Placental developmentStem cell statesControl of pluripotencyEpigenetic reprogrammingNovel technologies

Placental development

Karvas, R.M., David, L., and T.W. Theunissen (2022). Accessing the human trophoblast stem cell state from pluripotent and somatic cells. Cell. Mol. Life Sci. 79, 604

Dong, C., Fu, S., Karvas, R.M., Chew, B., Fischer, L.A., Xing, X., Harrison, J., Popli, P., Kommagani, R., Wang, T., Zhang, B., and T.W. Theunissen (2022). A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cell. Nature Communications, 13, 2548.

Karvas R.M., Khan, S.A., Verma, S., Yin, Y., Kulkarni, D., Dong, C., Park, K., Chew, B., Sane, E., Fischer, L.A., Kumar, D., Ma, L., Boon, A.C.M., Dietmann, S., Mysorekar, I.U., and T.W. Theunissen (2022). Stem-cell-derived trophoblast organoids model human placental development and susceptibility to emerging pathogens. Cell Stem Cell, 29, 810-825.

Dong, C., Beltcheva, M., Gontarz. P., Zhang, B., Popli, P., Fischer, L.A., Khan, S.A., Park, K., Yoon, E., Xing, X., Kommagani, R., Wang, T., Solnica-Krezel, L. and T.W. Theunissen (2020). Derivation of trophoblast stem cells from naive human pluripotent stem cells. eLife, 9, e52504.

Stem cell states

Khan, S.A., Park, K., Fischer, L.A., Dong, C., Lungjangwa, T., Jimenez, M., Casalena, D., Chew, B., Dietmann, S., Auld, D.S., Jaenisch, R. and T.W. Theunissen (2021). Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening. Cell Reports, 35, 109233.

Dong, C., Fischer, L.A. and T.W. Theunissen (2019). Recent insights into the naïve state of human pluripotency and its applications. Exp. Cell. Res., 111645.

Pontis, J., Planet, E., Offner, S., Turelli, P., Duc, J., Coudray, A., Theunissen, T.W., Jaenisch, R. and D. Trono (2019). Hominid-specific transposable elements and KZFPs facilitate human embryonic genome activation and control transcription in naive human ESCs. Cell Stem Cell, 24, 1-12.

Sahakyan, A., Kim, R., Chronis, C., Sabri, S., Bonora, G., Theunissen, T.W., Kuoy, E., Langerman, J., Clark, A.T., Jaenisch, R. and K. Plath (2017). Human naive pluripotent stem cells model X chromosome dampening and X inactivation. Cell Stem Cell 20, 1-15.

Theunissen, T.W.*, Friedli, M.*, He, Y.*, Planet, E., Oneil, R., Markoulaki, S., Pontis, J., Wang, H., Iouranova, A., Imbeault, M., Duc, J., Cohen, M.A., Wert, K.J., Castanon, R.G., Zhang, Z., Huang, Y., Nery, J.R., Drotar, J., Lungjangwa, T., Trono, D., Ecker, J.R. and R. Jaenisch (2016). Molecular criteria for defining the naive human pluripotent state. Cell Stem Cell 19, 1-14. *Co-first authors.

Theunissen, T.W.*, Powell, B.E.*, Wang, H.*, Mitalipova, M., Faddah, D., Maetzel, D., Ganz, K., Shi, L., Stelzer,Y., Zhang, J., Lungjangwa, T., Imsoonthornruksa, S., Rangajaran, S., Fan, Z.P., Young, R.A., Gray, N., and R. Jaenisch (2014). Systematic identification of culture conditions for induction and maintenance of naive human pluripotency, Cell Stem Cell 15, 471–487. *Co-first authors.

Control of pluripotency

Huang, X., Park, K., Gontarz, P., Zhang, B., Pan, J., McKenzie, Z., Fischer, L.A., Dong, C., Dietmann, S., Xing, X., Shliaha, P.V., Yang, J., Li, D., Ding, J., Lungjangwa, T., Mitalipova, M., Khan, S.A., Imsoonthornruksa, S., Jensen, N., Wang, T., Kadoch, C., Jaenisch, R., Wang, J., and T.W. Theunissen (2021). OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human. Nature Communications, 12, 5123.

Lawrence, M., Theunissen, T.W., Lombard, P., Adams, D.J., and J.C.R. Silva (2019). ZMYM2 inhibits NANOG-mediated reprogramming. Wellcome Open Research 4: 88.

Theunissen, T.W. and R. Jaenisch (2017). Mechanisms of gene regulation in human embryos and pluripotent stem cells. Development, 144: 4496-4509.

