# Publications Search Within Results Search Within Results search ## 22 results Show filters filter\_alt Sort by Year of PublicationAlphabetical A-Z sort ## 22 results Download 22 citations download- [BibTeX](/node/687026/export?format=bibtex) - [EndNote X3 XML](/node/687026/export?format=endnote8) - [EndNote 7 XML](/node/687026/export?format=endnote7) - [Endnote tagged](/node/687026/export?format=tagged) - [Marc](/node/687026/export?format=marc) - [PubMedId](/node/687026/export?format=pubmed_id) - [RIS](/node/687026/export?format=ris) ### 2025 Wanderley CWS, Michaud DE, Shimada K, Nelson A, Fu J, Schnitt SJ, Tolaney SM, Mittendorf EA, Barroso-Sousa R, Waks A, et al. [APOE+ Tumor-Associated Macrophages and CD4-DOCK4 T Cells Reveal Distinct Microenvironmental Features in HER2-Low and HER2-0 Hormone Receptor-Positive Breast Cancer](https://doi.org/10.1101/2025.09.04.674072). bioRxiv. 2025. Wanderley CWS, Michaud DE, Shimada K, Nelson A, Fu J, Schnitt SJ, Tolaney SM, Mittendorf EA, Barroso-Sousa R, Waks A, et al. [APOE+ Tumor-Associated Macrophages and CD4-DOCK4 T Cells Reveal Distinct Microenvironmental Features in HER2-Low and HER2-0 Hormone Receptor-Positive Breast Cancer](https://doi.org/10.1101/2025.09.04.674072). bioRxiv. 2025. - add\_circle do\_not\_disturb\_on Abstract Novel anti-HER2 antibody-drug conjugates (ADCs), such as trastuzumab deruxtecan (T-DXd), have shown efficacy in tumors with varying HER2 expression, including HER2-low and even tumors with minimal HER2 presence. This has sparked interest in the biology... ### 2024 Shimada K, Michaud DE, Cui YX, Zheng K, Goldberg J, Ju Z, Schnitt SJ, Pastorello R, Kania LD, Hoffer J, et al. [An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer](https://www.biorxiv.org/content/10.1101/2024.11.23.619172v1). bioRxiv. 2024. Shimada K, Michaud DE, Cui YX, Zheng K, Goldberg J, Ju Z, Schnitt SJ, Pastorello R, Kania LD, Hoffer J, et al. [An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer](https://www.biorxiv.org/content/10.1101/2024.11.23.619172v1). bioRxiv. 2024. - add\_circle do\_not\_disturb\_on Abstract T cells are generally sparse in hormone receptor-positive (HR+) breast cancer, potentially due to limited antigen presentation, but the driving mechanisms of low T cell abundance remains unclear. Therefore, we defined and investigated programs (‘gene... Guerriero JL, Lin J-R, Pastorello R, Du Z, Chen Y-A, Townsend MG, Shimada K, Hughes ME, Ren S, Tayob N, et al. [Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer](https://www.nature.com/articles/s41523-023-00605-3). NPJ Breast Cancer. 2024;10(1). Guerriero JL, Lin J-R, Pastorello R, Du Z, Chen Y-A, Townsend MG, Shimada K, Hughes ME, Ren S, Tayob N, et al. [Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer](https://www.nature.com/articles/s41523-023-00605-3). NPJ Breast Cancer. 2024;10(1). - add\_circle do\_not\_disturb\_on Abstract Emerging data suggests that HER2 intratumoral heterogeneity (ITH) is associated with therapy resistance, highlighting the need for new strategies to assess HER2 ITH. A promising approach is leveraging multiplexed tissue analysis techniques such as cyclic... ### 2021 Weng J-H, Koch PD, Luan H, Tu H-C, Shimada K, Ngan I, Ventura R, Jiang R, Mitchison T. [Colchicine acts selectively in the liver to induce hepatokines that inhibit myeloid cell activation](https://www.nature.com/articles/s42255-021-00366-y). Nat Metab. 2021;3(4):513–522. doi:10.1038/s42255-021-00366-y Weng J-H, Koch PD, Luan H, Tu H-C, Shimada K, Ngan I, Ventura R, Jiang R, Mitchison T. [Colchicine acts selectively in the liver to induce hepatokines that inhibit myeloid cell activation](https://www.nature.com/articles/s42255-021-00366-y). Nat Metab. 