1
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Ridnour LA, Heinz WF, Cheng RY, Wink AL, Kedei N, Pore M, Imtiaz F, Femino EL, Gonzalez AL, Coutinho L, Butcher D, Edmondson EF, Rangel MC, Kinders RJ, Lipkowitz S, Wong ST, Anderson SK, McVicar DW, Li X, Glynn SA, Billiar TR, Chang JC, Hewitt SM, Ambs S, Lockett SJ, Wink DA. NOS2 and COX2 Provide Key Spatial Targets that Determine Outcome in ER- Breast Cancer. bioRxiv 2023:2023.12.21.572859. [PMID: 38187532 PMCID: PMC10769386 DOI: 10.1101/2023.12.21.572859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Estrogen receptor-negative (ER-) breast cancer is an aggressive breast cancer subtype with limited therapeutic options. Upregulated expression of both inducible nitric oxide synthase (NOS2) and cyclo-oxygenase (COX2) in breast tumors predicts poor clinical outcomes. Signaling molecules released by these enzymes activate oncogenic pathways, driving cancer stemness, metastasis, and immune suppression. The influence of tumor NOS2/COX2 expression on the landscape of immune markers using multiplex fluorescence imaging of 21 ER- breast tumors were stratified for survival. A powerful relationship between tumor NOS2/COX2 expression and distinct CD8+ T cell phenotypes was observed at 5 years post-diagnosis. These results were confirmed in a validation cohort using gene expression data showing that ratios of NOS2 to CD8 and COX2 to CD8 are strongly associated with poor outcomes in high NOS2/COX2-expressing tumors. Importantly, multiplex imaging identified distinct CD8+ T cell phenotypes relative to tumor NOS2/COX2 expression in Deceased vs Alive patient tumors at 5-year survival. CD8+NOS2-COX2- phenotypes defined fully inflamed tumors with significantly elevated CD8+ T cell infiltration in Alive tumors expressing low NOS2/COX2. In contrast, two distinct phenotypes including inflamed CD8+NOS2+COX2+ regions with stroma-restricted CD8+ T cells and CD8-NOS2-COX2+ immune desert regions with abated CD8+ T cell penetration, were significantly elevated in Deceased tumors with high NOS2/COX2 expression. These results were supported by applying an unsupervised nonlinear dimensionality-reduction technique, UMAP, correlating specific spatial CD8/NOS2/COX2 expression patterns with patient survival. Moreover, spatial analysis of the CD44v6 and EpCAM cancer stem cell (CSC) markers within the CD8/NOS2/COX2 expression landscape revealed positive correlations between EpCAM and inflamed stroma-restricted CD8+NOS2+COX2+ phenotypes at the tumor/stroma interface in deceased patients. Also, positive correlations between CD44v6 and COX2 were identified in immune desert regions in deceased patients. Furthermore, migrating tumor cells were shown to occur only in the CD8-NOS2+COX2+ regions, identifying a metastatic hot spot. Taken together, this study shows the strength of spatial localization analyses of the CD8/NOS2/COX2 landscape, how it shapes the tumor immune microenvironment and the selection of aggressive tumor phenotypes in distinct regions that lead to poor clinical outcomes. This technique could be beneficial for describing tumor niches with increased aggressiveness that may respond to clinically available NOS2/COX2 inhibitors or immune-modulatory agents.
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Affiliation(s)
- Lisa A Ridnour
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Robert Ys Cheng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Adelaide L Wink
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Noemi Kedei
- Collaborative Protein Technology Resource (CPTR) Nanoscale Protein Analysis, OSTR, CCR, NCI, NIH
| | - Milind Pore
- Imaging Mass Cytometry Frederick National Laboratory for Cancer Research
| | - Fatima Imtiaz
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Elise L Femino
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Ana L Gonzalez
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Leandro Coutinho
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Donna Butcher
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for the National Cancer Institute
| | - Elijah F Edmondson
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for the National Cancer Institute
| | - M Cristina Rangel
- Center for Translational Research in Oncology, ICESP/HC, Faculdade de Medicina da Universidade de São Paulo and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Robert J Kinders
- Office of the Director, Division of Cancer Treatment and Diagnosis, NCI, Frederick, MD
| | | | | | - Stephen K Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Danial W McVicar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
| | - Sharon A Glynn
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Jenny C Chang
- Mary and Ron Neal Cancer Center, Houston Methodist Hospital and Weill Cornell Medicine, Houston, TX
| | | | - Stefan Ambs
- Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - David A Wink
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
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2
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Ridnour LA, Cheng RYS, Heinz WF, Pore M, Gonzalez AL, Femino EL, Moffat R, Wink AL, Imtiaz F, Coutinho L, Butcher D, Edmondson EF, Rangel MC, Wong STC, Lipkowitz S, Glynn S, Vitek MP, McVicar DW, Li X, Anderson SK, Paolocci N, Hewitt SM, Ambs S, Billiar TR, Chang JC, Lockett SJ, Wink DA. Spatial analysis of NOS2 and COX2 interaction with T-effector cells reveals immunosuppressive landscapes associated with poor outcome in ER- breast cancer patients. bioRxiv 2023:2023.12.21.572867. [PMID: 38187660 PMCID: PMC10769421 DOI: 10.1101/2023.12.21.572867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Multiple immunosuppressive mechanisms exist in the tumor microenvironment that drive poor outcomes and decrease treatment efficacy. The co-expression of NOS2 and COX2 is a strong predictor of poor prognosis in ER- breast cancer and other malignancies. Together, they generate pro-oncogenic signals that drive metastasis, drug resistance, cancer stemness, and immune suppression. Using an ER- breast cancer patient cohort, we found that the spatial expression patterns of NOS2 and COX2 with CD3+CD8+PD1- T effector (Teff) cells formed a tumor immune landscape that correlated with poor outcome. NOS2 was primarily associated with the tumor-immune interface, whereas COX2 was associated with immune desert regions of the tumor lacking Teff cells. A higher ratio of NOS2 or COX2 to Teff was highly correlated with poor outcomes. Spatial analysis revealed that regional clustering of NOS2 and COX2 was associated with stromal-restricted Teff, while only COX2 was predominant in immune deserts. Examination of other immunosuppressive elements, such as PDL1/PD1, Treg, B7H4, and IDO1, revealed that PDL1/PD1, Treg, and IDO1 were primarily associated with restricted Teff, whereas B7H4 and COX2 were found in tumor immune deserts. Regardless of the survival outcome, other leukocytes, such as CD4 T cells and macrophages, were primarily in stromal lymphoid aggregates. Finally, in a 4T1 model, COX2 inhibition led to a massive cell infiltration, thus validating the hypothesis that COX2 is an essential component of the Teff exclusion process and, thus, tumor evasion. Our study indicates that NOS2/COX2 expression plays a central role in tumor immunosuppression. Our findings indicate that new strategies combining clinically available NOS2/COX2 inhibitors with various forms of immune therapy may open a new avenue for the treatment of aggressive ER-breast cancers.
