Max Planck Research Group on Single Cell Genomics (Barbara Treutlein)
The major part of the Treutlein group has moved to the Department of Biosystems Science and Engineering (D-BSSE) of the ETH Zürich.
An understanding of what constitutes the biological basis for modern humans is of fundamental importance for understanding how modern humans came to dominate the biosphere. Single cell genomics is an emerging field providing unprecedented insights into the biology of complex tissues. We use single cell genomics data to reconstruct developmental pathways, lineage hierarchies, and tissue heterogeneity in humans. We integrate single cell measurements with signatures of positive selection and comparisons with great apes to understand the molecular mechanisms that define the modern human condition.
Read more about us here: https://bsse.ethz.ch/qdb
Reconstructing human development using single cell RNAseq
Recent advances in the field of stem cell biology and tissue engineering have made it possible to generate induced pluripotent stem (iPS) cells from somatic cells and to differentiate these iPS cells into many cell lineages and tissue types of the human body. We are using these technologies to study differentiation pathways and functional diversity of human cell types in controlled tissue culture environments. In parallel, we use single cell RNAseq to phenotype primary human tissues at multiple developmental stages in order to compare in vitro and in vivo patterns of development. Together, these approaches provide insight into the genetic mechanisms that build and maintain human organs.
Understanding human uniqueness through comparisons with great apes
In order to understand what makes humans unique, it is important to place our observations into an evolutionary context. To this end, we reconstruct great ape development using tissues and iPS cells generated from our closest living relatives including chimpanzee, bonobo, gorilla, and orangutan. We use CRISPR/Cas genome engineering to “ancestralize” human cells to a chimpanzee-like state in order to understand how specific genetic changes lead to innovations in the modern human lineage.
Methods development
We continue to apply and develop new technologies to understand how individual cells utilize their genome to self-organize into fantastically complex structuress.
Publications
2024
Micheel, J., Safrastyan, A., Aron, F., & Wollny, D. (2024). Exploring the impact of primer length on efficient gene detection via high-throughput sequencing. Nature Communications, 15: 5858. |
Open Access2023
Riesenberg, S., Kanis, P., Macak, D., Wollny, D., Düsterhöft, D., Kowalewski, J., Helmbrecht, N., Maricic, T., & Pääbo, S. (2023). Efficient high-precision homology-directed repair-dependent genome editing by HDRobust. Nature Methods, 20, 1388-1399. |
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Safrastyan, A., zu Siederdissen, C. H., & Wollny, D. (2023). Decoding cell-type contributions to the cfRNA transcriptomic landscape of liver cancer. Human Genomics, 17(1): 90. |
2022
Gerber, T., Loureiro, C., Schramma, N., Chen, S., Jain, A., Weber, A., Weigert, A., Santel, M., Alim, K., Treutlein, B., & Camp, J. G. (2022). Spatial transcriptomic and single-nucleus analysis reveals heterogeneity in a gigantic single-celled syncytium. eLife, 11: e69745. |
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He, Z., Maynard, A., Jain, A., Gerber, T., Petri, R., Lin, H.-C., Santel, M., Ly, K., Dupré, J.-S., Sidow, L., Sanchis Calleja, F., Jansen, S. M. J., Riesenberg, S., Camp, J. G., & Treutlein, B. (2022). Lineage recording in human cerebral organoids. Nature Methods, 19(1), 90-99.
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Krumm, J., Sekine, K., Samaras, P., Brazovskaja, A., Breunig, M., Yasui, R., Kleger, A., Taniguchi, H., Wilhelm, M., Treutlein, B., Camp, J. G., & Kuster, B. (2022). High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development. Cell Reports, 38: 110604. |
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Oskolkov, N., Santel, M., Parikh, H. M., Ekström, O., Camp, J. G., Miyamoto-Mikami, E., Ström, K., Mir, B. A., Kryvokhyzha, D., Lehtovirta, M., Kobayashi, H., Kakigi, R., Naito, H., Eriksson, K.-F., Nystedt, B., Fuku, N., Treutlein, B., Pääbo, S., & Hansson, O. (2022). High-throughput muscle fiber typing from RNA sequencing data. Skeletal Muscle, 12: 16. |
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Wollny, D., Vernot, B., Wang, J., Hondele, M., Safrastyan, A., Aron, F., Micheel, J., He, Z., Hyman, A., Weis, K., Camp, J. G., Tang, T. D., & Treutlein, B. (2022). Characterization of RNA content in individual phase-separated coacervate microdroplets. Nature Communications, 13: 2626.
