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Balasubramanian VK, Veličković D, Rubio Wilhelmi MDM, Anderton CR, Stewart CN, DiFazio S, Blumwald E, Ahkami AH. Spatiotemporal metabolic responses to water deficit stress in distinct leaf cell-types of poplar. Front Plant Sci 2024; 15:1346853. [PMID: 38495374 PMCID: PMC10940329 DOI: 10.3389/fpls.2024.1346853] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
The impact of water-deficit (WD) stress on plant metabolism has been predominantly studied at the whole tissue level. However, plant tissues are made of several distinct cell types with unique and differentiated functions, which limits whole tissue 'omics'-based studies to determine only an averaged molecular signature arising from multiple cell types. Advancements in spatial omics technologies provide an opportunity to understand the molecular mechanisms underlying plant responses to WD stress at distinct cell-type levels. Here, we studied the spatiotemporal metabolic responses of two poplar (Populus tremula× P. alba) leaf cell types -palisade and vascular cells- to WD stress using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI). We identified unique WD stress-mediated metabolic shifts in each leaf cell type when exposed to early and prolonged WD stresses and recovery from stress. During water-limited conditions, flavonoids and phenolic metabolites were exclusively accumulated in leaf palisade cells. However, vascular cells mainly accumulated sugars and fatty acids during stress and recovery conditions, respectively, highlighting the functional divergence of leaf cell types in response to WD stress. By comparing our MALDI-MSI metabolic data with whole leaf tissue gas chromatography-mass spectrometry (GC-MS)-based metabolic profile, we identified only a few metabolites including monosaccharides, hexose phosphates, and palmitic acid that showed a similar accumulation trend at both cell-type and whole leaf tissue levels. Overall, this work highlights the potential of the MSI approach to complement the whole tissue-based metabolomics techniques and provides a novel spatiotemporal understanding of plant metabolic responses to WD stress. This will help engineer specific metabolic pathways at a cellular level in strategic perennial trees like poplars to help withstand future aberrations in environmental conditions and to increase bioenergy sustainability.
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Affiliation(s)
- Vimal Kumar Balasubramanian
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | | | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, United States
| | - Stephen DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
| | - Amir H. Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
- Adjoint Faculty, School of Biological Science (SBS), Washington State University (WSU), Pullman, WA, United States
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2
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Gorman BL, Torti SV, Torti FM, Anderton CR. Mass spectrometry imaging of metals in tissues and cells: Methods and biological applications. Biochim Biophys Acta Gen Subj 2024; 1868:130329. [PMID: 36791830 PMCID: PMC10423302 DOI: 10.1016/j.bbagen.2023.130329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/24/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Metals are pervasive throughout biological processes, where they play essential structural and catalytic roles. Metals can also exhibit deleterious effects on human health. Powerful analytical techniques, such as mass spectrometry imaging (MSI), are required to map metals due to their low concentrations within biological tissue. SCOPE OF REVIEW This Mini Review focuses on key MSI technology that can image metal distributions in situ, describing considerations for each technique (e.g., resolution, sensitivity, etc.). We highlight recent work using MSI for mapping trace metals in tissues, detecting metal-based drugs, and simultaneously imaging metals and biomolecules. MAJOR CONCLUSIONS MSI has enabled significant advances in locating bioactive metals at high spatial resolution and correlating their distributions with that of biomolecules. The use of metal-based immunochemistry has enabled simultaneous high-throughput protein and biomolecule imaging. GENERAL SIGNIFICANCE The techniques and examples described herein can be applied to many biological questions concerning the important biological roles of metals, metal toxicity, and localization of metal-based drugs.
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Affiliation(s)
- Brittney L Gorman
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States of America
| | - Suzy V Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030, United States of America
| | - Frank M Torti
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, United States of America
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, United States of America.
