Sevim-Wunderlich, S., Dang, T., Rossius, J., Schnütgen, F., Kühn, R. (2024) An X-linked Chronic Granulomatous disease mouse model for CRISPR/Cas9 gene therapy development. Genes (in press)
2023
Seibert, M., Koschade, S.E., Stolp, V., Häupl, B., Wempe, F., Serve, H., Kurrle, N.*, Schnütgen, F.*, and von Metzler, I.* (2023) The MYC-Regulated RNA Binding Proteins hnRNPC and LARP1 are Drivers of Multiple Myeloma Cell Growth and Disease Progression and Negatively Predict Patient Survival. Cancers 15, 5508
Alshamleh, I., Kurrle, N., Makowka, P., Bhayadia, R., Kumar, R., Süsser, S., Seibert, M., Ludig, D., Wolf, S., Koschade, S., Stoschek, K., Kreitz, J., Fuhrmann, D., Toenges, R., Notaro, M., Comoglio, F., Schuringa, J.J., Berg, T., Brüne, B., Krause, D., Klusmann, J.H., Oellerich, T., Schnütgen, F.*, Schwalbe, H.*, and Serve, H.* (2023) PDP1 is a key metabolic gatekeeper and modulator of drug resistance in FLT3-ITD-positive acute myeloid leukemia. Leukemia 37, 2367-2382
Scheich, S., Chen, J., Liu, J., Schnütgen, F., Enssle, J., Ceribelli, M., Thomas, C.J., Choi, J., Morris, V., Hsiao, T., Nguyen, H., Wang, B., Bolomsky, A., Phelan, J.D., Corcoran, S., Young, R.M., Häupl, B., Wright, G.W., Huang, D.W., Ji, Y., Yu, X., Xu, W., Yang, Y., Zhao, H., Muppidi, J., Pan, K.-T., Oellerich, T., and Staudt, L.M. (2023) Targeting N-linked Glycosylation for the Therapy of Aggressive Lymphomas. Cancer Discovery 13, 1862-1883
Edwards-Faret, G., de Vin, F., Slezak, M., Karaman, R., Gollenbeck, L., Shinmyo, Y,. Batiuk, M.Y., Menacho Pando, C., Urschitz, J., Rincon, M.Y., Moisyadi, S., Schnütgen, F., Kawasaki, H., Schmucker, D., & Holt, M.G. (2023) A new technical approach for cross-species examination of neuronal wiring and adult neuron-glia functions. Neuroscience 508, 40-51
Nold, S.P., Sych, K., Imre, G., Fuhrmann, D., Pfeilschifter, J., Vutukuri, R., Schnütgen, F., Wittig, I., Frank, S. & Goren, I. (2023) Reciprocal abrogation of PKM isoforms: contradictory outcomes and differing impact of splicing signal on CRISPR/Cas9 mediated gene editing in keratinocytes. FEBS1111/febs.16625
2022
Seibert, M., Kurrle, N., Stolp, V., Nürnberger, H., Tzschentke, S., Börner, L., Wempe, F., Serve, H., & Schnütgen, F. (2022) Selection-free endogenous tagging of cell lines by bicistronic co-expression of the surface antigen NGFR. MethodsX 9,101929
Vilaplana-Lopera, N., Cuminetti, V., Almaghrabia, R., Papatzikas, G., Rout, A., Jeeves, M., González, E., Alyayhawi, Y., Cunningham, A., Erdem, A., Schnütgen, F., Raghavan, M., Potluri, S., Cazier, J.-B., Schuringa, J.J., Reed, M.A.C., Arranz, L., Günther, U.L., and Garcia, P. (2022) Crosstalk between AML and stromal cells triggers acetate secretion through the metabolic rewiring of stromal cells. Elife 11, e75908
Jayavelu, A.K., Wolf, S., Buettner, F., Alexe, G., Häupl, B., Comoglio, F., Schneider, C., Doebele, C., Fuhrmann, D., Wagner, S., Donato, E., Andresenm C., Wilke, A., Zindel, A., Jahn, D., Splettstoesser, B., Plessmann, U., Münch, S., Abou Elardat, K., Makowka, P., Acker, F., Enssle, J., Cremer, A., Schnütgen, F., Kurrle, N., Chapuy, B., Löber, J., Hartmann, S., Wild, P., Wittig, I., Hünschmann, D., Kaderali, L., Cox, J., Brüne, B., Röllig, C., Thiede, C., Steffen, B., Bornhäuser, M., Trumpp, A., Urlaub, H., Stegmaier, K., Serve, H., Mann, M., Oellerich, T. (2022) The Proteogenomic Subtypes of Acute Myeloid Leukemia. Cancer Cell 40, 301-317