Radzisheuskaya, A., Chia Gle, B., dos Santos, R.L., Theunissen, T.W., Castro, L.F., Nichols, J., and J.C. Silva (2013). A defined Oct4 level governs cell state transitions of pluripotency entry and differentiation into all embryonic lineages. Nature Cell Biology 15, 579-90.

Przybyla, L., Theunissen, T.W., Jaenisch, R., and J. Voldman (2013). Matrix remodeling maintains ESC self-renewal by activating Stat3, Stem Cells 31, 1097-106.

Tee, W.W., Pardo, M., Theunissen, T.W., Yu, L., Choudhary, J.S., Hajkova, P., and M.A. Surani (2010). Prmt5 is essential for early mouse development and acts in the cytoplasm to maintain ES cell pluripotency, Genes & Development 24, 2772-7.

Orkin, S.H., Wang, J., Kim, J., Chu, J., Rao, S., Theunissen, T.W., Shen, X., and D.N. Levasseur (2008). The transcriptional network controlling pluripotency in ES cells. Cold Spring Harbor Symposia on Quantitative Biology 73, 195-202.

Wang, J., Rao, S., Chu, J., Shen, X., Levasseur, D.N., Theunissen, T.W., and S.H. Orkin (2006). A protein interaction network for pluripotency of embryonic stem cells. Nature 444, 364-368.

Epigenetic reprogramming

De Los Angeles, A., Ferrari, F., Fujiwara, Y., Mathieu, R., Lee S., Lee, S., Tu, H.C., Ross, S., Chou, S., Nguyen, M., Wu, Z., Theunissen, T.W., Powell, B.E., Imsoonthornruksa, S., Chen, J., Borkent, M., Krupalnik, V., Lujan, E., Wernig, M., Hanna, J.H., Hochedlinger, K., Pei, D., Jaenisch, R., Deng, H., Orkin S.H., Park, P.J. and G.Q. Daley (2015). Failure to replicate the STAP cell phenomenon. Nature 525, E6-E9.

Theunissen, T.W. and R. Jaenisch (2014). Molecular control of induced pluripotency. Cell Stem Cell 14, 720-734.

Costa, Y.*, Ding, J.*, Theunissen, T.W.*, Faiola, F.*, Hore, T.A., Shliaha, P.V., Fidalgo, M., Saunders, A., Lawrence, M., Dietmann, S., Das, S., Levasseur, D.N., Li, Z., Xu, M., Reik, W., Silva, J.C.R.* and J. Wang* (2013). NANOG-dependent function of TET1 and TET2 in establishment of pluripotency, Nature 495, 370-4. *Co-first authors.

Theunissen, T.W., Costa, Y., Radzisheuskaya, A., van Oosten, A.L., Lavial, F., Pain, B., Castro, L.F.C., and J.C.R. Silva (2011). Reprogramming capacity of Nanog is functionally conserved in vertebrates and resides in a unique homeodomain. Development138, 4853-4865.

Theunissen, T.W., van Oosten, A., Castelo-Branco, G., Hall, J. Smith, A., and J.C.R. Silva (2011). Nanog overcomes reprogramming barriers and induces pluripotency in minimal conditions, Current Biology 21, 65-71.

Yang, J., van Oosten, A., Theunissen, T.W., Guo, G., Silva, J.C.R., and A. Smith (2010). STAT3 activation is limiting for reprogramming to ground state pluripotency. Cell Stem Cell 7, 319-328.

Silva, J., Nichols. J., Theunissen, T.W., Guo, G., van Oosten, A., Barrandon, O., Wray, J., Yamanaka, S., Chambers, I., and A. Smith (2009). Nanog is the gateway to the pluripotent ground state. Cell 138(4), 722-37.

Silva, J., Barrandon, O., Nichols, J., Kawaguchi, J., Theunissen, T.W., and A. Smith (2008). Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biology 6(10), e253.

Novel technologies

Dong, C. and Theunissen, T.W. (2022). Generating trophoblast stem cells from human naïve pluripotent stem cells. Methods Mol Biol. 2416, 91-104.

Fischer, L.A., Khan, S.A., and Theunissen, T.W. (2022). Induction of human naïve pluripotency using 5i/L/A medium. Methods Mol Biol. 2416, 13-28.

Cheng, A.W., Wang, H., Yang, H., Shi, L., Katz, Y., Theunissen T.W., Rangarajan, S., Shivalila, C.S., Dadon, D.B., and Jaenisch, R (2013). Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Research 23, 1163-71.

Wang, J., Theunissen, T.W., and S.H. Orkin (2007). Site-directed, virus-free and inducible RNAi in embryonic stem cells. PNAS. 104, 20850-5.