Studies that used DAPCEL gene optimization
In these studies, the protein was expressed from a gene redesigned by Dapcel.
Activities of Ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling
Genes & Development (2010) 24, 1787–1801
Skabkin, M.A., Skabkina, O.V., Dhote, V., Komar, A.A., Hellen, C.U., Pestova, T.V.
The earliest study listed here. The gene for human DHX29 (a 1369-amino-acid DExH-box protein) was redesigned by selecting rare synonymous codons to support correct co-translational folding in E. coli. The protein was expressed in active, soluble form and purified to homogeneity; its activity matched that of the protein previously purified from mammalian cells (Pisareva, V.P., Pisarev, A.V., Komar, A.A., Hellen, C.U., Pestova, T.V. (2008) Translation initiation on mammalian mRNAs with structured 5'UTRs requires DExH-box protein DHX29. Cell, 135, 1237-1250).
Later studies that used DAPCEL-optimized genes:
Roles of individual domains in the function of DHX29, an essential factor required for translation of structured mammalian mRNAs
Proceedings of the National Academy of Sciences (2012) 109, E3150–E3159
Dhote, V., Sweeney, T.R., Kim, N., Hellen, C.U., Pestova, T.V.
Facilitates chromatin transcription complex is an "accelerator" of tumor transformation and potential marker and target of aggressive cancers
Cell Reports (2013) 4, 159–173
Garcia, H., Miecznikowski, J.C., Safina, A., Commane, M., Ruusulehto, A., Kilpinen, S., Leach, R.W., Attwood, K., Li, Y., Degan, S., Omilian, A.R., Guryanova, O., Papantonopoulou, O., Wang, J., Buck, M., Liu, S., Morrison, C., Gurova, K.V.
The mechanism of translation initiation on Type 1 picornavirus IRESs
The EMBO Journal (2014) 33, 76–92
Sweeney, T.R., Abaeva, I.S., Pestova, T.V., Hellen, C.U.
Regulation of Murine Ovarian Epithelial Carcinoma by Vaccination against the Cytoplasmic Domain of Anti-Müllerian Hormone Receptor II
Journal of Immunology Research (2015) 2015, 630287
Sakalar, C., Mazumder, S., Johnson, J.M., Altuntas, C.Z., Jaini, R., Aguilar, R., Naga Prasad, S.V., Connolly, D.C., Tuohy, V.K.
Targeted Vaccination against Human α-Lactalbumin for Immunotherapy and Primary Immunoprevention of Triple Negative Breast Cancer
Cancers (2016) 8, 56
Tuohy, V.K., Jaini, R., Johnson, J.M., Loya, M.G., Wilk, D., Downs-Kelly, E., Mazumder, S.
Primary Immunoprevention of Epithelial Ovarian Carcinoma by Vaccination against the Extracellular Domain of Anti-Müllerian Hormone Receptor II
Cancer Prevention Research (2017) 10, 612–624
Mazumder, S., Johnson, J.M., Swank, V., Dvorina, N., Martelli, E., Ko, J., Tuohy, V.K.
GTPase ROP2 binds and promotes activation of target of rapamycin, TOR, in response to auxin
The EMBO Journal (2017) 36, 886–903
Schepetilnikov, M., Makarian, J., Srour, O., Geldreich, A., Yang, Z., Chicher, J., Hammann, P., Ryabova, L.A.
Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain
Proteins: Structure, Function, and Bioinformatics (2019) 87, 157–167
Gay, J.C., Eckenroth, B.E., Evans, C.M., Langini, C., Carlson, S., Lloyd, J.T., Caflisch, A., Glass, K.C.
Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome
Molecular Cell (2020) 80, 127–139.e6
Bertram, K., El Ayoubi, L., Dybkov, O., Agafonov, D.E., Will, C.L., Hartmuth, K., Urlaub, H., Kastner, B., Stark, H., Lührmann, R.
Functional role and ribosomal position of the unique N-terminal region of DHX29, a factor required for initiation on structured mammalian mRNAs
Nucleic Acids Research (2021) 49, 12955–12969
Sweeney, T.R., Dhote, V., Guca, E., Hellen, C.U.T., Hashem, Y., Pestova, T.V.
Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain
International Journal of Molecular Sciences (2021) 22, 9128
Evans, C.M., Phillips, M., Malone, K.L., Tonelli, M., Cornilescu, G., Cornilescu, C., Holton, S.J., Gorjánácz, M., Wang, L., Carlson, S., Gay, J.C., Nix, J.C., Demeler, B., Markley, J.L., Glass, K.C.
The kinetic landscape of an RNA-binding protein in cells
Nature (2021) 591, 152–156
Sharma, D., Zagore, L.L., Brister, M.M., Ye, X., Crespo-Hernández, C.E., Licatalosi, D.D., Jankowsky, E.
Aurintricarboxylic acid is a canonical disruptor of the TAZ-TEAD transcriptional complex
PLOS ONE (2022) 17, e0266143
Che, K., Pobbati, A.V., Seavey, C.N., Fedorov, Y., Komar, A.A., Burtscher, A., Ma, S., Rubin, B.P.
Targeted Modification of Mammalian DNA by a Novel Type V Cas12a Endonuclease from Ruminococcus bromii
International Journal of Molecular Sciences (2022) 23, 9289
Vasilev, R., Gunitseva, N., Shebanova, R., Korzhenkov, A., Vlaskina, A., Evteeva, M., Polushkina, I., Nikitchina, N., Toshchakov, S., Kamenski, P., Patrushev, M., Mazunin, I.
Formulation of an ovarian cancer vaccine with the squalene-based AddaVax adjuvant inhibits the growth of murine epithelial ovarian carcinomas
Clinical and Experimental Vaccine Research (2022) 11, 163–172
Mazumder, S., Swank, V., Dvorina, N., Johnson, J.M., Tuohy, V.K.