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2021
Kyrousi, C., O’Neill, A. C., Brazovskaja, A., He, Z., Kielkowski, P., Coquand, L., Di Giaimo, R., D’ Andrea, P., Belka, A., Forero Echeverry, A., Mei, D., Lenge, M., Cruceanu, C., Buchsbaum, I. Y., Khattak, S., Fabien, G., Binder, E., Elmslie, F., Guerrini, R., Baffet, A. D., Sieber, S. A., Treutlein, B., Robertson, S. P., & Cappello, S. (2021). Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity. Nature Communications, 12(1): 6298. |
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Lin, H.-C., He, Z., Ebert, S., Schörnig, M., Santel, M., Nikolova, M. T., Weigert, A., Hevers, W., Kasri, N. N., Taverna, E., Camp, J. G., & Treutlein, B. (2021). NGN2 induces diverse neuron types from human pluripotency. Stem Cell Reports, 16, 2118-2127. |
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Lin, T.-Y., Gerber, T., Taniguchi-Sugiura, Y., Murawala, P., Hermann, S., Grosser, L., Shibata, E., Treutlein, B., & Tanaka, E. M. (2021). Fibroblast dedifferentiation as a determinant of successful regeneration. Developmental Cell, 56(10), 1541-1551.e6. |
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Schörnig, M., Ju, X.-C., Fast, L., Weigert, A., Schaffer, T., Ebert, S., Treutlein, B., Kasri, N. N., Peter, B., Hevers, W., & Taverna, E. (2021). Comparison of induced neurons reveals slower structural and functional maturation in humans than in apes. eLife, 10: e59323. |
2020
Dannemann, M., He, Z., Heide, C., Vernot, B., Sidow, L., Kanton, S., Weigert, A., Treutlein, B., Pääbo, S., Kelso, J., & Camp, J. G. (2020). Human stem cell resources are an inroad to Neandertal DNA functions. Stem Cell Reports, 15, 214-225. |
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He, Z., Brazovskaja, A., Ebert, S., Camp, J. G., & Treutlein, B. (2020). CSS: Cluster similarity spectrum integration of single-cell genomics data. Genome Biology, 21: 224. |
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He, Z., Gerber, T., Maynard, A., Jain, A., Petri, R., Santel, M., Ly, K., Sidow, L., Sanchís-Calleja, F., Riesenberg, S., Camp, J. G., & Treutlein, B. (2020). Lineage recording reveals dynamics of cerebral organoid regionalization. bioRxiv. |
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Kanton, S., Treutlein, B., & Camp, J. G. (2020). Single-cell genomic analysis of human cerebral organoids. In J. R. Spence ( |
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Khrameeva, E., Kurochkin, I., Han, D., Guijarro, P., Kanton, S., Santel, M., Qian, Z., Rong, S., Mazin, P., Sabirov, M., Bulat, M., Efimova, O., Tkachev, A., Guo, S., Sherwood, C. C., Camp, J. G., Pääbo, S., Treutlein, B., & Khaitovich, P. (2020). Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains. Genome Research, 30(5), 776-789. |
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Miller, A. J., Yu, Q., Czerwinski, M., Tsai, Y.-H., Conway, R. F., Wu, A., Holloway, E. M., Walker, T., Glass, I. A., Treutlein, B., Camp, J. G., & Spence, J. R. (2020). In vitro and in vivo development of the human airway at single-cell resolution. Developmental Cell, 53(1): e6, pp. 117-128. |
2019
Brazovskaja, A., Treutlein, B., & Camp, J. G. (2019). High-throughput single-cell transcriptomics on organoids. Current Opinion in Biotechnology, 55, 167-171. |
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Gerber, T. (2019). Dissecting limb regeneration and cancer heterogeneity using single-cell RNA-seq. PhD Thesis, Universität, Leipzig. |
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Kanton, S. (2019). Dissecting human cortical development, evolution and malformation using organoids and single-cell transcriptomics. PhD Thesis, Universität, Leipzig. |