Wilke, A., Doebele, C., Zindel, A., Lee, K.S., Rieke, S., Ceribelli, M., Comoglio, F., Phelan, J., Wang, J., Pikman, A., Jahn, D., Häupl, B., Schneider, C., Scheich, S., Tosto, F., Bohnenberger, H., Stauder, P., Schnütgen, F., Słabicki, M., Coulibaly, Z., Wolf, S., Bojarczuk, K., Chapuy, B., Brandts, B., Stroebel, P., Lewis, C., Engelke, M., Xu, X., Kim, H., Dang, T.H., Schmitz, R., Hodson, D.J., Stegmaier, K., Urlaub, H., Serve, H., Schmitt, C., Kreuz, F., Knittel, G., Rabinowitz, J., Reinhardt, H., Vander Heiden, M., Thomas, C., Staudt, L., Zenz, T., and Oellerich, T. (2022) SHMT2 inhibition disrupts the TCF3 TCF3 transcriptional survival program in Burkitt lymphoma. Blood, doi: 10.1182/blood.2021012081
Koschade, SE., Klann, K., Shaid, S., Vick, B., Stratmann, JA., Thölken, M., Meyer, LM., Nguyen, TD., Campe, J., Moser, LM., Hock, S., Baker, F., Meyer, CT., Wempe, F., Serve, H., Ullrich, E., Jeremias, I., Münch, C., Brandts, CH. Translatome proteomics identifies autophagy as a resistance mechanism to on-target FLT3 inhibitors in acute myeloid leukemia. Leukemia 36(1):2396-2407
2021
Clees, A., Stolp, V., Häupl, B., Fuhrmann, D.C., Wempe, F., Seibert, M., Weber, S., Banning, A., Tikkanen, R., Williams, R., Brüne, B., Serve, H., Schnütgen, F.*, von Metzler, I.*, and Kurrle, N.* (2021) Identification of the Cysteine Protease Legumain as a Potential Chronic Hypoxia-Specific Multiple Myeloma Target Gene. Cells 11, 292
Karakitsou, E, Foguet, C., Contreras Mostazo, M.G., Kurrle, N., Schnütgen, F., Michaelis, M., Cinatl, J., Marin, S., and Cascante, M. (2021) Genome-scale integration of transcriptome and metabolome unveils squalene synthase and dihydrofolate reductase as targets against AML cells resistant to chemotherapy. Computational and Structural Biotechnology Journal. 10.1016/j.csbj.2021.06.049
Nimbarte, V.D., Wirmer-Bartoschek, J., Gande, S.L., Alshamleh, I., Seibert, M., Nasiri, H.R., Schnütgen, F., Serve, H., and Schwalbe, H. (2021) Fragment-based Lead Discovery and Design of Indole-derived c-Myc Promoter G-Quadruplex Binders to Down-regulate c-Myc Expression in Cancer Cells. ChemMedChem 1002/cmdc.202000835
Malkomes, P., Lunger, I., Oppermann, E., Abou-El-Ardat, K., Oellerich, T., Guenther, S., Canbulat, C., Bothur, S., Schnütgen, F., Yu, W., Wingert, S., Haetscher, N., Catapano, C., Dietz, M.S., Heilemann, M., Kvasnicka, H.-M., Holzer, K., Serve, H., Bechstein, W.O., and Rieger, M. (2021) Transglutaminase 2 promotes tumorigenicity of colon cancer cells by inactivation of the tumor suppressor p53. Oncogene 40, 4352-4367
Seibert, M., Kurrle, N., Schnütgen, F., and Serve, H. (2021) Amino acid sensory complex proteins in mTORC1 and macroautophagy regulation. Matrix Biol. doi: 10.1016/j.matbio.2021.01.001
Makowka, P., Stolp, V., Stoschek K., Serve H. (2021) Molecular determinants of therapy response of venetoclax-based combinations in acute myeloid leukemia. Biol Chem. 402(12):1547-1564
2020
Weber, S., Parmon, A., N., Schnütgen, F., and Serve, H. (2020) The clinical significance of iron overload and iron metabolism, in myelodysplastic syndrome and acute myeloid leukemia. Front. Immunol. 11, 627-662
Contreras Mostazo, M.G., Kurrle, N., Casado, M., Fuhrmann, D., Alshamleh, I., Häupl, B., Martín-Sanz, P., Brüne, B., Serve, H., Schwalbe, H., Schnütgen, F.*, Marin, S.*, and Cascante, M.* (2020) Metabolic plasticity is an essential requirement of acquired tyrosine kinase inhibitor resistance in Chronic Myeloid Leukemia. Cancers 12, 3443
Alshamleh, I., Krause, N., Richter, C., Kurrle, N., Serve, H., Günther, UL., Schwalbe, H. (2020) Real-time NMR spectroscopy for studying metabolism. Angew Chem Int Ed Engl. 59(6):2304-2308
Kumar, R., Pereira, R.S., Zanetti, C., Minciacchi, V.R., Merten, M., Meister, M., Niemann, J., Dietz, M.S., Rüssel, N., Schnütgen, F., Tamai, M., Akahane, K., Inukai, T., Oellerich, T., Kvasnicka, H.M., Pfeifer, H., Nicolini, F.E., Heilemann, M., Van Etten, R.A., & Krause, D. (2020) Specific, targetable interactions with the microenvironment influence imatinib-resistant chronic myeloid leukemia. Leukemia 34, 2087-2101
2019
