[ { "id": "authors:p1a52-w7j03", "collection": "authors", "collection_id": "p1a52-w7j03", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211209-231124000", "type": "monograph", "title": "Stereochemical engineering of a peptide macrocycle allosteric inhibitor of phospho-Akt2 controls cell penetration by fine-tuning macrocycle-cell membrane interactions", "author": [ { "family_name": "Nag", "given_name": "Arundhati", "orcid": "0000-0002-1328-1695", "clpid": "Nag-Arundhati" }, { "family_name": "Mafi", "given_name": "Amirhossein", "orcid": "0000-0002-8366-6785", "clpid": "Mafi-Amirhossein" }, { "family_name": "Das", "given_name": "Samir", "clpid": "Das-Samir" }, { "family_name": "Yu", "given_name": "Mary Beth", "clpid": "Yu-Mary-Beth" }, { "family_name": "Alvarez-Villalonga", "given_name": "Belen", "clpid": "Alvarez-Villalonga-Belen" }, { "family_name": "Goddard", "given_name": "William A., III", "orcid": "0000-0003-0097-5716", "clpid": "Goddard-W-A-III" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "abstract": "We report the development of a cell-penetrant cyclic loop biligand that selectively binds, in vitro, to the phosphorylated Ser474 site of Protein Kinase B (p-Akt2) with high affinity (K_D = 10 nM). The cyclic loop biligand consists of a linear peptide joined to a macrocycle peptide through triazole linkage, and it was isolated through two iterative in situ screens. This biligand allosterically inhibited kinase activity of Akt2 but it was cell-impermeable, as isolated from the screening process. Since Akt2 is an oncoprotein hyperactivated via phosphorylation at Ser474 in cancers, we sought to visualize p-Akt2 in live cancer cells using the developed biligand. To this end, we matured this biligand into a cell-penetrant reagent through systematic iterations of its chemical structure to promote cell-penetrating properties, while retaining its binding and inhibition for p-Akt2. Two retro-inverso, N-methylated versions of the macrocyclic ligand were developed which were uptaken by live cancer cells, while retaining their high affinities for pAkt2. Interestingly, the stereochemistry of two amino acid residues in the cell-penetrant ligands exhibited strong influence on their extent of cell penetration. This phenomenon of difference in cell penetration was explored through metadynamics simulations of each ligand in the cell membrane. It was found that the ligand uptaken to a greater extent by cells had more intramolecular interactions with itself and had fewer cholesterol molecules associated with it, which aided in its cell-penetration.", "doi": "10.26434/chemrxiv-2021-kldh7", "publication_date": "2021-11-24" }, { "id": "authors:wpsjb-te013", "collection": "authors", "collection_id": "wpsjb-te013", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201120-071520503", "type": "monograph", "title": "Shared Antigen-specific CD8\u207a T cell Responses Against the SARS-COV-2 Spike Protein in HLA A*02:01 COVID-19 Participants", "author": [ { "family_name": "Chour", "given_name": "William", "orcid": "0000-0003-1817-0123", "clpid": "Chour-William" }, { "family_name": "Xu", "given_name": "Alexander M.", "orcid": "0000-0003-4877-4358", "clpid": "Xu-Alexander-M" }, { "family_name": "Ng", "given_name": "Alphonsus H. C.", "orcid": "0000-0003-0074-4598", "clpid": "Ng-Alphonsus-H-C" }, { "family_name": "Choi", "given_name": "Jongchan", "clpid": "Choi-Jongchan" }, { "family_name": "Xie", "given_name": "Jingyi", "clpid": "Xie-Jingyi" }, { "family_name": "Yuan", "given_name": "Dan", "clpid": "Yuan-Dan" }, { "family_name": "Delucia", "given_name": "Diane C.", "clpid": "Delucia-Diane-C" }, { "family_name": "Edmark", "given_name": "Rick A.", "clpid": "Edmark-Rick-A" }, { "family_name": "Jones", "given_name": "Lesley C.", "clpid": "Jones-Lesley-C" }, { "family_name": "Schmitt", "given_name": "Thomas M.", "clpid": "Schmitt-Thomas-M" }, { "family_name": "Chaffee", "given_name": "Mary E.", "clpid": "Chaffee-Mary-E" }, { "family_name": "Duvvuri", "given_name": "Venkata R.", "clpid": "Duvvuri-Venkata-R" }, { "family_name": "Murray", "given_name": "Kim