2021;3(4):513–522. doi:10.1038/s42255-021-00366-y - add\_circle do\_not\_disturb\_on Abstract Colchicine has served as a traditional medicine for millennia and remains widely used to treat inflammatory and other disorders. Colchicine binds tubulin and depolymerizes microtubules, but it remains unclear how this mechanism blocks myeloid cell... Shimada K, Bachman J, Muhlich J, Mitchison T. [shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data](https://elifesciences.org/articles/57116). Elife. 2021;10. doi:10.7554/eLife.57116 Shimada K, Bachman J, Muhlich J, Mitchison T. [shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data](https://elifesciences.org/articles/57116). Elife. 2021;10. doi:10.7554/eLife.57116 - add\_circle do\_not\_disturb\_on Abstract Individual cancers rely on distinct essential genes for their survival. The Cancer Dependency Map (DepMap) is an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines. To make this drug discovery resource more accessible to... ### 2020 Stokes M, Small JC, Vasciaveo A, Shimada K, Hirschhorn T, Califano A, Stockwell B. [Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation](https://www.nature.com/articles/s41598-020-67310-0). Sci Rep. 2020;10(1):10748. doi:10.1038/s41598-020-67310-0 Stokes M, Small JC, Vasciaveo A, Shimada K, Hirschhorn T, Califano A, Stockwell B. [Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation](https://www.nature.com/articles/s41598-020-67310-0). Sci Rep. 2020;10(1):10748. doi:10.1038/s41598-020-67310-0 - add\_circle do\_not\_disturb\_on Abstract The identification of targeted agents with high therapeutic index is a major challenge for cancer drug discovery. We found that screening chemical libraries across neuroblastoma (NBL) tumor subtypes for selectively-lethal compounds revealed metabolic... ### 2019 Nakanishi M, Mitchell R, Benoit Y, Orlando L, Reid J, Shimada K, Davidson K, Shapovalova Z, Collins T, Nagy A, et al. [Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells](https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(19)30275-2). Cell. 2019;177(4):910–924.e22. doi:10.1016/j.cell.2019.03.013 Nakanishi M, Mitchell R, Benoit Y, Orlando L, Reid J, Shimada K, Davidson K, Shapovalova Z, Collins T, Nagy A, et al. [Human Pluripotency Is Initiated and Preserved by a Unique Subset of Founder Cells](https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(19)30275-2). Cell. 2019;177(4):910–924.e22. doi:10.1016/j.cell.2019.03.013 - add\_circle do\_not\_disturb\_on Abstract The assembly of organized colonies is the earliest manifestation in the derivation or induction of pluripotency in vitro. However, the necessity and origin of this assemblance is unknown. Here, we identify human pluripotent founder cells (hPFCs) that... Shimada K, Mitchison T. [Unsupervised identification of disease states from high-dimensional physiological and histopathological profiles](https://link.springer.com/article/10.15252/msb.20188636). Mol Syst Biol. 2019;15(2):e8636. doi:10.15252/msb.20188636 Shimada K, Mitchison T. [Unsupervised identification of disease states from high-dimensional physiological and histopathological profiles](https://link.springer.com/article/10.15252/msb.20188636). Mol Syst Biol. 2019;15(2):e8636. doi:10.15252/msb.20188636 - add\_circle do\_not\_disturb\_on Abstract The liver and kidney in mammals play central roles in protecting the organism from xenobiotics and are at high risk of xenobiotic-induced injury. Xenobiotic-induced tissue injury has been extensively studied from both classical histopathological and... ### 2018 Shimada K, Reznik E, Stokes M, Krishnamoorthy L, Bos P, Song Y, Quartararo C, Pagano N, Carpizo D, , et al. [Copper-Binding Small Molecule Induces Oxidative Stress