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Affiliation(s)
- Lisa A Ridnour
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Robert Y S Cheng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Milind Pore
- Imaging Mass Cytometry Frederick National Laboratory for Cancer Research
| | - Ana L Gonzalez
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Elise L Femino
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Rebecca Moffat
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Adelaide L Wink
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Fatima Imtiaz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Leandro Coutinho
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
- Faculdade de Medicina da Universidade de São Paulo and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Donna Butcher
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for the National Cancer Institute
| | - Elijah F Edmondson
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for the National Cancer Institute
| | - M Cristina Rangel
- Faculdade de Medicina da Universidade de São Paulo and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Sharon Glynn
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
| | | | - Daniel W McVicar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
| | - Stephen K Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
- Basic Science Program, Frederick National Laboratory for Cancer Research
| | - Nazareno Paolocci
- Division of Cardiology, Department of Medicine, Johns Hopkins University, and Department of Biomedical Sciences, University of Padova, Italy
- Laboratory of Pathology CCR, NCI, NIH
| | | | - Stefan Ambs
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Timothy R Billiar
- Mary and Ron Neal Cancer Center, Houston Methodist Hospital and Weill Cornell Medicine, Houston, TX
| | - Jenny C Chang
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
- Imaging Mass Cytometry Frederick National Laboratory for Cancer Research
- Faculdade de Medicina da Universidade de São Paulo and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for the National Cancer Institute
- Houston Methodist Weill Cornell Medical College, Houston TX
- Women's Malignancies Branch, CCR, NCI, NIH
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
- (Mike Duke)
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
- Basic Science Program, Frederick National Laboratory for Cancer Research
- Division of Cardiology, Department of Medicine, Johns Hopkins University, and Department of Biomedical Sciences, University of Padova, Italy
- Laboratory of Pathology CCR, NCI, NIH
- Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA
- Mary and Ron Neal Cancer Center, Houston Methodist Hospital and Weill Cornell Medicine, Houston, TX
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - David A Wink
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
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Il Ahn J, Zhang L, Ravishankar H, Fan L, Kirsch K, Zeng Y, Meng L, Park JE, Yun HY, Ghirlando R, Ma B, Ball D, Ku B, Nussinov R, Schmit JD, Heinz WF, Kim SJ, Karpova T, Wang YX, Lee KS. Author Correction: Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells. Commun Biol 2023; 6:784. [PMID: 37500946 PMCID: PMC10374603 DOI: 10.1038/s42003-023-05162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Affiliation(s)
- Jong Il Ahn
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liang Zhang
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Harsha Ravishankar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Klara Kirsch
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yan Zeng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lingjun Meng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jung-Eun Park
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- School of Pharmacy, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - David Ball
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Tatiana Karpova
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kyung S Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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4
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Il Ahn J, Zhang L, Ravishankar H, Fan L, Kirsch K, Zeng Y, Meng L, Park JE, Yun HY, Ghirlando R, Ma B, Ball D, Ku B, Nussinov R, Schmit JD, Heinz WF, Kim SJ, Karpova T, Wang YX, Lee KS. Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells. Commun Biol 2023; 6:712. [PMID: 37433832 PMCID: PMC10336005 DOI: 10.1038/s42003-023-05067-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Proper organization of intracellular assemblies is fundamental for efficient promotion of biochemical processes and optimal assembly functionality. Although advances in imaging technologies have shed light on how the centrosome is organized, how its constituent proteins are coherently architected to elicit downstream events remains poorly understood. Using multidisciplinary approaches, we showed that two long coiled-coil proteins, Cep63 and Cep152, form a heterotetrameric building block that undergoes a stepwise formation into higher molecular weight complexes, ultimately generating a cylindrical architecture around a centriole. Mutants defective in Cep63•Cep152 heterotetramer formation displayed crippled pericentriolar Cep152 organization, polo-like kinase 4 (Plk4) relocalization to the procentriole assembly site, and Plk4-mediated centriole duplication. Given that the organization of pericentriolar materials (PCM) is evolutionarily conserved, this work could serve as a model for investigating the structure and function of PCM in other species, while offering a new direction in probing the organizational defects of PCM-related human diseases.
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Affiliation(s)
- Jong Il Ahn
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liang Zhang
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Harsha Ravishankar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-ray Scattering Core Facility, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Klara Kirsch
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yan Zeng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lingjun Meng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jung-Eun Park
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Hye-Yeoung Yun
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- School of Pharmacy, Shanghai Jiao Tong University, 200240, Shanghai, P R China
| | - David Ball
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Tatiana Karpova
- Laboratory of Receptor Biology and Gene Expression, Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Kyung S Lee
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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5
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Degenhardt MFS, Degenhardt HF, Bhandari YR, Lee YT, Ding J, Heinz WF, Stagno JR, Schwieters CD, Zhang J, Wang YX. Determining structures of individual RNA conformers using atomic force microscopy images and deep neural networks. Res Sq 2023:rs.3.rs-2798658. [PMID: 37425706 PMCID: PMC10327248 DOI: 10.21203/rs.3.rs-2798658/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The vast percentage of the human genome is transcribed into RNA, many of which contain various structural elements and are important for functions. RNA molecules are conformationally heterogeneous and functionally dyanmics1, even when they are structured and well-folded2, which limit the applicability of methods such as NMR, crystallography, or cryo-EM. Moreover, because of the lack of a large structure RNA database, and no clear correlation between sequence and structure, approaches like AlphaFold3 for protein structure prediction, do not apply to RNA. Therefore determining the structures of heterogeneous RNA is an unmet challenge. Here we report a novel method of determining RNA three-dimensional topological structures using deep neural networks and atomic force microscopy (AFM) images of individual RNA molecules in solution. Owing to the high signal-to-noise ratio of AFM, our method is ideal for capturing structures of individual conformationally heterogeneous RNA. We show that our method can determine 3D topological structures of any large folded RNA conformers, from ~ 200 to ~ 420 residues, the size range that most functional RNA structures or structural elements fall into. Thus our method addresses one of the major challenges in frontier RNA structural biology and may impact our fundamental understanding of RNA structure.
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Affiliation(s)
- Maximilia F S Degenhardt
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute; Frederick, USA
| | - Hermann F Degenhardt
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute; Frederick, USA
| | - Yuba R Bhandari
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute; Frederick, USA
| | - Yun-Tzai Lee
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute; Frederick, USA
| | - Jienyu Ding
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute; Frederick, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute; Frederick, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda, USA
| | - Jinwei Zhang
- Structural Biology of Noncoding RNAs and Ribonucleoproteins Section, Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health; Bethesda, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, National Cancer Institute; Frederick, USA
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6
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Cheng RYS, Ridnour LA, Wink AL, Gonzalez AL, Femino EL, Rittscher H, Somasundaram V, Heinz WF, Coutinho L, Rangel MC, Edmondson EF, Butcher D, Kinders RJ, Li X, Wong STC, McVicar DW, Anderson SK, Pore M, Hewitt SM, Billiar TR, Glynn SA, Chang JC, Lockett SJ, Ambs S, Wink DA. Interferon-gamma is quintessential for NOS2 and COX2 expression in ER - breast tumors that lead to poor outcome. Cell Death Dis 2023; 14:319. [PMID: 37169743 PMCID: PMC10175544 DOI: 10.1038/s41419-023-05834-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/13/2023]
Abstract
A strong correlation between NOS2 and COX2 tumor expression and poor clinical outcomes in ER breast cancer has been established. However, the mechanisms of tumor induction of these enzymes are unclear. Analysis of The Cancer Genome Atlas (TCGA) revealed correlations between NOS2 and COX2 expression and Th1 cytokines. Herein, single-cell RNAseq analysis of TNBC cells shows potent NOS2 and COX2 induction by IFNγ combined with IL1β or TNFα. Given that IFNγ is secreted by cytolytic lymphocytes, which improve clinical outcomes, this role of IFNγ presents a dichotomy. To explore this conundrum, tumor NOS2, COX2, and CD8+ T cells were spatially analyzed in aggressive ER-, TNBC, and HER2 + breast tumors. High expression and clustering of NOS2-expressing tumor cells occurred at the tumor/stroma interface in the presence of stroma-restricted CD8+ T cells. High expression and clustering of COX2-expressing tumor cells extended into immune desert regions in the tumor core where CD8+ T cell penetration was limited or absent. Moreover, high NOS2-expressing tumor cells were proximal to areas with increased satellitosis, suggestive of cell clusters with a higher metastatic potential. Further in vitro experiments revealed that IFNγ + IL1β/TNFα increased the elongation and migration of treated tumor cells. This spatial analysis of the tumor microenvironment provides important insight into distinct neighborhoods where stroma-restricted CD8+ T cells exist proximal to NOS2-expressing tumor niches that could have increased metastatic potential.
