Macromolecular modeling and design in Rosetta: recent methods and frameworks

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes

Interleukin-2 (IL-2) is a cytokine required for effector T cell expansion, survival, and function, especially for engineered T cells in adoptive cell immunotherapy, but its pleiotropy leads to simultaneous stimulation and suppression of immune responses as well as systemic toxicity, limiting its therapeutic use. We engineered IL-2 cytokine-receptor orthogonal (ortho) pairs that interact with one another, transmitting native IL-2 signals, but do not interact with their natural cytokine and receptor counterparts. Introduction of orthoIL-2Rβ into T cells enabled the selective cellular targeting of orthoIL-2 to engineered CD4⁺ and CD8⁺ T cells in vitro and in vivo, with limited off-target effects and negligible toxicity. OrthoIL-2 pairs were efficacious in a preclinical mouse cancer model of adoptive cell therapy and may therefore represent a synthetic approach to achieving selective potentiation of engineered cells.

Antitumor effect of VNP20009, an attenuated Salmonella, in murine tumor models

VNP20009, a genetically modified strain of Salmonella typhimurium with deletions in the msbB and purI loci, exhibited antitumor activities when given systemically to tumor-bearing mice. VNP20009 inhibited the growth of subcutaneously implanted B16F10 murine melanoma, and the human tumor xenografts Lox, DLD-1, A549, WiDr, HTB177, and MDA-MB-231. A single intravenous injection of VNP20009, at doses ranging from 1 x 10(4) to 3 x 10(6) cfu/mouse, produced tumor growth inhibitions of 57-95%. Tumor volume doubling time, another indicator for tumor growth inhibition, also significantly increased in mice treated with VNP20009. Using mice with immune system deficiencies, we also demonstrated that the antitumor effects of VNP20009 did not depend on the presence of T and B cells. In addition, VNP20009, given intravenously, inhibited the growth of lung metastases in mice. Only live bacteria showed the antitumor effect.

Tumor amplified protein expression therapy: Salmonella as a tumor-selective protein delivery vector

Attenuated strains of Salmonella typhimurium, VNP20009 and YS7212, when injected systemically to tumor-bearing mice, accumulated preferentially in tumors at levels at least 200-fold and, more commonly, 1000-fold greater than in other normal tissues. This selectivity occurred in subcutaneously implanted murine tumors, including B16F10 melanoma, M27 lung carcinoma, and colon 38 carcinoma. The preferential accumulation was also manifested in animals bearing human tumor xenografts, including Lox, C8186, DLD1, SW620, HCT116, HTB177, DU145, MDA-MB-231, and Caki. Four to five days after a single IV injection of 1 x 10(6) colony-forming unit (cfu)/mouse, we routinely detected VNP20009 proliferation and accumulation at levels ranging from 1 x 10(8) to 2 x 10(9) cfu/g tumor. The amount of VNP20009 accumulated in the liver ranged from 3 x 10(4) to 2 x 10(6) cfu/g. The distribution of Salmonella in tumors was homogenous; YS7212 could be detected from the periphery to the interior portion of the tumors. Using mice with various immunodeficiencies, we also discovered the same preferential accumulation of Salmonella in tumors implanted in these mice. The use of Salmonella as a protein delivery vector was shown by IV administration of the bacteria expressing either green fluorescent protein (GFP) or cytosine deaminase (CD) into tumor-bearing mice. GFP and CD were detected in tumors, but not in livers, taken from mice inoculated with Salmonella carrying these genes. Bacteria accumulation and CD expression persisted in the tumors for up to 14 days after a single bolus IV administration of bacteria to tumor-bearing mice.

Detection of in vivo differentiation of murine WEHI-3B D+ leukemia cells transfected with the lac-Z marker gene using two-color flow cytometry

The in vivo induction of the differentiation of murine WEHI-3B D+ myelomonocytic leukemia cells was measured by flow cytometry, simultaneously staining leukemia cells for the marker exogenous beta-galactosidase and for differentiation by the antigen Mac-1 (CD11b/CD18). The WEHI-3B D+ leukemia cells were transfected with the E. coli lac-Z gene by electroporation and subclones that constitutively expressed high levels of the lac-Z gene product beta-galactosidase were established. Flow cytometric analyses of cells in the peritoneal cavities of mice bearing leukemia cells showed that cells continued to express beta-galactosidase for at least 14 days, and they were distinguishable from host-derived cells in vivo by their expression of the transfected gene. Simultaneous determination of the beta-galactosidase activity and Mac-1 content of cells in the peritoneal cavities of mice revealed that administration of recombinant human granulocyte colony-stimulating factor (rhG-CSF) to the mice enhanced the expression of Mac-1 antigen by beta-galactosidase-positive cells. The results demonstrate that G-CSF may have clinical potential as a therapeutic differentiating agent, and that flow cytometric analysis provides a useful in vivo system to evaluate the therapeutic potential of agents capable of inducing terminal differentiation.

High throughput assay for inhibitors of the epidermal growth factor receptor-associated tyrosine kinase

We have developed a colorimetric assay for the examination of inhibitors of epidermal growth factor (EGF) receptor-associated tyrosine kinase in intact cells. EGF receptor from cells treated with inhibitors is captured by an anti-EGF receptor antibody and the phosphotyrosine content is measured by an anti-phosphotyrosine antibody. The quantitative assay does not use radioactive substances and is configured for a high-throughput format. Since it is performed in intact cells, substances lower the phosphotyrosine content on the receptor by different mechanisms will be identified. One distinct feature of the assay is that it uses the natural substrate inside the cell as compared to others using artificial substrates in an unphysiological environment. This assay is easy to perform, is reproducible, and is compatible with many organic solvents and tissue culture media. Thus, it is useful for the discovery of EGF receptor kinase inhibitors from natural products or synthetic compounds and is particularly suitable for large-scale screening.

Nonradioactive ligand binding assay for epidermal growth factor receptor

A rapid and sensitive nonradioactive ligand binding assay for identifying the agonists and antagonists of epidermal growth factor receptor is described. The assay is easy to perform, has a within-assay error of less than 15%, and does not use radioactive substances. Nonspecific binding is less than 10% and the assay is sensitive enough to detect epidermal growth factor (EGF) antagonists at as little as 10 nM, if the antagonist has the same affinity as EGF. The assay is carried out in 96-well plates and is particularly suitable for large-scale screening. This report includes description of the methods that we used to assess the validity of the assay system, and the results of that assessment.

The relationship between epidermal growth factor receptors and the terminal differentiation of A431 carcinoma cells

The replication of human epidermoid carcinoma A431 cells is inhibited by epidermal growth factor (EGF), with 5 ng/ml of EGF causing 50% inhibition of cellular proliferation. EGF resistant clones isolated from A431 cells were able to replicate in the presence of 100 ng/ml of EGF. That this insensitivity to EGF was probably due to a decrease in the expression of EGF receptors (EGFR) on the cell surface was shown using an EGFR cDNA probe to detect a 68% to 85% decrease relative to parental cells in the amount of EGFR mRNA in the EGF resistant clones. A corresponding decrease in surface EGFR levels was also detected in EGF resistant clones as measured by 125I-EGF binding. Eighteen percent of A431 cells cultured in serum-free medium for 6 days entered a pathway of terminal differentiation, as expressed by the formation of envelope-competent cells, whereas EGF resistant clones exhibited a considerably greater capacity to mature, even when cultured in serum-containing medium. The findings suggest that the concentration of EGFRs is important for the capacity of epidermal cells to undergo terminal differentiation in vitro.