and Cell-Cycle Arrest in Glioblastoma-Patient-Derived Cells](https://linkinghub.elsevier.com/retrieve/pii/S2451-9456(18)30074-6). Cell Chem Biol. 2018;25(5):585–594.e7. doi:10.1016/j.chembiol.2018.02.010 Shimada K, Reznik E, Stokes M, Krishnamoorthy L, Bos P, Song Y, Quartararo C, Pagano N, Carpizo D, , et al. [Copper-Binding Small Molecule Induces Oxidative Stress and Cell-Cycle Arrest in Glioblastoma-Patient-Derived Cells](https://linkinghub.elsevier.com/retrieve/pii/S2451-9456(18)30074-6). Cell Chem Biol. 2018;25(5):585–594.e7. doi:10.1016/j.chembiol.2018.02.010 - add\_circle do\_not\_disturb\_on Abstract Transition metals are essential, but deregulation of their metabolism causes toxicity. Here, we report that the compound NSC319726 binds copper to induce oxidative stress and arrest glioblastoma-patient-derived cells at picomolar concentrations... ### 2017 Viswanathan V, Ryan M, Dhruv H, Gill S, Eichhoff O, Seashore-Ludlow B, Kaffenberger S, Eaton J, Shimada K, Aguirre A, et al. [Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway](https://www.nature.com/articles/nature23007). Nature. 2017;547(7664):453–457. doi:10.1038/nature23007 Viswanathan V, Ryan M, Dhruv H, Gill S, Eichhoff O, Seashore-Ludlow B, Kaffenberger S, Eaton J, Shimada K, Aguirre A, et al. [Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway](https://www.nature.com/articles/nature23007). Nature. 2017;547(7664):453–457. doi:10.1038/nature23007 - add\_circle do\_not\_disturb\_on Abstract Plasticity of the cell state has been proposed to drive resistance to multiple classes of cancer therapies, thereby limiting their effectiveness. A high-mesenchymal cell state observed in human tumours and cancer cell lines has been associated with... ### 2016 Shimada K, Skouta R, Kaplan A, Yang WS, Hayano M, Dixon S, Brown L, Valenzuela C, Wolpaw A, Stockwell B. [Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis.](https://www.nature.com/articles/nchembio.2079) Nat Chem Biol. 2016;12(7):497–503. doi:10.1038/nchembio.2079 Shimada K, Skouta R, Kaplan A, Yang WS, Hayano M, Dixon S, Brown L, Valenzuela C, Wolpaw A, Stockwell B. [Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis.](https://www.nature.com/articles/nchembio.2079) Nat Chem Biol. 2016;12(7):497–503. doi:10.1038/nchembio.2079 - add\_circle do\_not\_disturb\_on Abstract Apoptosis is one type of programmed cell death. Increasingly, non-apoptotic cell death is recognized as being genetically controlled, or 'regulated'. However, the full extent and diversity of alternative cell death mechanisms remain uncharted. Here we... Shimada K, Stockwell B. [tRNA synthase suppression activates de novo cysteine synthesis to compensate for cystine and glutathione deprivation during ferroptosis.](https://www.tandfonline.com/doi/10.1080/23723556.2015.1091059?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed) Mol Cell Oncol. 2016;3(2):e1091059. doi:10.1080/23723556.2015.1091059 Shimada K, Stockwell B. [tRNA synthase suppression activates de novo cysteine synthesis to compensate for cystine and glutathione deprivation during ferroptosis.](https://www.tandfonline.com/doi/10.1080/23723556.2015.1091059?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed) Mol Cell Oncol. 2016;3(2):e1091059. doi:10.1080/23723556.2015.1091059 - add\_circle do\_not\_disturb\_on Abstract Glutathione is a major endogenous reducing agent in cells, and cysteine is a limiting factor in glutathione synthesis. Cysteine is obtained by uptake or biosynthesis, and mammalian cells often rely on either one or the other pathway. Because of the... - Previous page chevron\_left - [1](?page=0 "Current page") - [2](?page=1 "Go to page 2") - [ Next page chevron\_right ](?page=1 "Go to next page")