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Affiliation(s)
- Robert Y S Cheng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Lisa A Ridnour
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Adelaide L Wink
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD, USA
| | - Ana L Gonzalez
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elise L Femino
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Helene Rittscher
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Veena Somasundaram
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD, USA
| | - Leandro Coutinho
- Center for Translational Research in Oncology, ICESP/HC, Faculdade de Medicina da Universidade de São Paulo; and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
| | - M Cristina Rangel
- Center for Translational Research in Oncology, ICESP/HC, Faculdade de Medicina da Universidade de São Paulo; and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Elijah F Edmondson
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for NCI, Frederick, MD, USA
| | - Donna Butcher
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for NCI, Frederick, MD, USA
| | - Robert J Kinders
- Office of the Director, Division of Cancer Treatment and Diagnosis, NCI, Frederick, MD, USA
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Stephen T C Wong
- Systems Medicine and Bioengineering Department, Houston Methodist Neal Cancer Center, Houston Methodist Hospital and Weill Cornell Medicine, Houston, TX, USA
| | - Daniel W McVicar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Stephen K Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Milind Pore
- Imaging Mass Cytometry Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Sharon A Glynn
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
| | - Jenny C Chang
- Mary and Ron Neal Cancer Center, Houston Methodist Hospital and Weill Cornell Medicine, Houston, TX, USA
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD, USA
| | - David A Wink
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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7
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Cheng RY, Ridnour LA, Wink AL, Gonzalez AL, Femino EL, Rittscher H, Somasundarum V, Heinz WF, Coutinho L, Cristina Rangel M, Edmondson EF, Butcher D, Kinders RJ, Li X, Wong STC, McVicar DW, Anderson SK, Pore M, Hewitt SM, Billiar TR, Glynn S, Chang JC, Lockett SJ, Ambs S, Wink DA. Interferon-gamma is Quintessential for NOS2 and COX2 Expression in ER - Breast Tumors that Lead to Poor Outcome. bioRxiv 2023:2023.04.06.535916. [PMID: 37066331 PMCID: PMC10104135 DOI: 10.1101/2023.04.06.535916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
A strong correlation between NOS2 and COX2 tumor expression and poor clinical outcomes in ER-breast cancer has been established. However, mechanisms of tumor induction of these enzymes are unclear. Analysis of The Cancer Genome Atlas (TCGA) revealed correlations between NOS2 and COX2 expression and Th1 cytokines. Herein, single cell RNAseq analysis of TNBC cells shows potent NOS2 and COX2 induction by IFNγ combined with IL1β or TNFα. Given that IFNγ is secreted by cytolytic lymphocytes, which improve clinical outcomes, this role of IFNγpresents a dichotomy. To explore this conundrum, tumor NOS2, COX2, and CD8 + T cells were spatially analyzed in aggressive ER-, TNBC, and HER2+ breast tumors. High expression and clustering of NOS2-expressing tumor cells occurred at the tumor/stroma interface in the presence of stroma-restricted CD8 + T cells. High expression and clustering of COX2-expressing tumor cells extended into immune desert regions in the tumor core where CD8 + T cell penetration was limited or absent. Moreover, high NOS2-expressing tumor cells were proximal to areas with increased satellitosis suggestive of cell clusters with a higher metastatic potential. Further in vitro experiments revealed that IFNγ+IL1β/TNFα increased elongation and migration of treated tumor cells. This spatial analysis of the tumor microenvironment provides important insight of distinct neighborhoods where stroma-restricted CD8 + T cells exist proximal to NOS2-expressing tumor niches that could have increased metastatic potential.
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8
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Lee HK, Conrad CE, Magidson V, Heinz WF, Pauly G, Yu P, Ramakrishnan S, Stagno JR, Wang YX. Developing methods to study conformational changes in RNA crystals using a photocaged ligand. Front Mol Biosci 2022; 9:964595. [PMID: 36052167 PMCID: PMC9424638 DOI: 10.3389/fmolb.2022.964595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Crystallographic observation of structural changes in real time requires that those changes be uniform both spatially and temporally. A primary challenge with time-resolved ligand-mixing diffraction experiments is asynchrony caused by variable factors, such as efficiency of mixing, rate of diffusion, crystal size, and subsequently, conformational heterogeneity. One method of minimizing such variability is use of a photolabile caged ligand, which can fully saturate the crystal environment (spatially), and whose photoactivation can rapidly (temporally) trigger the reaction in a controlled manner. Our recently published results on a ligand-mixing experiment using time-resolved X-ray crystallography (TRX) with an X-ray free electron laser (XFEL) demonstrated that large conformational changes upon ligand binding resulted in a solid-to-solid phase transition (SSPT), while maintaining Bragg diffraction. Here we investigate this SSPT by polarized video microscopy (PVM) after light-triggered release of a photo-caged adenine (pcADE). In general, the mean transition times and transition widths of the SSPT were less dependent on crystal size than what was observed in previous PVM studies with direct ADE mixing. Instead, the photo-induced transition appears to be heavily influenced by the equilibrium between caged and uncaged ADE due to relatively low sample exposure and uncaging efficiency. Nevertheless, we successfully demonstrate a method for the characterization of phase transitions in RNA crystals that are inducible with a photocaged ligand. The transition data for three crystals of different sizes were then applied to kinetic analysis by fitting to the known four-state model associated with ligand-induced conformational changes, revealing an apparent concentration of uncaged ADE in crystal of 0.43–0.46 mM. These results provide further insight into approaches to study time-resolved ligand-induced conformational changes in crystals, and in particular, highlight the feasibility of triggering phase transitions using a light-inducible system. Developing such approaches may be paramount for the rapidly emerging field of time-resolved crystallography.
