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Palande S, Kaste JAM, Roberts MD, Segura Abá K, Claucherty C, Dacon J, Doko R, Jayakody TB, Jeffery HR, Kelly N, Manousidaki A, Parks HM, Roggenkamp EM, Schumacher AM, Yang J, Percival S, Pardo J, Husbands AY, Krishnan A, Montgomery BL, Munch E, Thompson AM, Rougon-Cardoso A, Chitwood DH, VanBuren R. Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants. PLoS Biol 2023; 21:e3002397. [PMID: 38051702 PMCID: PMC10723737 DOI: 10.1371/journal.pbio.3002397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 12/15/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests that there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function.
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Affiliation(s)
- Sourabh Palande
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Joshua A. M. Kaste
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Miles D. Roberts
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Kenia Segura Abá
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Carly Claucherty
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Jamell Dacon
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Rei Doko
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Thilani B. Jayakody
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Hannah R. Jeffery
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Nathan Kelly
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Andriana Manousidaki
- Department of Statistics and Probability, Michigan State University, East Lansing, Michigan, United States of America
| | - Hannah M. Parks
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Emily M. Roggenkamp
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Ally M. Schumacher
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jiaxin Yang
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Sarah Percival
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeremy Pardo
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Aman Y. Husbands
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Arjun Krishnan
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Beronda L Montgomery
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Elizabeth Munch
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Mathematics, Michigan State University, East Lansing, Michigan, United States of America
| | - Addie M. Thompson
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, United States of America
| | - Alejandra Rougon-Cardoso
- Laboratory of Agrigenomic Sciences, Universidad Nacional Autónoma de México, ENES-León, León, Mexico
- Laboratorio Nacional Plantecc, ENES-León, León, Mexico
| | - Daniel H. Chitwood
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, United States of America
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Heath BR, Gong W, Taner HF, Broses L, Okuyama K, Cheng W, Jin M, Fitzsimonds ZR, Manousidaki A, Wu Y, Zhang S, Wen H, Chinn SB, Bartee E, Xie Y, Moon JJ, Lei YL. Saturated fatty acids dampen the immunogenicity of cancer by suppressing STING. Cell Rep 2023; 42:112303. [PMID: 36952341 PMCID: PMC10514241 DOI: 10.1016/j.celrep.2023.112303] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/21/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
Oncogenes destabilize STING in epithelial cell-derived cancer cells, such as head and neck squamous cell carcinomas (HNSCCs), to promote immune escape. Despite the abundance of tumor-infiltrating myeloid cells, HNSCC presents notable resistance to STING stimulation. Here, we show how saturated fatty acids in the microenvironment dampen tumor response to STING stimulation. Using single-cell analysis, we found that obesity creates an IFN-I-deprived tumor microenvironment with a massive expansion of suppressive myeloid cell clusters and contraction of effector T cells. Saturated fatty acids, but not unsaturated fatty acids, potently inhibit the STING-IFN-I pathway in HNSCC cells. Myeloid cells from obese mice show dampened responses to STING stimulation and are more suppressive of T cell activation. In agreement, obese hosts exhibited increased tumor burden and lower responsiveness to STING agonist. As a mechanism, saturated fatty acids induce the expression of NLRC3, depletion of which results in a T cell inflamed tumor microenvironment and IFN-I-dependent tumor control.
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Affiliation(s)
- Blake R Heath
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Wang Gong
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Hülya F Taner
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, USA; Graduate Program in Oral Health Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Luke Broses
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Kohei Okuyama
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Wanqing Cheng
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Max Jin
- Homer Stryker M.D. School of Medicine, Western Michigan University, Kalamazoo, MI, USA
| | - Zackary R Fitzsimonds
- Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Andriana Manousidaki
- Department of Computational Mathematics, Science, and Engineering, Department of Statistics, Michigan State University, East Lansing, MI, USA
| | - Yuesong Wu
- Department of Computational Mathematics, Science, and Engineering, Department of Statistics, Michigan State University, East Lansing, MI, USA
| | - Shaoping Zhang
- Department of Periodontics, University of Iowa College of Dentistry, Iowa City, IA, USA
| | - Haitao Wen
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Steven B Chinn
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, USA
| | - Eric Bartee
- Department of Internal Medicine, Division of Molecular Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Yuying Xie
- Department of Computational Mathematics, Science, and Engineering, Department of Statistics, Michigan State University, East Lansing, MI, USA
| | - James J Moon
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Yu Leo Lei
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Periodontics and Oral Medicine, University of Michigan, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Graduate Program in Oral Health Sciences, University of Michigan School of Dentistry, Ann Arbor, MI, USA; Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, USA.
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