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Kanton, S., Boyle, M. J., He, Z., Santel, M., Weigert, A., Sanchís-Calleja, F., Guijarro, P., Sidow, L., Fleck, J. S., Han, D., Qian, Z., Heide, M., Huttner, W. B., Khaitovich, P., Pääbo, S., Treutlein, B., & Camp, J. G. (2019). Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature, 574(7778), 418-422. |
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Klaus, J., Kanton, S., Kyrousi, C., Ayo-Martin, A. C., Giaimo, R. D., Riesenberg, S., O’Neill, A. C., Camp, J. G., Tocco, C., Santel, M., Rusha, E., Drukker, M., Schroeder, M., Götz, M., Robertson, S. P., Treutlein, B., & Cappello, S. (2019). Altered neuronal migratory trajectories in human cerebral organoids derived from individuals with neuronal heterotopia. Nature Medicine, 25, 561-568. |
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Klein, A. M., & Treutlein, B. (2019). Single cell analyses of development in the modern era. Development, 146(12): dev181396. |
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Parra, R. G., Papadopoulos, N., Ahumada-Arranz, L., El Kholtei, J., Mottelson, N., Horokhovsky, Y., Treutlein, B., & Soeding, J. (2019). Reconstructing complex lineage trees from scRNA-seq data using MERLoT. Nucleic Acids Research, 47(17), 8961-8974. |
2018
Camp, J. G., Wollny, D., & Treutlein, B. (2018). Single-cell genomics to guide human stem cell and tissue engineering. Nature Methods, 15(9), 661-667. |
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Fei, J.-F., Lou, W.-P.-K., Knapp, D., Murawala, P., Gerber, T., Taniguchi, Y., Nowoshilow, S., Khattak, S., & Tanaka, E. M. (2018). Application and optimization of CRISPR–Cas9-mediated genome engineering in axolotl ( Ambystoma mexicanum ). Nature Protocols, 13, 2908-2943. |
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Gerber, T., Murawala, P., Knapp, D., Masselink, W., Schuez, M., Hermann, S., Gac-Santel, M., Nowoshilow, S., Kageyama, J., Khattak, S., Currie, J. D., Camp, J. G., Tanaka, E. M., & Treutlein, B. (2018). Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration. Science, 362(6413): eaaq0681. |
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Kageyama, J., Wollny, D., Treutlein, B., & Camp, J. G. (2018). ShinyCortex: Exploring single-cell transcriptome data from the developing human cortex. Frontiers in Neuroscience, 12: 315. |
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Karow, M., Camp, J. G., Falk, S., Gerber, T., Pataskar, A., Gac-Santel, M., Kageyama, J., Brazovskaja, A., Garding, A., Fan, W., Riedemann, T., Casamassa, A., Smiyakin, A., Schichor, C., Goetz, M., Tiwari, V. K., Treutlein, B., & Berninger, B. (2018). Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. Nature Reviews Neurology, 21, 932-940. |
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Vaid, S., Camp, J. G., Hersemann, L., Oegema, C. E., Heninger, A.-K., Winkler, S., Brandl, H., Sarov, M., Treutlein, B., Huttner, W. B., & Namba, T. (2018). A novel population of Hopx-dependent basal radial glial cells in the developing mouse neocortex. Development, 145(20): dev169276. |
2017
Camp, J. G., & Treutlein, B. (2017). Advances in mini-brain technology. Nature, 545(7652), 39-40. |
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Camp, J. G., & Treutlein, B. (2017). Human organomics: A fresh approach to understanding human development using single-cell transcriptomics. Development, 144(9), 1584-1587. |