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Affiliation(s)
- Hyun Kyung Lee
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Chelsie E. Conrad
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - William F. Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Gary Pauly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Ping Yu
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Saminathan Ramakrishnan
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Jason R. Stagno
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
- *Correspondence: Jason R. Stagno, ; Yun-Xing Wang,
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
- *Correspondence: Jason R. Stagno, ; Yun-Xing Wang,
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9
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Trofka A, Huang BL, Zhu J, Heinz WF, Magidson V, Shibata Y, Shi YB, Tarchini B, Stadler HS, Kabangu M, Al Haj Baddar NW, Voss SR, Mackem S. Genetic basis for an evolutionary shift from ancestral preaxial to postaxial limb polarity in non-urodele vertebrates. Curr Biol 2021; 31:4923-4934.e5. [PMID: 34610275 DOI: 10.1016/j.cub.2021.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/30/2021] [Accepted: 09/03/2021] [Indexed: 11/24/2022]
Abstract
In most tetrapod vertebrates, limb skeletal progenitors condense with postaxial dominance. Posterior elements (such as ulna and fibula) appear prior to their anterior counterparts (radius and tibia), followed by digit-appearance order with continuing postaxial polarity. The only exceptions are urodele amphibians (salamanders), whose limb elements develop with preaxial polarity and who are also notable for their unique ability to regenerate complete limbs as adults. The mechanistic basis for this preaxial dominance has remained an enigma and has even been proposed to relate to the acquisition of novel genes involved in regeneration. However, recent fossil evidence suggests that preaxial polarity represents an ancestral rather than derived state. Here, we report that 5'Hoxd (Hoxd11-d13) gene deletion in mouse is atavistic and uncovers an underlying preaxial polarity in mammalian limb formation. We demonstrate this shift from postaxial to preaxial dominance in mouse results from excess Gli3 repressor (Gli3R) activity due to the loss of 5'Hoxd-Gli3 antagonism and is associated with cell-cycle changes promoting precocious cell-cycle exit in the anterior limb bud. We further show that Gli3 knockdown in axolotl results in a shift to postaxial dominant limb skeleton formation, as well as expanded paddle-shaped limb-bud morphology and ensuing polydactyly. Evolutionary changes in Gli3R activity level, which also played a key role in the fin-to-limb transition, appear to be fundamental to the shift from preaxial to postaxial polarity in formation of the tetrapod limb skeleton.
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Affiliation(s)
- Anna Trofka
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Bau-Lin Huang
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Jianjian Zhu
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yuki Shibata
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver NICHD, Bethesda, MD, USA
| | - Yun-Bo Shi
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver NICHD, Bethesda, MD, USA
| | | | - H Scott Stadler
- Division of Skeletal Biology, Shriners Hospitals for Children, Portland, OR, USA; Department of Orthopaedics and Rehabilitation, Oregon Health & Science University, Portland, OR, USA
| | - Mirindi Kabangu
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, USA
| | - Nour W Al Haj Baddar
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, USA
| | - S Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, USA.
| | - Susan Mackem
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA.
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10
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Stagno JR, Ramakrishnan S, Heinz WF, Magidson V, Zuo X, Wang YX. Solid–solid phase transition in adenine riboswitch crystals driven by large conformational changes induced by ligand. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321091649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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11
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Stagno J, Ramikrishnan S, Heinz WF, Magidson V, Zuo X, Yu P, Wang YX. Solid–solid phase transition in adenine riboswitch crystals driven by large conformational changes induced by ligand. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321099256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Ramakrishnan S, Stagno JR, Heinz WF, Zuo X, Yu P, Wang YX. The mechanism driving a solid-solid phase transition in a biomacromolecular crystal. IUCrJ 2021; 8:655-664. [PMID: 34258013 PMCID: PMC8256710 DOI: 10.1107/s2052252521004826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/06/2021] [Indexed: 06/13/2023]
Abstract
Solid-solid phase transitions (SSPTs) occur between distinguishable crystalline forms. Because of their importance in application and theory in materials science and condensed-matter physics, SSPTs have been studied most extensively in metallic alloys, inorganic salts and small organic molecular crystals, but much less so in biomacromolecular crystals. In general, the mechanisms of SSPTs at the atomic and molecular levels are not well understood. Here, the ordered molecular rearrangements in biomacromolecular crystals of the adenine riboswitch aptamer are described using real-time serial crystallography and solution atomic force microscopy. Large, ligand-induced conformational changes drive the initial phase transition from the apo unit cell (AUC) to the trans unit cell 1 (TUC1). During this transition, coaxial stacking of P1 duplexes becomes the dominant packing interface, whereas P2-P2 interactions are almost completely disrupted, resulting in 'floating' layers of molecules. The coupling points in TUC1 and their local conformational flexibility allow the molecules to reorganize to achieve the more densely packed and energetically favorable bound unit cell (BUC). This study thus reveals the interplay between the conformational changes and the crystal phases - the underlying mechanism that drives the phase transition. Using polarized video microscopy to monitor SSPTs in small crystals at high ligand concentration, the time window during which the major conformational changes take place was identified, and the in crystallo kinetics have been simulated. Together, these results provide the spatiotemporal information necessary for informing time-resolved crystallography experiments. Moreover, this study illustrates a practical approach to characterization of SSPTs in transparent crystals.
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Affiliation(s)
- Saminathan Ramakrishnan
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason R. Stagno
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - William F. Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Ping Yu
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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13
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Ramakrishnan S, Stagno JR, Magidson V, Heinz WF, Wang YX. A combined approach to characterize ligand-induced solid-solid phase transitions in biomacromolecular crystals. J Appl Crystallogr 2021; 54:787-796. [PMID: 34194289 PMCID: PMC8202036 DOI: 10.1107/s1600576721003137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/24/2021] [Indexed: 11/10/2022] Open
Abstract
Solid-solid phase transitions (SSPTs) are widespread naturally occurring phenomena. Understanding the molecular mechanisms and kinetics of SSPTs in various crystalline materials, however, has been challenging due to technical limitations. In particular, SSPTs in biomacromolecular crystals, which may involve large-scale changes and particularly complex sets of interactions, are largely unexplored, yet may have important implications for time-resolved crystallography and for developing synthetic biomaterials. The adenine riboswitch (riboA) is an RNA control element that uses ligand-induced conformational changes to regulate gene expression. Crystals of riboA, upon the addition of a ligand, undergo an SSPT from monoclinic to triclinic to orthorhombic. Here, solution atomic force microscopy (AFM) and polarized video microscopy (PVM) are used to characterize the multiple transition states throughout the SSPT in both the forward and the reverse directions. This contribution describes detailed protocols for growing crystals directly on mica or glass surfaces for AFM and PVM characterization, respectively, as well as methods for image processing and phase-transition kinetics analysis.
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Affiliation(s)
- Saminathan Ramakrishnan
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason R. Stagno
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - William F. Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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14
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Rausch JW, Heinz WF, Payea MJ, Sherpa C, Gorospe M, Le Grice SFJ. Characterizing and circumventing sequence restrictions for synthesis of circular RNA in vitro. Nucleic Acids Res 2021; 49:e35. [PMID: 33406226 DOI: 10.1093/nar/gkaa1256] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/27/2020] [Accepted: 12/18/2020] [Indexed: 01/10/2023] Open
Abstract
Just as eukaryotic circular RNA (circRNA) is a product of intracellular backsplicing, custom circRNA can be synthesized in vitro using a transcription template in which transposed halves of a split group I intron flank the sequence of the RNA to be circularized. Such permuted intron-exon (PIE) constructs have been used to produce circRNA versions of ribozymes, mimics of viral RNA motifs, a streptavidin aptamer, and protein expression vectors for genetic engineering and vaccine development. One limitation of this approach is the obligatory incorporation of small RNA segments (E1 and E2) into nascent circRNA at the site of end-joining. This restriction may preclude synthesis of small circRNA therapeutics and RNA nanoparticles that are sensitive to extraneous sequence, as well as larger circRNA mimics whose sequences must precisely match those of the native species on which they are modelled. In this work, we used serial mutagenesis and in vitro selection to determine how varying E1 and E2 sequences in a thymidylate synthase (td) group I intron PIE transcription template construct affects circRNA synthesis yield. Based on our collective findings, we present guidelines for the design of custom-tailored PIE transcription templates from which synthetic circRNAs of almost any sequence may be efficiently synthesized.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Matthew J Payea
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Chringma Sherpa
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
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15
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Ramakrishnan S, Stagno JR, Magidson V, Heinz WF, Wang YX. Dependence of phase transition uniformity on crystal sizes characterized using birefringence. Struct Dyn 2021; 8:034301. [PMID: 34235229 PMCID: PMC8248999 DOI: 10.1063/4.0000098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 06/13/2023]
Abstract
Solid-solid phase transitions (SSPTs) have been widely observed in crystals of organic or inorganic small-molecules. Although SSPTs in macromolecular crystals have been reported, the majority involve local atomic changes, such as those induced by changes in hydration. SSPTs driven by large conformational changes, however, can be more difficult to characterize since they often significantly disrupt lattice packing interactions. Such drastic changes make the cooperativity of molecular motion at the atomic level less easily achieved and more dependent on intrinsic properties of the crystal that define lattice order. Here, we investigate the effect of crystal size on the uniformity of SSPT in thin plate-like crystals of the adenine riboswitch aptamer RNA (riboA) by monitoring changes in crystal birefringence upon the diffusion of adenine ligand. The birefringence intensity is directly related to molecular order and the concurrent changes to polarizability of molecules that results from structural changes throughout the phase transition. The riboA crystals were loosely grouped into three categories (small, medium, and large) based on the surface area of the crystal plates. The time width of transition increased as a function of crystal size, ranging from ∼13 s for small crystals to ∼40 s for the largest crystal. Whereas the transitions in small crystals (<10 μm2) were mostly uniform throughout, the medium and large crystals exhibited large variations in the time and width of the transition peak depending on the region of the crystal being analyzed. Our study provides insight into the spatiotemporal behavior of phase transitions in crystals of biological molecules and is of general interest to time-resolved crystallographic studies, where the kinetics of conformational changes may be governed by the kinetics of an associated SSPT.