Kreitz, J., Schönfeld, C., Seibert, M., Stolp, V., Alshamleh, I., Oellerich, T., Steffen, B., Schwalbe, H., Schnütgen, F., Kurrle, N., & Serve, H. (2019) Metabolic Plasticity of Acute Myeloid Leukemia. Cells 8, 805
Fuhrmann, D., Olesch, C., Kurrle, N., Schnütgen, F., Zukunft, S., Fleming, I., & Brüne, B. (2019) Chronic hypoxia enhances β-oxidation-dependent electron transport via electron transferring flavoproteins. Cells 8, 172
Thöne, F.M.B., Kurrle, N., von Melchner, H., & Schnütgen, F. (2019) CRISPR/Cas9-mediated generic protein tagging in mammalian cells. Methods 164-165, 59-66
Barth, J., Abou-El-Ardat, K., Dalic, D., Kurrle, N., Maier, AM., Mohr, S., Schütte, J., Vassen, L., Greve, G., Schulz-Fincke, J., Schmitt, M., Tosic, M., Metzger, E., Bug, G., Khandanpour, C., Wagner, SA., Lübbert, M., Jung, M., Serve, H., Schüle, R., Berg, T. (2019) LSD1 inhibition by tranylcypromine derivatives interferes with GFI1-mediated repression of PU.1 target genes and induces differentiation in AML. Leukemia 33(6):1411-1426
Master Thesis Project in Computational Single Cell Biology –
Computational analysis of tRNA expression at a single-cell level
The labs of Florian Büttner and Michael Rieger are looking for a motivated Master student to
develop a computational workflow for the analysis of tRNA expression single cell data. The
Büttner and Rieger labs are internationally renowned in the fields of computational cancer
research and stem cell research. Moreover, the collaborative environment of the University
Hospital Frankfurt fosters interdisciplinary excellence and provides an ideal research
infrastructure. Furthermore, the topic has been defined as an emerging field of the Excellence
Cluster Cardio-Pulmonary Institute, with excellent support for early career researchers.
Our labs are currently developing a method to quantify transfer RNAs (tRNAs) at a single cell
level. We have established experimental protocols, generated preliminary datasets and we need
to develop a specific computational approach. This will allow to elucidate how tRNA
abundance and codon usage orchestrate cellular systems, focusing on hematopoietic stem cells
and primary leukemia cells. The applicant will analyze single-cell sequencing data (tRNAs and
mRNA transcriptomes) from patient derived material, visualize the results and discuss their
findings with the other scientists involved in the project of both research groups.
The computational analysis of tRNAs at a single cell level pose multiple exciting challenges:
The accurate genome mapping is made difficult by the high sequence similarity between tRNAs and by their post-transcriptional modifications;
The functional analysis can be performed at multiple levels: single tRNAs, isodecoder
(all tRNAs sharing a specific anticodon), and isoaccepter (all tRNAs carrying the same
amino-acid).
Some tRNA genes are located in introns of coding genes; therefore tRNA expression
could be regulated independently or conditioned to mRNA expression, the genomic
position of the tRNAs should therefore be considered in the analysis
We will consider applicants studying Bioinformatics, Biology, Molecular Medicine,
Pharmaceutical Sciences or any related field. The optimal candidate has strong programming
skills (Python, R, linux command) and a good understanding of sequence alignment algorithms
and analysis of transcriptomic data. Beyond the focus on bioinformatic analyses of the data, the
applicant has the possibility to contribute to the wet lab research.
If you are interested, please send your CV, a short cover letter and a copy of your Bachelor’s degree to:
Adrien Jolly (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein.) and/or Marius Külp (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein.)