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Camp, J. G., Sekine, K., Gerber, T., Loeffler-Wirth, H., Binder, H., Gac, M., Kanton, S., Kageyama, J., Damm, G., Seehofer, D., Belicova, L., Bickle, M., Barsacchi, R., Okuda, R., Yoshizawa, E., Kimura, M., Ayabe, H., Taniguchi, H., Takebe, T., & Treutlein, B. (2017). Multilineage communication regulates human liver bud development from pluripotency. Nature, 546(7659), 533-538. |
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Gansauge, M.-T., Gerber, T., Glocke, I., Korlevic, P., Lippik, L., Nagel, S., Riehl, L. M., Schmidt, A., & Meyer, M. (2017). Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Research, 45(10): e79. |
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Gerber, T., Willscher, E., Loeffler-Wirth, H., Hopp, L., Schadendorf, D., Schartl, M., Anderegg, U., Camp, G., Treutlein, B., Binder, H., & Kunz, M. (2017). Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq. Oncotarget, 8(1), 846-862. |
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Sundaramoorthy, R., Hughes, A. L., Singh, V., Wiechens, N., Ryan, D. P., El-Mkami, H., Petoukhov, M., Svergun, D. I., Treutlein, B., Quack, S., Fischer, M., Michaelis, J., Böttcher, B., Norman, D. G., & Owen-Hughes, T. (2017). Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. eLife, 6: e22510. |
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Wapinski, O. L., Lee, Q. Y., Chen, A. C., Li, R., Corces, M. R., Ang, C. E., Treutlein, B., Xiang, C., Baubet, V., Suchy, F. P., Sankar, V., Sim, S., Quake, S. R., Dahmane, N., Wernig, M., & Chang, H. Y. (2017). Rapid chromatin switch in the direct reprogramming of fibroblasts to neurons. Cell Reports, 20(13), 3236-3247. |
2016
Gokce, O., Stanley, G. M., Treutlein, B., Neff, N. F., Camp, J. G., Malenka, R. C., Rothwell, P. E., Fuccillo, M. V., Südhof, T. C., & Quake, S. R. (2016). Cellular taxonomy of the mouse striatum as revealed by single-cell RNA-seq. Cell Reports, 16(4), 1126-1137. |
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Mora-Bermúdez, F., Badsha, F., Kanton, S., Camp, J. G., Vernot, B., Köhler, K., Voigt, B., Okita, K., Maricic, T., He, Z., Lachmann, R., Pääbo, S., Treutlein, B., & Huttner, W. B. (2016). Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development. eLife, e18683. |
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Treutlein, B., Lee, Q. Y., Camp, J. G., Mall, M., Koh, W., Shariati, S. A. M., Sim, S., Neff, N. F., Skotheim, J. M., Wernig, M., & Quake, S. R. (2016). Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature, 534(7607), 391-395. |
2015
Camp, J. G., Badsha, F., Florio, M., Kanton, S., Gerber, T., Wilsch-Bräuninger, M., Lewitus, E., Sykes, A., Hevers, W., Lancaster, M., Knoblich, J. A., Lachmann, R., Pääbo, S., Huttner, W. B., & Treutlein, B. (2015). Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proceedings of the National Academy of Sciences of the United States of America, 112(51), 15672-15677. |
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Korlević, P., Gerber, T., Gansauge, M.-T., Hajdinjak, M., Nagel, S., Ayinuer-Petri, A., & Meyer, M. (2015). Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. BioTechniques, 59(2), 87-93. |
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Vaughan, A. E., Brumwell, A. N., Xi, Y., Gotts, J. E., Brownfield, D. G., Treutlein, B., Tan, K., Tan, V., Liu, F. C., Looney, M. R., Matthay, M. A., Rock, J. R., & Chapman, H. A. (2015). Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury. Nature, 517(7536), 621-625. |
2014
Hajdinjak, M., Korlević, P., Gansauge, M.-T., Dabney, J., Slon, V., Glocke, I., Sawyer, S., Nickel, B., Nagel, S., Gerber, T., Hopfe, C., Stenzel, U., Renaud, G., Andrés, A. M., Castellano, S., Kelso, J., Prüfer, K., Meyer, M., & Pääbo, S. (2014). Neandertal genetic diversity. Poster presented at XVII World UISPP Congress, Burgos, Spain. |