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Affiliation(s)
- Saminathan Ramakrishnan
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Jason R. Stagno
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - William F. Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
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16
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Gilmore AC, Flaherty SJ, Somasundaram V, Scheiblin DA, Lockett SJ, Wink DA, Heinz WF. An in vitro tumorigenesis model based on live-cell-generated oxygen and nutrient gradients. Commun Biol 2021; 4:477. [PMID: 33859337 PMCID: PMC8050328 DOI: 10.1038/s42003-021-01954-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 03/02/2021] [Indexed: 01/06/2023] Open
Abstract
The tumor microenvironment (TME) is multi-cellular, spatially heterogenous, and contains cell-generated gradients of soluble molecules. Current cell-based model systems lack this complexity or are difficult to interrogate microscopically. We present a 2D live-cell chamber that approximates the TME and demonstrate that breast cancer cells and macrophages generate hypoxic and nutrient gradients, self-organize, and have spatially varying phenotypes along the gradients, leading to new insights into tumorigenesis.
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Affiliation(s)
- Anne C Gilmore
- Optical Microscopy and Analysis Laboratory, Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sarah J Flaherty
- Optical Microscopy and Analysis Laboratory, Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Veena Somasundaram
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - David A Scheiblin
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - David A Wink
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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17
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Ramakrishnan S, Stagno JR, Conrad CE, Ding J, Yu P, Bhandari YR, Lee YT, Pauly G, Yefanov O, Wiedorn MO, Knoska J, Oberthür D, White TA, Barty A, Mariani V, Li C, Brehm W, Heinz WF, Magidson V, Lockett S, Hunter MS, Boutet S, Zatsepin NA, Zuo X, Grant TD, Pandey S, Schmidt M, Spence JCH, Chapman HN, Wang YX. Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nat Commun 2021; 12:1762. [PMID: 33741910 PMCID: PMC7979858 DOI: 10.1038/s41467-021-21838-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 11/20/2022] Open
Abstract
Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals. Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.
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Affiliation(s)
| | - Jason R Stagno
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Chelsie E Conrad
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.,Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jienyu Ding
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Ping Yu
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yuba R Bhandari
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yun-Tzai Lee
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Gary Pauly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Max O Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Chufeng Li
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen Lockett
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ, USA.,Department of Chemistry and Physics, ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Victoria, Australia
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Suraj Pandey
- Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Marius Schmidt
- Kenwood Interdisciplinary Research Complex Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ, USA
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.,Department of Physics, Universität Hamburg, Hamburg, Germany.,Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA.
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18
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Kasprzak WK, Zakrevsky P, Bindewald E, Heinz WF, Wu W, Kahnt H, Dorjsuren N, Fields EA, de Val N, Jaeger L, Shapiro BA. Design and Modeling of a Tetrahedron Nanostructure for Enhanced Delivery of RNAi Substrates. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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19
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Zakrevsky P, Kasprzak WK, Heinz WF, Wu W, Khant H, Bindewald E, Dorjsuren N, Fields EA, de Val N, Jaeger L, Shapiro BA. Truncated tetrahedral RNA nanostructures exhibit enhanced features for delivery of RNAi substrates. Nanoscale 2020; 12:2555-2568. [PMID: 31932830 DOI: 10.1039/c9nr08197f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using RNA as a material for nanoparticle construction provides control over particle size and shape at the nano-scale. RNA nano-architectures have shown promise as delivery vehicles for RNA interference (RNAi) substrates, allowing multiple functional entities to be combined on a single particle in a programmable fashion. Rather than employing a completely bottom-up approach to scaffold design, here multiple copies of an existing synthetic supramolecular RNA nano-architecture serve as building blocks along with additional motifs for the design of a novel truncated tetrahedral RNA scaffold, demonstrating that rationally designed RNA assemblies can themselves serve as modular pieces in the construction of larger rationally designed structures. The resulting tetrahedral scaffold displays enhanced characteristics for RNAi-substrate delivery in comparison to similar RNA-based scaffolds, as evidenced by its increased functional capacity, increased cellular uptake and ultimately an increased RNAi efficacy of its adorned Dicer substrate siRNAs. The unique truncated tetrahedral shape of the nanoparticle core appears to contribute to this particle's enhanced function, indicating the physical characteristics of RNA scaffolds merit significant consideration when designing platforms for delivery of functional RNAs via RNA nanoparticles.
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Affiliation(s)
- Paul Zakrevsky
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Htet Khant
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Eckart Bindewald
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Nomongo Dorjsuren
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Eric A Fields
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA and Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD 21701, USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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20
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Sun Z, Cagliero C, Izard J, Chen Y, Zhou YN, Heinz WF, Schneider TD, Jin DJ. Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli. Nucleic Acids Res 2019; 47:3970-3985. [PMID: 30843055 DOI: 10.1093/nar/gkz159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 11/14/2022] Open
Abstract
RNA polymerase (RNAP), the transcription machinery, shows dynamic binding across the genomic DNA under different growth conditions. The genomic features that selectively redistribute the limited RNAP molecules to dictate genome-wide transcription in response to environmental cues remain largely unknown. We chose the bacterial osmotic stress response model to determine genomic features that direct genome-wide redistribution of RNAP during the stress. Genomic mapping of RNAP and transcriptome profiles corresponding to the different temporal states after salt shock were determined. We found rapid redistribution of RNAP across the genome, primarily at σ70 promoters. Three subsets of genes exhibiting differential salt sensitivities were identified. Sequence analysis using an information-theory based σ70 model indicates that the intergenic regions of salt-responsive genes are enriched with a higher density of σ70 promoter-like sites than those of salt-sensitive genes. In addition, the density of promoter-like sites has a positive linear correlation with RNAP binding at different salt concentrations. The RNAP binding contributed by the non-initiating promoter-like sites is important for gene transcription at high salt concentration. Our study demonstrates that hyperdensity of σ70 promoter-like sites in the intergenic regions of salt-responsive genes drives the RNAP redistribution for reprograming the transcriptome to counter osmotic stress.
