatenate which often leads to insertion as multimer. Adding bulky moieties like biotin to both ends of a donor-PCR-fragment prevents multimerisation of the donor and favors single-molecule-insertion during homology repair.
in fish: Efficient single-copy HDR by 5’ modified long dsDNA donors
and mouse: Efficient single copy integration via homology-directed repair (scHDR) by 5'modification of large DNA donor fragments in mice

biotinylated PCR donor stays monomeric, improving single copy integration via HDR
de novo PAM generation increases base editing range

Applying base editing in a staggered mode, the „inception“ approach 
broadens the targeting scope of base editors by 60 %. De novo PAM generation to reach initially inaccessible target sites for base editing

“inception” - de novo PAM generation allaws editing nucleotides previously out of reach

List of Preprints

Gierten, J., Welz, B., Fitzgerald, T., Thumberger, T., Hummel, O., Leger, A., Weber, P., Hassel, D., Hübner, N., Birney, E., Wittbrodt, J., 2023. Natural genetic variation quantitatively regulates heart rate and dimension. bioRxiv, 2023.2009.2001.555906, 10.1101/2023.09.01.555906.

Publication list

2024

Suzuki, R., Woo, J.Z., Thumberger, T., Hofmann, G., Wittbrodt, J., Tavhelidse-Suck, T., 2024. Characterizing medaka visual features using a high-throughput optomotor response assay. PLoS One 19, e0302092, 10.1371/journal.pone.0302092.

2023

Pakari, K., Wittbrodt, J., Thumberger, T., 2023. CRISPR-Fortschritte—Schnitt für Schnitt zu neuen Möglichkeiten. BIOspektrum 29, 25-28, 10.1007/s12268-023-1893-z.

Pakari, K., Wittbrodt, J., Thumberger, T., 2023. De novo PAM generation to reach initially inaccessible target sites for base editing. Development 150, 10.1242/dev.201115.

Medert, R., Thumberger, T., Tavhelidse-Suck, T., Hub, T., Kellner, T., Oguchi, Y., Dlugosz, S., Zimmermann, F., Wittbrodt, J., Freichel, M., 2023. Efficient single copy integration via homology-directed repair (scHDR) by 5'modification of large DNA donor fragments in mice. Nucleic Acids Res 51, e14, 10.1093/nar/gkac1150.

Gierten, J., Welz, B., Fitzgerald, T., Thumberger, T., Hummel, O., Leger, A., Weber, P., Hassel, D., Hubner, N., Birney, E., Wittbrodt, J., 2023. Natural genetic variation quantitatively regulates heart rate and dimension. bioRxiv, 10.1101/2023.09.01.555906.

Doering, L., Cornean, A., Thumberger, T., Benjaminsen, J., Wittbrodt, B., Kellner, T., Hammouda, O.T., Gorenflo, M., Wittbrodt, J., Gierten, J., 2023. CRISPR-based knockout and base editing confirm the role of MYRF in heart development and congenital heart disease. Dis Model Mech 16, 10.1242/dmm.049811.

2022

Thumberger, T., Tavhelidse-Suck, T., Gutierrez-Triana, J.A., Cornean, A., Medert, R., Welz, B., Freichel, M., Wittbrodt, J., 2022. Boosting targeted genome editing using the hei-tag. Elife 11, 10.7554/eLife.70558.

Leger, A., Brettell, I., Monahan, J., Barton, C., Wolf, N., Kusminski, N., Herder, C., Aadepu, N., Becker, C., Gierten, J., Hammouda, O.T., Hasel, E., Lischik, C., Lust, K., Sokolova, N., Suzuki, R., Tavhelidse, T., Thumberger, T., Tsingos, E., Watson, P., Welz, B., Naruse, K., Loosli, F., Wittbrodt, J., Birney, E., Fitzgerald, T., 2022. Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. Genome Biol 23, 58, 10.1186/s13059-022-02602-4.

Fitzgerald, T., Brettell, I., Leger, A., Wolf, N., Kusminski, N., Monahan, J., Barton, C., Herder, C., Aadepu, N., Gierten, J., Becker, C., Hammouda, O.T., Hasel, E., Lischik, C., Lust, K., Sokolova, N., Suzuki, R., Tsingos, E., Tavhelidse, T., Thumberger, T., Watson, P., Welz, B., Khouja, N., Naruse, K., Birney, E., Wittbrodt, J., Loosli, F., 2022. The Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. Genome Biol 23, 59, 10.1186/s13059-022-02623-z.