M.", "clpid": "Murray-Kim-M" }, { "family_name": "Peng", "given_name": "Songming", "orcid": "0000-0002-2742-6584", "clpid": "Peng-Songming" }, { "family_name": "Wallick", "given_name": "Julie", "clpid": "Wallick-Julie" }, { "family_name": "Algren", "given_name": "Heather A.", "clpid": "Algren-Heather-A" }, { "family_name": "Berrington", "given_name": "William R.", "clpid": "Berrington-William-R" }, { "family_name": "O'Mahoney", "given_name": "D. Shane", "clpid": "O'Mahoney-D-Shane" }, { "family_name": "Lee", "given_name": "John K.", "orcid": "0000-0003-4077-0395", "clpid": "Lee-John-K" }, { "family_name": "Greenberg", "given_name": "Philip D.", "clpid": "Greenberg-Philip-D" }, { "family_name": "Goldman", "given_name": "Jason D.", "orcid": "0000-0002-3825-6832", "clpid": "Goldman-Jason-D" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "abstract": "We report here on antigens from the SARS-CoV-2 virus spike protein, that when presented by Class I MHC, can lead to cytotoxic CD8\u207a T cell anti-viral responses in COVID-19 patients. We present a method in which the SARS-CoV-2 spike protein is converted into a library of peptide antigen-Major Histocompatibility Complexes (pMHCs) as single chain trimers that contain the peptide antigen, the MHC HLA allele, and the \u03b2-2 microglobulin sub-unit. That library is used to detect the evolution of virus-specific T cell populations from two COVID-19 patients, at two time points over the course of infection. Both patients exhibit similar virus-specific T cell populations, but very different time-trajectories of those populations. These results can be used to track those virus-specific T cell populations over the course of an infection, thus providing deep insight into the variations in immune system trajectories observed in different COVID-19 patients.", "doi": "10.1101/2020.05.04.20085779", "publication_date": "2020-05-08" }, { "id": "authors:35565-f8k34", "collection": "authors", "collection_id": "35565-f8k34", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190913-074926949", "type": "monograph", "title": "Trajectories from Snapshots: Integrated proteomic and metabolic single-cell assays reveal multiple independent adaptive responses to drug tolerance in a BRAF-mutant melanoma cell line", "author": [ { "family_name": "Su", "given_name": "Yapeng", "clpid": "Su-Yapeng" }, { "family_name": "Li", "given_name": "Guideng", "orcid": "0000-0003-0840-7262", "clpid": "Li-Guideng" }, { "family_name": "Ko", "given_name": "Melissa E.", "clpid": "Ko-Melissa-E" }, { "family_name": "Cheng", "given_name": "Hanjun", "clpid": "Cheng-Hanjun" }, { "family_name": "Zhu", "given_name": "Ronghui", "clpid": "Zhu-Ronghui" }, { "family_name": "Xue", "given_name": "Min", "clpid": "Xue-Min" }, { "family_name": "Wang", "given_name": "Jessica", "orcid": "0000-0003-1421-4969", "clpid": "Wang-Jessica-K" }, { "family_name": "Lee", "given_name": "Jihoon W.", "clpid": "Lee-Jihoon-W" }, { "family_name": "Frankiw", "given_name": "Luke", "clpid": "Frankiw-L-S" }, { "family_name": "Xu", "given_name": "Alexander", "orcid": "0000-0003-4877-4358", "clpid": "Xu-Alexander-M" }, { "family_name": "Wong", "given_name": "Stephanie", "clpid": "Wong-Stephanie" }, { "family_name": "Robert", "given_name": "Lidia", "clpid": "Robert-L" }, { "family_name": "Takata", "given_name": "Kaitlyn", "orcid": "0000-0003-4864-9741", "clpid": "Takata-Kaitlyn-L" }, { "family_name": "Huang", "given_name": "Sui", "clpid": "Huang-Sui" }, { "family_name": "Ribas", "given_name": "Antoni", "clpid": "Ribas-A" }, { "family_name": "Levine", "given_name": "Raphael", "clpid": "Levine-R-D" }, { "family_name": "Nolan", "given_name": "Garry P.", "clpid": "Nolan-Garry-P" }, { "family_name": "Wei", "given_name": "Wei", "orcid": "0000-0002-1018-7708", "clpid": "Wei-Wei" }, { "family_name": "Plevritis", "given_name": "Sylvia K.", "clpid": "Plevritis-S-K" }, { "family_name": "Baltimore", "given_name": "David", "orcid": "0000-0001-8723-8190", "clpid": "Baltimore-D" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" } ], "abstract": "The determination of individual cell trajectories through a high-dimensional cell-state space is an outstanding