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Affiliation(s)
- Zhe Sun
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Cedric Cagliero
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jerome Izard
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yixiong Chen
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yan Ning Zhou
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Thomas D Schneider
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ding Jun Jin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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21
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Somasundaram V, Gilmore AC, Basudhar D, Palmieri EM, Scheiblin DA, Heinz WF, Cheng RYS, Ridnour LA, Altan-Bonnet G, Lockett SJ, McVicar DW, Wink DA. Inducible nitric oxide synthase-derived extracellular nitric oxide flux regulates proinflammatory responses at the single cell level. Redox Biol 2019; 28:101354. [PMID: 31683257 PMCID: PMC6920088 DOI: 10.1016/j.redox.2019.101354] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/04/2019] [Accepted: 10/18/2019] [Indexed: 02/01/2023] Open
Abstract
The role of nitric oxide (NO) in cancer progression has largely been studied in the context of tumor NOS2 expression. However, pro- versus anti-tumor signaling is also affected by tumor cell-macrophage interactions. While these cell-cell interactions are partly regulated by NO, the functional effects of NO flux on proinflammatory (M1) macrophages are unknown. Using a triple negative murine breast cancer model, we explored the potential role of macrophage Nos2 on 4T1 tumor progression. The effects of NO on macrophage phenotype were examined in bone marrow derived macrophages from wild type and Nos2−/− mice following in vitro stimulation with cytokine/LPS combinations to produce low, medium, and high NO flux. Remarkably, Nos2 induction was spatially distinct, where Nos2high cells expressed low cyclooxygenase-2 (Cox2) and vice versa. Importantly, in vitro M1 polarization with IFNγ+LPS induced high NO flux that was restricted to cells harboring depolarized mitochondria. This flux altered the magnitude and spatial extent of hypoxic gradients. Metabolic and single cell analyses demonstrated that single cell Nos2 induction limited the generation of hypoxic gradients in vitro, and Nos2-dependent and independent features may collaborate to regulate M1 functionality. It was found that Cox2 expression was important for Nos2high cells to maintain NO tolerance. Furthermore, Nos2 and Cox2 expression in 4T1 mouse tumors was spatially orthogonal forming distinct cellular neighborhoods. In summary, the location and type of Nos2high cells, NO flux, and the inflammatory status of other cells, such as Cox2high cells in the tumor niche contribute to Nos2 inflammatory mechanisms that promote disease progression of 4T1 tumors.
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Affiliation(s)
- Veena Somasundaram
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, USA
| | - Anne C Gilmore
- Optical Microscopy and Analysis Laboratory, Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, USA
| | - Debashree Basudhar
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, USA
| | - Erika Mariana Palmieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, USA
| | - David A Scheiblin
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert Y S Cheng
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, USA
| | - Lisa A Ridnour
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, USA
| | - Grégoire Altan-Bonnet
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, USA
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Daniel W McVicar
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, USA
| | - David A Wink
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, USA.
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22
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Nunn N, Prabhakar N, Reineck P, Magidson V, Kamiya E, Heinz WF, Torelli MD, Rosenholm J, Zaitsev A, Shenderova O. Brilliant blue, green, yellow, and red fluorescent diamond particles: synthesis, characterization, and multiplex imaging demonstrations. Nanoscale 2019; 11:11584-11595. [PMID: 31169858 PMCID: PMC6642439 DOI: 10.1039/c9nr02593f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Until recently, the number of emission colors available from fluorescent diamond particles was primarily limited to red to near-infrared fluorescence from the nitrogen-vacancy color center in type Ib synthetic diamond and green fluorescence associated with the nitrogen-vacancy-nitrogen center in type Ia natural diamond. Using our recently reported rapid thermal annealing technique, we demonstrate the capability of producing fluorescent diamond particles that exhibit distinctive blue, green, yellow, and red fluorescence from the same synthetic diamond starting material. Utilizing these multiple colored diamonds, we analyze their fluorescence characteristics both in-solution as well as on-substrate and additionally evaluate their viability in simple multiplex imaging and cellular bioimaging experiments. While there are still challenges associated with their immediate use in traditional multiplex imaging, this novel approach opens new opportunities to enhance the capability and flexibility of fluorescent diamond particles at the nanoscale.
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Affiliation(s)
- Nicholas Nunn
- Adámas Nanotechnologies, Inc. 8100 Brownleigh Drive, Suite 120 Raleigh, NC 27617, USA
| | - Neeraj Prabhakar
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Tykistokatu 6A, Turku 20520, Finland
| | - Phillip Reineck
- ARC Centre of Excellence for Nanoscale BioPhotonics & School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Erina Kamiya
- Optical Microscopy and Analysis Laboratory, Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - William F. Heinz
- Optical Microscopy and Analysis Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marco D. Torelli
- Adámas Nanotechnologies, Inc. 8100 Brownleigh Drive, Suite 120 Raleigh, NC 27617, USA
| | - Jessica Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Tykistokatu 6A, Turku 20520, Finland
| | - Alexander Zaitsev
- College of Staten Island (CUNY), 2800 Victory Blvd., Staten Island, NY 10312, USA
| | - Olga Shenderova
- Adámas Nanotechnologies, Inc. 8100 Brownleigh Drive, Suite 120 Raleigh, NC 27617, USA
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23
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Matarlo JS, Krumpe LRH, Heinz WF, Oh D, Shenoy SR, Thomas CL, Goncharova EI, Lockett SJ, O'Keefe BR. The Natural Product Butylcycloheptyl Prodiginine Binds Pre-miR-21, Inhibits Dicer-Mediated Processing of Pre-miR-21, and Blocks Cellular Proliferation. Cell Chem Biol 2019; 26:1133-1142.e4. [PMID: 31155509 DOI: 10.1016/j.chembiol.2019.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/15/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022]
Abstract
Identification of RNA-interacting pharmacophores could provide chemical probes and, potentially, small molecules for RNA-based therapeutics. Using a high-throughput differential scanning fluorimetry assay, we identified small-molecule natural products with the capacity to bind the discrete stem-looped structure of pre-miR-21. The most potent compound identified was a prodiginine-type compound, butylcycloheptyl prodiginine (bPGN), with the ability to inhibit Dicer-mediated processing of pre-miR-21 in vitro and in cells. Time-dependent RT-qPCR, western blot, and transcriptomic analyses showed modulation of miR-21 expression and its target genes such as PDCD4 and PTEN upon treatment with bPGN, supporting on-target inhibition. Consequently, inhibition of cellular proliferation in HCT-116 colorectal cancer cells was also observed when treated with bPGN. The discovery that bPGN can bind and modulate the expression of regulatory RNAs such as miR-21 helps set the stage for further development of this class of natural product as a molecular probe or therapeutic agent against miRNA-dependent diseases.