Cornean, A., Gierten, J., Welz, B., Mateo, J.L., Thumberger, T., Wittbrodt, J., 2022. Precise in vivo functional analysis of DNA variants with base editing using ACEofBASEs target prediction. Elife 11, 10.7554/eLife.72124.

Beedgen, L., Hullen, A., Gucum, S., Thumberger, T., Wittbrodt, J., Thiel, C., 2022. A rapid and simple procedure for the isolation and cultivation of fibroblast-like cells from medaka and zebrafish embryos and fin clip biopsies. Lab Anim 56, 270-278, 10.1177/00236772211045483.

2021

Zilova, L., Weinhardt, V., Tavhelidse, T., Schlagheck, C., Thumberger, T., Wittbrodt, J., 2021. Fish primary embryonic pluripotent cells assemble into retinal tissue mirroring in vivo early eye development. Elife 10, 10.7554/eLife.66998.

Hammouda, O.T., Wu, M.Y., Kaul, V., Gierten, J., Thumberger, T., Wittbrodt, J., 2021. In vivo identification and validation of novel potential predictors for human cardiovascular diseases. PLoS One 16, e0261572, 10.1371/journal.pone.0261572.

Gucum, S., Sakson, R., Hoffmann, M., Grote, V., Becker, C., Pakari, K., Beedgen, L., Thiel, C., Rapp, E., Ruppert, T., Thumberger, T., Wittbrodt, J., 2021. A patient-based medaka alg2 mutant as a model for hypo-N-glycosylation. Development 148, 10.1242/dev.199385.

Cirksena, K., Hutte, H.J., Shcherbakova, A., Thumberger, T., Sakson, R., Weiss, S., Jensen, L.R., Friedrich, A., Todt, D., Kuss, A.W., Ruppert, T., Wittbrodt, J., Bakker, H., Buettner, F.F.R., 2021. The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development. Mol Cell Proteomics 20, 100092, 10.1016/j.mcpro.2021.100092.

Aghaallaei, N., Dick, A.M., Tsingos, E., Inoue, D., Hasel, E., Thumberger, T., Toyoda, A., Leptin, M., Wittbrodt, J., Bajoghli, B., 2021. alphabeta/gammadelta T cell lineage outcome is regulated by intrathymic cell localization and environmental signals. Sci Adv 7, 10.1126/sciadv.abg3613.

2020

Meyer, H.V., Dawes, T.J.W., Serrani, M., Bai, W., Tokarczuk, P., Cai, J., de Marvao, A., Henry, A., Lumbers, R.T., Gierten, J., Thumberger, T., Wittbrodt, J., Ware, J.S., Rueckert, D., Matthews, P.M., Prasad, S.K., Costantino, M.L., Cook, S.A., Birney, E., O'Regan, D.P., 2020. Genetic and functional insights into the fractal structure of the heart. Nature 584, 589-594, 10.1038/s41586-020-2635-8.

Mederer, T., Schmitteckert, S., Volz, J., Martinez, C., Roth, R., Thumberger, T., Eckstein, V., Scheuerer, J., Thoni, C., Lasitschka, F., Carstensen, L., Gunther, P., Holland-Cunz, S., Hofstra, R., Brosens, E., Rosenfeld, J.A., Schaaf, C.P., Schriemer, D., Ceccherini, I., Rusmini, M., Tilghman, J., Luzon-Toro, B., Torroglosa, A., Borrego, S., Sze-Man Tang, C., Garcia-Barcelo, M., Tam, P., Paramasivam, N., Bewerunge-Hudler, M., De La Torre, C., Gretz, N., Rappold, G.A., Romero, P., Niesler, B., 2020. A complementary study approach unravels novel players in the pathoetiology of Hirschsprung disease. PLoS Genet 16, e1009106, 10.1371/journal.pgen.1009106.

Bosze, B., Ono, Y., Mattes, B., Sinner, C., Gourain, V., Thumberger, T., Tlili, S., Wittbrodt, J., Saunders, T.E., Strahle, U., Schug, A., Scholpp, S., 2020. Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish. Histochem Cell Biol 154, 463-480, 10.1007/s00418-020-01887-5.