Functional analogs of mammalian 4E-BPs reveal a role for TOR in global plant translation
Cell Reports (2023) 42, 112892
Dong, Y., Srour, O., Lukhovitskaya, N., Makarian, J., Baumberger, N., Galzitskaya, O., Elser, D., Schepetilnikov, M., Ryabova, L.A.
Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains
Journal of Medicinal Chemistry (2024) 67, 8186–8200
Phillips, M., Malone, K.L., Boyle, B.W., Montgomery, C., Kressy, I.A., Joseph, F.M., Bright, K.M., Boyson, S.P., Chang, S., Nix, J.C., Young, N.L., Jeffers, V., Frietze, S., Glass, K.C.
The Catalytic Activity of Human REV1 on Undamaged and Damaged DNA
International Journal of Molecular Sciences (2024) 25, 4107
Stolyarenko, A.D., Novikova, A.A., Shilkin, E.S., Poltorachenko, V.A., Makarova, A.V.
Studies that used Dapcel proteins
These studies used Dapcel catalog or custom-made proteins.
p38MAPK builds a hyaluronan cancer niche to drive lung tumorigenesis
Genes & Development (2016) 30, 2623–2636
Brichkina, A., Bertero, T., Loh, H.M., Nguyen, N.T., Emelyanov, A., Rigade, S., Ilie, M., Hofman, P., Gaggioli, C., Bulavin, D.V.
STAT3-mediated SMAD3 activation underlies Oncostatin M-induced Senescence
Cell Cycle (2017) 16, 319–334
Bryson, B.L., Junk, D.J., Cipriano, R., Jackson, M.W.
Oncostatin M promotes cancer cell plasticity through cooperative STAT3-SMAD3 signaling
Oncogene (2017) 36, 4001–4013
Junk, D.J., Bryson, B.L., Smigiel, J.M., Parameswaran, N., Bartel, C.A., Jackson, M.W.
Potent EMT and CSC Phenotypes Are Induced By Oncostatin-M in Pancreatic Cancer
Molecular Cancer Research (2017) 15, 478–488
Smigiel, J.M., Parameswaran, N., Jackson, M.W.
IFN-γ, IL-17A, or zonulin rapidly increase the permeability of the blood-brain and small intestinal epithelial barriers: Relevance for neuro-inflammatory diseases
Biochemical and Biophysical Research Communications (2018) 507, 274–279
Rahman, M.T., Ghosh, C., Hossain, M., Linfield, D., Rezaee, F., Janigro, D., Marchi, N., van Boxel-Dezaire, A.H.H.
The opposing effects of interferon-beta and oncostatin-M as regulators of cancer stem cell plasticity in triple-negative breast cancer
Breast Cancer Research (2019) 21, 54
Doherty, M.R., Parvani, J.G., Tamagno, I., Junk, D.J., Bryson, B.L., Cheon, H.J., Stark, G.R., Jackson, M.W.
Aberrant Induction of a Mesenchymal/Stem Cell Program Engages Senescence in Normal Mammary Epithelial Cells
Molecular Cancer Research (2021) 19, 651–666
Bryson, B.L., Tamagno, I., Taylor, S.E., Parameswaran, N., Chernosky, N.M., Balasubramaniam, N., Jackson, M.W.
Oncostatin-M and OSM-Receptor Feed-Forward Activation of MAPK Induces Separable Stem-like and Mesenchymal Programs
Molecular Cancer Research (2023) 21, 975–990
Polak, K.L., Tamagno, I., Parameswaran, N., Smigiel, J., Chan, E.R., Yuan, X., Rios, B., Jackson, M.W.
Pericentromeric satellite lncRNAs are induced in cancer-associated fibroblasts and regulate their functions in lung tumorigenesis
Cell Death & Disease (2023) 14, 19
Enukashvily, N.I., Ponomartsev, N.V., Ketkar, A., Suezov, R., Chubar, A.V., Prjibelski, A.D., Shafranskaya, D.D., Elmshäuser, S., Keber, C.U., Stefanova, V.N., Akopov, A.L., Klingmüller, U., Pfefferle, P.I., Stiewe, T., Lauth, M., Brichkina, A.I.
A multicentric consortium study demonstrates that dimethylarginine dimethylaminohydrolase 2 is not a dimethylarginine dimethylaminohydrolase
Nature Communications (2023) 14, 3392. Collaboration with Dapcel scientists.
Ragavan, V.N., Nair, P.C., Jarzebska, N., Angom, R.S., Ruta, L., Bianconi, E., Grottelli, S., Tararova, N.D., Ryazanskiy, D., Lentz, S.R., Tommasi, S., Martens-Lobenhoffer, J., Suzuki-Yamamoto, T., Kimoto, M., Rubets, E., Chau, S., Chen, Y., Hu, X., Bernhardt, N., Spieth, P.M., Weiss, N., Bornstein, S.R., Mukhopadhyay, D., Bode-Böger, S.M., Maas, R., Wang, Y., Macchiarulo, A., Mangoni, A.A., Cellini, B., Rodionov, R.N.
Toll-Like receptor 3-mediated interferon-β production is suppressed by oncostatin m and a broader epithelial-mesenchymal transition program
Breast Cancer Research (2024) 26, 167
Chernosky, N.M., Tamagno, I., Polak, K.L., Chan, E.R., Yuan, X., Jackson, M.W.
These are a selection of the published studies that have used our genes and proteins.
Reviews that discuss DAPCEL technology
Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry
BMC Evolutionary Biology (2015) 15, 76
Anisimova, M.
A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell
Biochemistry (Moscow) (2021) 86, 976–991
Komar, A.A.