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Affiliation(s)
- Joe S Matarlo
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Lauren R H Krumpe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Daniel Oh
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Shilpa R Shenoy
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Cheryl L Thomas
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ekaterina I Goncharova
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Biomedical Informatics and Data Science Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Barry R O'Keefe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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24
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Basudhar D, Glynn S, Greer M, Somasundaram V, No JH, Scheiblin DA, Garrido P, Heinz WF, Ryan AE, Weiss JM, Cheng RY, Ridnour LA, Lockett SJ, McVicar DW, Ambs S, Wink DA. Abstract 3789: Role of NOS2-COX2 crosstalk in tumor microenvironment of estrogen receptor-negative breast cancer and its therapeutic implications. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tumor is often described as a wound that never heals. This leads to a chronic inflammatory tumor microenvironment characterized by infiltration of M2 macrophages and Th2 cells causing dysregulated release of multiple cytokines, chemokines and growth factors, thus creating a conducive environment for tumor growth and metastasis. In spite of significant progress in breast cancer treatment, metastatic breast cancer still remains a major health hazard with a high mortality rate among women. Moreover, there is cellular heterogeneity within and among different breast tumors, which poses a significant challenge in developing effective therapeutics, thus making it important to understand subtype-specific mechanisms. Our laboratory and other groups have previously shown that inducible nitric oxide synthase (NOS2), an enzyme involved in production and regulation of endogenous nitric oxide (NO), is a predictor of poor survival among highly metastatic ER-negative (ER-) breast cancer patients. Another proinflammatory enzyme, cyclooxygenase-2 (COX2,) responsible for conversion of arachidonic acid to prostaglandin E2 (PGE2), is also highly expressed in breast cancer and is detectable in ductal carcinoma in situ, invasive breast carcinoma, and metastatic lesions. We investigated the role of inflammation associated enzymes, NOS2 and COX2, and established that their simultaneous elevated expression significantly reduced patient survival (33%) when compared to greater than 95% survival of ER- patients with low NOS2/COX2 tumor expression. We further investigated their tumor subtype specific novel signaling mechanism in vitro and showed TNFα and/or endoplasmic reticulum stress as key players. Proinflammatory cytokines present in tumor microenvironment play a key role in regulation of this pathway and effectiveness of chemotherapeutics. Moreover, the ability of NOS2 and COX2 to regulate different cytokines in the tumor microenvironment further emphasizes the importance of their crosstalk in tumor progression, metastasis and ability of cancer cells to escape immune surveillance. Last, we demonstrated that simultaneous inhibition of COX2 and NOS2 using commercially available inhibitors significantly reduced tumor growth in murine models of ER- breast cancer, thus suggesting the beneficial effects of dual NOS2/COX2 therapy.
Citation Format: Debashree Basudhar, Sharon Glynn, Madison Greer, Veena Somasundaram, Jae H. No, David A. Scheiblin, Pablo Garrido, William F. Heinz, Aideen E. Ryan, Jonathan M. Weiss, Robert Y. Cheng, Lisa A. Ridnour, Stephen J. Lockett, Daniel W. McVicar, Stefan Ambs, David A. Wink. Role of NOS2-COX2 crosstalk in tumor microenvironment of estrogen receptor-negative breast cancer and its therapeutic implications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3789.
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Affiliation(s)
| | - Sharon Glynn
- 2National University of Ireland Galway, Galway, Ireland
| | | | | | - Jae H. No
- 1National Cancer Institute, Frederick, MD
| | | | - Pablo Garrido
- 2National University of Ireland Galway, Galway, Ireland
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25
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Heinz WF, Werbin J, Hoh JH. Restricted Exchange Environment Chambers for Creating and Manipulating Diffusive Gradients in 2D Cell Culture. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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26
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Hoh JH, Heinz WF. Bacterial Chemotactic Tumble Angles Reduce Backtracking and Maximize Information Gathering. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.3275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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27
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Hoh JH, Heinz WF, Werbin JL. Spatial information dynamics during early zebrafish development. Dev Biol 2013; 377:126-37. [PMID: 23438813 DOI: 10.1016/j.ydbio.2013.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 02/01/2013] [Accepted: 02/06/2013] [Indexed: 10/27/2022]
Abstract
During development inherited information directs growth and specifies the complex spatial organization of cells and molecules. Here we show that a new information metric, the k-space information (kSI), captures the growth and emergence of spatial organization in a developing embryo. Using zebrafish as a model, we quantify the rate of development over the first 24h and demonstrate that important developmental landmarks are associated with well-defined transitions in information dynamics. The rate of development during this time is highest immediately before and after gastrulation, as well early in the segmentation period. We also find that the majority of the information arises from spatial correlations on the length scale of 20-80 μm, but there are contributions from many length scales that change over time. A comparison of the information dynamics in the maternal-zygotic one-eyed pinhead mutant, which is defective in mesoderm induction, with the wild-type embryo shows that the information dynamics diverge near the onset of gastrulation. Subsequently the mutant lacks a peak in the information dynamics that appears to be associated with the formation of trunk somites in the wild-type embryo. These findings provide a common and objective basis by which to quantify spatial organization, compare mutants and quantify developmental dynamics. The kSI can also be applied to any form of developmental data of arbitrary dimensions, and it offers a broad conceptual framework with which to organize the large amounts of data emerging from various sources.
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Affiliation(s)
- Jan H Hoh
- Department of Physiology, Johns Hopkins School of Medicine, 725N. Wolfe Street, Baltimore, MD 21205, USA.
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28
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Abstract
Protein micropatterned substrates have emerged as important tools for studying how cells interact with their environment, as well as allowing useful experimental control over, for example, cell shape and cell position on a surface. Here we present a new approach for protein micropatterning in which a focused laser is used to locally inactivate proteins on a protein-coated substrate. By translating the laser relative to the substrate, protein patterns of essentially arbitrary shape can be produced. This approach has a number of useful features. To begin, it is a maskless writing approach. Thus new patterns can be designed and implemented quickly. Laser inactivation can also be performed on a number of different substrate materials, ranging from glass to polydimethylsiloxane. Further, the inactivation is dose dependent, thus complex gradients and other non-uniform distributions of proteins can be produced. Because the focus of the laser can be changed quickly, laser-based patterning can also be applied to substrates with complex topographies or enclosed surfaces--as long as an optical path is available. To demonstrate this capability, protein patterns were made on the inside of small quartz capillary tubes. Patterned substrates produced using laser inactivation constrain cell shape in predictable ways, and we show that these substrates are compatible with a number of different eukaryotic cell lines.
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Affiliation(s)
- William F Heinz
- Department of Physiology, Johns Hopkins School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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29
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Hoh M, Werbin JL, Dumas JK, Heinz WF, Hoh JH. Nanometer-scale embossing of polydimethylsiloxane. Langmuir 2010; 26:2187-2190. [PMID: 20067244 DOI: 10.1021/la9029886] [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] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Microstructured polydimethylsiloxane (PDMS) is an important and widely used material in biology and chemistry. Here we report that micrometer- and nanometer-scale features can be introduced into the surface of PDMS in a process that is functionally equivalent to embossing. We show that surface features <50 nm can be replicated onto the surface of previously cured PDMS at room temperature and at low pressure. This type of embossing can be performed on samples in solution. It also allows one template to be used for many different types of microstructures by changing the embossing time or serial embossing at different alignments. The balance between elastic and plastic properties of the PDMS has the effect of high-pass filtering the features that are captured and produces a sample that is suitable for sensitive surface characterization technologies such as atomic force microscopy. These findings extend the applications of PDMS as well as open the possibility for new uses.
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Affiliation(s)
- Maria Hoh
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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30
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Abstract
One powerful approach to understanding how cells process spatially variant signals is based on using micropatterned substrates to control the distribution of signaling molecules. However, quantifying spatially complex signals requires an appropriate metric. Here we propose that the Shannon information theory formalism provides a robust and useful way to quantify the organization of proteins in micropatterned systems. To demonstrate the use of informational entropy as a metric, we produced patterns of lines of fibronectin with varying information content. Fibroblasts grown on these patterns were sensitive to very small changes in informational entropy (6.6 bits), and the responses depended on the scale of the pattern.