2019

Hammouda, O.T., Bottger, F., Wittbrodt, J., Thumberger, T., 2019. Swift Large-scale Examination of Directed Genome Editing. PLoS One 14, e0213317, 10.1371/journal.pone.0213317.

2018

Vick, P., Kreis, J., Schneider, I., Tingler, M., Getwan, M., Thumberger, T., Beyer, T., Schweickert, A., Blum, M., 2018. An Early Function of Polycystin-2 for Left-Right Organizer Induction in Xenopus. iScience 2, 76-85, 10.1016/j.isci.2018.03.011.

Gutierrez-Triana, J.A., Tavhelidse, T., Thumberger, T., Thomas, I., Wittbrodt, B., Kellner, T., Anlas, K., Tsingos, E., Wittbrodt, J., 2018. Efficient single-copy HDR by 5' modified long dsDNA donors. Elife 7, 10.7554/eLife.39468.

2017

Ulmer, B., Tingler, M., Kurz, S., Maerker, M., Andre, P., Monch, D., Campione, M., Deissler, K., Lewandoski, M., Thumberger, T., Schweickert, A., Fainsod, A., Steinbeisser, H., Blum, M., 2017. A novel role of the organizer gene Goosecoid as an inhibitor of Wnt/PCP-mediated convergent extension in Xenopus and mouse. Sci Rep 7, 43010, 10.1038/srep43010.

Tisler, M., Thumberger, T., Schneider, I., Schweickert, A., Blum, M., 2017. Leftward Flow Determines Laterality in Conjoined Twins. Curr Biol 27, 543-548, 10.1016/j.cub.2016.12.049.

Stemmer, M., Thumberger, T., Del Sol Keyer, M., Wittbrodt, J., Mateo, J.L., 2017. Correction: CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS One 12, e0176619, 10.1371/journal.pone.0176619.

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, 10.1016/j.gde.2017.02.002.

Kuri, P., Schieber, N.L., Thumberger, T., Wittbrodt, J., Schwab, Y., Leptin, M., 2017. Dynamics of in vivo ASC speck formation. J Cell Biol 216, 2891-2909, 10.1083/jcb.201703103.

Kuri, P., Schieber, N.L., Thumberger, T., Wittbrodt, J., Schwab, Y., Leptin, M., 2017. Correction: Dynamics of in vivo ASC speck formation. J Cell Biol 216, 3423-3424, 10.1083/JCB.20170310308302017c.

Inoue, D., Stemmer, M., Thumberger, T., Ruppert, T., Barenz, F., Wittbrodt, J., Gruss, O.J., 2017. Expression of the novel maternal centrosome assembly factor Wdr8 is required for vertebrate embryonic mitoses. Nat Commun 8, 14090, 10.1038/ncomms14090.

2016

Tisler, M., Wetzel, F., Mantino, S., Kremnyov, S., Thumberger, T., Schweickert, A., Blum, M., Vick, P., 2016. Cilia are required for asymmetric nodal induction in the sea urchin embryo. BMC Dev Biol 16, 28, 10.1186/s12861-016-0128-7.

Kromm, D., Thumberger, T., Wittbrodt, J., 2016. An eye on light-sheet microscopy. Methods Cell Biol 133, 105-123, 10.1016/bs.mcb.2016.01.001.

Bert, B., Chmielewska, J., Bergmann, S., Busch, M., Driever, W., Finger-Baier, K., Hossler, J., Kohler, A., Leich, N., Misgeld, T., Noldner, T., Reiher, A., Schartl, M., Seebach-Sproedt, A., Thumberger, T., Schonfelder, G., Grune, B., 2016. Considerations for a European animal welfare standard to evaluate adverse phenotypes in teleost fish. EMBO J 35, 1151-1154, 10.15252/embj.201694448.

2015

Stemmer, M., Thumberger, T., Del Sol Keyer, M., Wittbrodt, J., Mateo, J.L., 2015. CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS One 10, e0124633, 10.1371/journal.pone.0124633.

Bajoghli, B., Kuri, P., Inoue, D., Aghaallaei, N., Hanelt, M., Thumberger, T., Rauzi, M., Wittbrodt, J., Leptin, M., 2015. Noninvasive In Toto Imaging of the Thymus Reveals Heterogeneous Migratory Behavior of Developing T Cells. J Immunol 195, 2177-2186, 10.4049/jimmunol.1500361.