challenge, with relevance towards understanding biological changes ranging from cellular differentiation to epigenetic (adaptive) responses of diseased cells to drugging. We report on a combined experimental and theoretic method for determining the trajectories that specific highly plastic BRAFV600E mutant patient-derived melanoma cancer cells take between drug-naive and drug-tolerant states. Recent studies have implicated non-genetic, fast-acting resistance mechanisms are activated in these cells following BRAF inhibition. While single-cell highly multiplex omics tools can yield snapshots of the cell state space landscape sampled at any given time point, individual cell trajectories must be inferred from a kinetic series of snapshots, and that inference can be confounded by stochastic cell state switching. Using a microfludic-based single-cell integrated proteomic and metabolic assay, we assayed for a panel of signaling, phenotypic, and metabolic regulators at four time points during the first five days of drug treatment. Dimensional reduction of the resultant data set, coupled with information theoretic analysis, uncovered a complex cell state landscape and identified two distinct paths connecting drug-naive and drug-tolerant states. Cells are shown to exclusively traverse one of the two pathways depending on the level of the lineage restricted transcription factor MITF in the drug-naive cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities, and are independently druggable. Our results update the paradigm of adaptive resistance development in an isogenic cell population and offer insight into the design of more effective combination therapies.", "doi": "10.1101/767988", "publication_date": "2019-09-12" }, { "id": "authors:fhc9f-zwt87", "collection": "authors", "collection_id": "fhc9f-zwt87", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190805-155608943", "type": "monograph", "title": "Kinetic Inference Resolves Epigenetic Mechanism of Drug Resistance in Melanoma", "author": [ { "family_name": "Su", "given_name": "Yapeng", "clpid": "Su-Yapeng" }, { "family_name": "Lee", "given_name": "Jihoon W.", "clpid": "Lee-Jihoon-W" }, { "family_name": "Ng", "given_name": "Rachel", "clpid": "Ng-Rachel" }, { "family_name": "Liu", "given_name": "Victoria", "orcid": "0000-0003-1845-2497", "clpid": "Liu-Victoria" }, { "family_name": "Peng", "given_name": "Songming", "orcid": "0000-0002-2742-6584", "clpid": "Peng-Songming" }, { "family_name": "Xue", "given_name": "Min", "clpid": "Xue-Min" }, { "family_name": "Heath", "given_name": "James R.", "orcid": "0000-0001-5356-4385", "clpid": "Heath-J-R" }, { "family_name": "Li", "given_name": "Guideng", "orcid": "0000-0003-0840-7262", "clpid": "Li-Guideng" }, { "family_name": "Wong", "given_name": "Stephanie", "clpid": "Wong-Stephanie" }, { "family_name": "Baltimore", "given_name": "David", "orcid": "0000-0001-8723-8190", "clpid": "Baltimore-D" } ], "abstract": "We resolved a mechanism connecting tumor epigenetic plasticity with non-genetic adaptive resistance to therapy, with MAPK inhibition of BRAF-mutant melanomas providing the model. These cancer cells undergo multiple, reversible drug-induced cell-state transitions, ultimately yielding a drug-resistant mesenchymal-like phenotype. A kinetic series of transcriptome and epigenome data, collected over two months of drug treatment and release, revealed changing levels of thousands of genes and extensive chromatin remodeling. However, a 3-step computational algorithm greatly simplified the interpretation of these changes, and revealed that the whole adaptive process was controlled by a gene module activated within just three days of treatment, with RelA driving chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes. These findings were confirmed across several patient-derived cell lines and in melanoma patients under MAPK inhibitor treatment. Co-targeting BRAF and histone-modifying enzymes arrests adaptive transitions towards drug tolerance in epigenetically plastic melanoma cells and may be exploited therapeutically.", "doi": "10.1101/724740", "publication_date": "2019-08-05" } ]