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Affiliation(s)
- Jeffrey L Werbin
- Department of Physiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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31
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Pesen D, Heinz WF, Werbin JL, Hoh JH, Haviland DB. Electron beam patterning of fibronectin nanodots that support focal adhesion formation. Soft Matter 2007; 3:1280-1284. [PMID: 32900093 DOI: 10.1039/b710659a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nanodots of fibronectin which have radii as small as 100 nm and are biofunctional at the cellular level, can be rapidly fabricated in arbitrary spatial patterns using a technique based on electron beam exposure of a protein monolayer with subsequent backfilling of a second protein species.
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Affiliation(s)
- Devrim Pesen
- KTH Royal Institute of Technology, Department of Applied Physics, Roslagstullsbacken 21, SE-10691, Stockholm, Sweden.
| | - William F Heinz
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey L Werbin
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jan H Hoh
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David B Haviland
- KTH Royal Institute of Technology, Department of Applied Physics, Roslagstullsbacken 21, SE-10691, Stockholm, Sweden.
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Rundqvist J, Mendoza B, Werbin JL, Heinz WF, Lemmon C, Romer LH, Haviland DB, Hoh JH. High Fidelity Functional Patterns of an Extracellular Matrix Protein by Electron Beam-Based Inactivation. J Am Chem Soc 2006; 129:59-67. [PMID: 17199283 DOI: 10.1021/ja063698a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [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] [Indexed: 01/22/2023]
Abstract
Controlling the organization of proteins on surfaces provides a powerful biochemical tool for determining how cells interpret the spatial distribution of local signaling molecules. Here, we describe a general high fidelity approach based on electron beam writing to pattern the functional properties of protein-coated surfaces at length scales ranging from tens of nanometers to millimeters. A silicon substrate is first coated with the extracellular matrix protein fibronectin, which is then locally inactivated by exposure to a highly focused electron beam. Biochemical inactivation of the protein is established by the loss of antibody binding to the fibronectin. Functional inactivation is determined by the inability of cells to spread or form focal adhesions on the inactivated substrate, resulting in cell shapes constrained to the pattern, while they do both (and are unconstrained) on the remaining fibronectin. These protein patterns have very high fidelity, and typical patterns agree with the input dimensions of the pattern to within 2%. Further, the feature edges are well defined and approach molecular dimensions in roughness. Inactivation is shown to be dose dependent with observable suppression of the specific binding at 2 microC cm(-2) and complete removal of biochemical activity at approximately 50 microC cm(-2) for 5 keV electrons. The critical dose for inactivation also depends on accelerating voltage, and complete loss of antibody binding was achieved at approximately 4-7 microC cm(-2) for 1 keV electrons, which corresponds to approximately 50-90 electrons per cross-sectional area of a whole fibronectin dimer and ~2-4 electrons per type III fibronectin domain. AFM analysis of the pattern surfaces revealed that electron beam exposure does not remove appreciable amounts of material from the surface, suggesting that the patterning mechanism involves local inactivation rather than the ablation that has been observed in several organic thin film systems.
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Affiliation(s)
- Jonas Rundqvist
- Nanostructure Physics, Royal Institute of Technology, AlbaNova University Center, Roslagsvägen 30B, SE-106 91 Stockholm, Sweden
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Heinz WF, Antonik MD, Hoh JH. Reconstructing Local Interaction Potentials from Perturbations to the Thermally Driven Motion of an Atomic Force Microscope Cantilever. J Phys Chem B 2000. [DOI: 10.1021/jp993394t] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
The spatial distribution of intermolecular forces governs macromolecular interactions. The atomic force microscope, a relatively new tool for investigating interaction forces between nanometer-scale objects, can be used to produce spatially resolved maps of the surface or material properties of a sample; these include charge density, adhesion and stiffness, as well as the force required to break specific ligand-receptor bonds. Maps such as these will provide fundamental insights into biological structure and will become an important tool for characterizing technologically important biological systems.
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Affiliation(s)
- W F Heinz
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Abstract
An experimental approach for producing relative charge density maps of biological surfaces using the atomic force microscope is presented. This approach, called D minus D (D-D) mapping, uses isoforce surfaces collected at different salt concentrations to remove topography and isolate electrostatic contributions to the tip-sample interaction force. This approach is quantitative for surface potentials below 25 mV, and does not require prior knowledge of the cantilever spring constant, tip radius, or tip charge. In addition, D-D mapping does not require tip-sample contact. The performance of D-D mapping is demonstrated on surfaces of constant charge and varying topography (mechanically roughened mica and stacked bilayers of dipalmitolphosphatidylserine), a surface of varying charge and varying topography (patches of dipalmitolphosphatidylcholine on mica), and bacteriorhopsin membranes adsorbed to mica.
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Affiliation(s)
- W F Heinz
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 USA
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A-Hassan E, Heinz WF, Antonik MD, D'Costa NP, Nageswaran S, Schoenenberger CA, Hoh JH. Relative microelastic mapping of living cells by atomic force microscopy. Biophys J 1998; 74:1564-78. [PMID: 9512052 PMCID: PMC1299502 DOI: 10.1016/s0006-3495(98)77868-3] [Citation(s) in RCA: 306] [Impact Index Per Article: 11.8] [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] [Indexed: 02/06/2023] Open
Abstract
The spatial and temporal changes of the mechanical properties of living cells reflect complex underlying physiological processes. Following these changes should provide valuable insight into the biological importance of cellular mechanics and their regulation. The tip of an atomic force microscope (AFM) can be used to indent soft samples, and the force versus indentation measurement provides information about the local viscoelasticity. By collecting force-distance curves on a time scale where viscous contributions are small, the forces measured are dominated by the elastic properties of the sample. We have developed an experimental approach, using atomic force microscopy, called force integration to equal limits (FIEL) mapping, to produce robust, internally quantitative maps of relative elasticity. FIEL mapping has the advantage of essentially being independent of the tip-sample contact point and the cantilever spring constant. FIEL maps of living Madine-Darby canine kidney (MDCK) cells show that elasticity is uncoupled from topography and reveal a number of unexpected features. These results present a mode of high-resolution visualization in which the contrast is based on the mechanical properties of the sample.
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Affiliation(s)
- E A-Hassan
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Ronan RS, Heinz WF, Kempner ES. High-energy electron irradiation of proteins and nucleic acids: collisional stopping power and average energy loss. Radiat Environ Biophys 1996; 35:159-162. [PMID: 8880957 DOI: 10.1007/s004110050025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Inactivation of proteins due to the direct action of ionizing radiation and the electron energy loss spectra of organic materials indicate that an average of 60-66 eV of energy is lost from high energy electrons in each inelastic collision with target molecules. The average energy loss per inelastic collision with high energy electrons in solid, carbon-based materials, proteins and nucleic acids is calculated from mass collisional stopping powers and empirical total inelastic cross-sections. Bragg's Additivity Law is used for the calculation of the mean excitation energy of molecules. For simple organic compounds, the calculated average energy loss is close to that obtained by direct observation of the energy loss suffered by electrons as they pass through thin films of organic material. The density effect correction for the rate of energy loss, important in the more complex case of proteins irradiated with 10 MeV electrons, is determined using the comparable mass collisional stopping power of water and proteins. In this manner, a value is obtained for the average energy per inelastic collision of high energy electrons with proteins, which is similar to the average energy per inactivating event of proteins. Analogous calculations for nucleic acids are also presented.
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Affiliation(s)
- R S Ronan
- Laboratory of Physical Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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