2014

Walentek, P., Bogusch, S., Thumberger, T., Vick, P., Dubaissi, E., Beyer, T., Blum, M., Schweickert, A., 2014. A novel serotonin-secreting cell type regulates ciliary motility in the mucociliary epidermis of Xenopus tadpoles. Development 141, 1526-1533, 10.1242/dev.102343.

Blum, M., Feistel, K., Thumberger, T., Schweickert, A., 2014. The evolution and conservation of left-right patterning mechanisms. Development 141, 1603-1613, 10.1242/dev.100560.

2013

Hagenlocher, C., Walentek, P., C, M.L., Thumberger, T., Feistel, K., 2013. Ciliogenesis and cerebrospinal fluid flow in the developing Xenopus brain are regulated by foxj1. Cilia 2, 12, 10.1186/2046-2530-2-12.

2012

Walentek, P., Beyer, T., Thumberger, T., Schweickert, A., Blum, M., 2012. ATP4a is required for Wnt-dependent Foxj1 expression and leftward flow in Xenopus left-right development. Cell Rep 1, 516-527, 10.1016/j.celrep.2012.03.005.

Thumberger, T., Hagenlocher, C., Tisler, M., Beyer, T., Tietze, N., Schweickert, A., Feistel, K., Blum, M., 2012. Ciliary and non-ciliary expression and function of PACRG during vertebrate development. Cilia 1, 13, 10.1186/2046-2530-1-13.

Schweickert, A., Walentek, P., Thumberger, T., Danilchik, M., 2012. Linking early determinants and cilia-driven leftward flow in left-right axis specification of Xenopus laevis: a theoretical approach. Differentiation 83, S67-77, 10.1016/j.diff.2011.11.005.

Hockendorf, B., Thumberger, T., Wittbrodt, J., 2012. Quantitative analysis of embryogenesis: a perspective for light sheet microscopy. Dev Cell 23, 1111-1120, 10.1016/j.devcel.2012.10.008.

Beyer, T., Thumberger, T., Schweickert, A., Blum, M., 2012. Connexin26-mediated transfer of laterality cues in Xenopus. Biol Open 1, 473-481, 10.1242/bio.2012760.

Beyer, T., Danilchik, M., Thumberger, T., Vick, P., Tisler, M., Schneider, I., Bogusch, S., Andre, P., Ulmer, B., Walentek, P., Niesler, B., Blum, M., Schweickert, A., 2012. Serotonin signaling is required for Wnt-dependent GRP specification and leftward flow in Xenopus. Curr Biol 22, 33-39, 10.1016/j.cub.2011.11.027.

2010

Schweickert, A., Vick, P., Getwan, M., Weber, T., Schneider, I., Eberhardt, M., Beyer, T., Pachur, A., Blum, M., 2010. The nodal inhibitor Coco is a critical target of leftward flow in Xenopus. Curr Biol 20, 738-743, 10.1016/j.cub.2010.02.061.

2009

Vick, P., Schweickert, A., Weber, T., Eberhardt, M., Mencl, S., Shcherbakov, D., Beyer, T., Blum, M., 2009. Flow on the right side of the gastrocoel roof plate is dispensable for symmetry breakage in the frog Xenopus laevis. Dev Biol 331, 281-291, 10.1016/j.ydbio.2009.05.547.

Maisonneuve, C., Guilleret, I., Vick, P., Weber, T., Andre, P., Beyer, T., Blum, M., Constam, D.B., 2009. Bicaudal C, a novel regulator of Dvl signaling abutting RNA-processing bodies, controls cilia orientation and leftward flow. Development 136, 3019-3030, 10.1242/dev.038174.

Blum, M., Weber, T., Beyer, T., Vick, P., 2009. Evolution of leftward flow. Semin Cell Dev Biol 20, 464-471, 10.1016/j.semcdb.2008.11.005.

Blum, M., Beyer, T., Weber, T., Vick, P., Andre, P., Bitzer, E., Schweickert, A., 2009. Xenopus, an ideal model system to study vertebrate left-right asymmetry. Dev Dyn 238, 1215-1225, 10.1002/dvdy.21855.

2007

Schweickert, A., Weber, T., Beyer, T., Vick, P., Bogusch, S., Feistel, K., Blum, M., 2007. Cilia-driven leftward flow determines laterality in Xenopus. Curr Biol 17, 60-66, 10.1016/j.cub.2006.10.067.