[ { "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" }, { "id": "authors:sg60e-p1s82", "collection": "authors", "collection_id": "sg60e-p1s82", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190312-085351129", "type": "monograph", "title": "T Cell Receptor Immunotherapy Drives Human Immunodeficiency Virus Evolution in Humanized Mice", "author": [ { "family_name": "Joglekar", "given_name": "Alok V.", "orcid": "0000-0001-7554-7447", "clpid": "Joglekar-A-V" }, { "family_name": "Swift", "given_name": "Margaret", "clpid": "Swift-M" }, { "family_name": "Leonard", "given_name": "Michael T.", "orcid": "0000-0001-9084-2647", "clpid": "Leonard-M-T" }, { "family_name": "Jeppson", "given_name": "John D.", "clpid": "Jeppson-J-D" }, { "family_name": "Sandoval", "given_name": "Salemiz", "clpid": "Sandoval-S" }, { "family_name": "Baltimore", "given_name": "David", "orcid": "0000-0001-8723-8190", "clpid": "Baltimore-D" } ], "abstract": "Effective CD8+ T cell responses targeted to the KK10 epitope of HIV presented by HLA-B*27:05, a protective HLA allele, correlate with the ability to control infection without antiretroviral therapy (ART). Here, we report an immunotherapy approach using two B*27:05-KK10-specific T Cell Receptors (TCRs) isolated from HIV controllers. Immunocompromised mice engrafted with human Hematopoietic Stem/Progenitor Cells (HSPCs) encoding for the TCRs showed differentiation into functionally active engineered T cells. Following infection with HIV, both TCRs showed sustained, albeit modest, viral suppression over 32 weeks, accompanied by a concomitant increase in CD4+ T cells. Sequencing of viral quasi-species from the plasma of infected mice demonstrated clear evidence for viral evolution under selection pressure from the TCRs. The most commonly observed mutation in the KK10 epitope was L6M, which preserved viral fitness but showed attenuated recognition by the TCRs. These studies show that TCR-immunotherapy was able to suppress HIV infection long-term while driving HIV evolution in humanized mice.", "doi": "10.1101/574608", "publication_date": "2019-03-12" }, { "id": "authors:vpry4-n7x96", "collection": "authors", "collection_id": "vpry4-n7x96", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181030-074928774", "type": "monograph", "title": "Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression", "author": [ { "family_name": "Majumdar", "given_name": "Devdoot S.", "clpid": "Majumdar-D-S" }, { "family_name": "Frankiw", "given_name": "Luke", "clpid": "Frankiw-L-S" }, { "family_name": "Burns", "given_name": "Christian H.", "clpid": "Burns-C-H" }, { "family_name": "Garcia-Flores", "given_name": "Yvette", "clpid": "Garcia-Flores-Yvette" }, { "family_name": "Baltimore", "given_name": "David", "orcid": "0000-0001-8723-8190", "clpid": "Baltimore-D" } ], "abstract": "Inflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-kB transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. In many cases, this is attributable to poor splice donor sequences that are evolutionarily conserved. When these introns were altered by ~2 base pairs to yield stronger splice donors, gene expression levels increased markedly for several genes in the context of a reporter system. We propose that such splice sites represent a regulatory mechanism that determines the timing of production of the mRNAs from certain inflammatory genes and may also limit mRNA expression from these genes. Further work will be needed to understand the roles of this regulation in the inflammatory response. The suggestion of extensive temporal regulation of pre-mRNA splicing as a regulatory process in inflammation raises the question of where else in biology there may be timed processes with a similar underlying cause.", "doi": "10.1101/443796", "publication_date": "2018-10-15" } ]