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3
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Veličković D, Zemaitis KJ, Bhattacharjee A, Anderton CR. Mass spectrometry imaging of natural carbonyl products directly from agar-based microbial interactions using 4-APEBA derivatization. mSystems 2024; 9:e0080323. [PMID: 38064548 PMCID: PMC10804984 DOI: 10.1128/msystems.00803-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/31/2023] [Indexed: 01/24/2024] Open
Abstract
Aliphatic carboxylic acids, aldehydes, and ketones play diverse roles in microbial adaptation to their microenvironment, from excretion as toxins to adaptive metabolites for membrane fluidity. However, the spatial distribution of these molecules throughout biofilms and how microbes in these environments exchange these molecules remain elusive for many of these bioactive species due to inefficient molecular imaging strategies. Herein, we apply on-tissue chemical derivatization (OTCD) using 4-(2-((4-bromophenethyl)dimethylammonio)ethoxy)benzenaminium dibromide (4-APEBA) on a co-culture of a soil bacterium (Bacillus subtilis NCIB 3610) and fungus (Fusarium sp. DS 682) grown on agar as our model system. Using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), we spatially resolved more than 300 different metabolites containing carbonyl groups within this model system. Various spatial patterns are observable in these species, which indicate possible extracellular or intercellular processes of the metabolites and their up- or downregulation during microbial interaction. The unique chemistry of our approach allowed us to bring additional confidence in accurate carbonyl identification, especially when multiple isomeric candidates were possible, and this provided the ability to generate hypotheses about the potential role of some aliphatic carbonyls in this B. subtilis/Fusarium sp. interaction. The results shown here demonstrate the utility of 4-ABEBA-based OTCD MALDI-MSI in probing interkingdom interactions directly from microbial co-cultures, and these methods will enable future microbial interaction studies with expanded metabolic coverage.IMPORTANCEThe metabolic profiles within microbial biofilms and interkingdom interactions are extremely complex and serve a variety of functions, which include promoting colonization, growth, and survival within competitive and symbiotic environments. However, measuring and differentiating many of these molecules, especially in an in situ fashion, remains a significant analytical challenge. We demonstrate a chemical derivatization strategy that enabled highly sensitive, multiplexed mass spectrometry imaging of over 300 metabolites from a model microbial co-culture. Notably, this approach afforded us to visualize over two dozen classes of ketone-, aldehyde-, and carboxyl-containing molecules, which were previously undetectable from colonies grown on agar. We also demonstrate that this chemical derivatization strategy can enable the discrimination of isobaric and isomeric metabolites without the need for orthogonal separation (e.g., online chromatography or ion mobility). We anticipate that this approach will further enhance our knowledge of metabolic regulation within microbiomes and microbial systems used in bioengineering applications.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kevin J. Zemaitis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Arunima Bhattacharjee
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
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4
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Gorman BL, Taylor MJ, Tesfay L, Lukowski JK, Hegde P, Eder JG, Bloodsworth KJ, Kyle JE, Torti S, Anderton CR. Applying Multimodal Mass Spectrometry to Image Tumors Undergoing Ferroptosis Following In Vivo Treatment with a Ferroptosis Inducer. J Am Soc Mass Spectrom 2024; 35:5-12. [PMID: 38079508 DOI: 10.1021/jasms.3c00193] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Epithelial ovarian cancer (EOC) is the most common form of ovarian cancer. The poor prognosis generally associated with this disease has led to the search for improved therapies such as ferroptosis-inducing agents. Ferroptosis is a form of regulated cell death that is dependent on iron and is characterized by lipid peroxidation. Precise mapping of lipids and iron within tumors exposed to ferroptosis-inducing agents may provide insight into processes of ferroptosis in vivo and ultimately assist in the optimal deployment of ferroptosis inducers in cancer therapy. In this work, we present a method for combining matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) with secondary ion mass spectrometry (SIMS) to analyze changes in spatial lipidomics and metal composition, respectively, in ovarian tumors following exposure to a ferroptosis inducer. Tumors were obtained by injecting human ovarian cancer tumor-initiating cells into mice, followed by treatment with the ferroptosis inducer erastin. SIMS imaging detected iron accumulation in the tumor tissue, and sequential MALDI-MS imaging of the same tissue section displayed two chemically distinct regions of lipids. One region was associated with the iron-rich area detected with SIMS, and the other region encompassed the remainder of the tissue section. Bulk lipidomics confirmed the lipid assignments putatively assigned from the MALDI-MS data. Overall, we demonstrate the ability of multimodal MSI to identify the spatial locations of iron and lipids in the same tissue section and associate these regions with clinical pathology.
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Affiliation(s)
- Brittney L Gorman
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Michael J Taylor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Lia Tesfay
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut 06030, United States
| | - Jessica K Lukowski
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- School of Medicine, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Poornima Hegde
- Department of Pathology and Laboratory Medicine, University of Connecticut Health, Farmington, 06030, Connecticut United States
| | - Josie G Eder
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kent J Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jennifer E Kyle
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Suzy Torti
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, Connecticut 06030, United States
| | - Christopher R Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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5
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Kim H, Gorman BL, Taylor MJ, Anderton CR. Atomistic simulations for investigation of substrate and salt effects on lipid in-source fragmentation in secondary ion mass spectrometry: A follow-up study. Biointerphases 2024; 19:011003. [PMID: 38341772 DOI: 10.1116/6.0003281] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/16/2024] [Indexed: 02/13/2024] Open
Abstract
In-source fragmentation (ISF) poses a significant challenge in secondary ion mass spectrometry (SIMS). These fragment ions increase the spectral complexity and can lead to incorrect annotation of fragments as intact species. The presence of salt that is ubiquitous in biological samples can influence the fragmentation and ionization of analytes in a significant manner, but their influences on SIMS have not been well characterized. To elucidate the effect of substrates and salt on ISF in SIMS, we have employed experimental SIMS in combination with atomistic simulations of a sphingolipid on a gold surface with various NaCl concentrations as a model system. Our results revealed that a combination of bond dissociation energy and binding energy between N-palmitoyl-sphingomyelin and a gold surface is a good predictor of fragment ion intensities in the absence of salt. However, ion-fragment interactions play a significant role in determining fragment yields in the presence of salt. Additionally, the charge distribution on fragment species may be a major contributor to the varying effects of salt on fragmentation. This study demonstrates that atomistic modeling can help predict ionization potential when salts are present, providing insights for more accurate interpretations of complex biological spectra.
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Affiliation(s)
- Hoshin Kim
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Brittney L Gorman
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Michael J Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
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6
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King WL, Yates CF, Cao L, O'Rourke-Ibach S, Fleishman SM, Richards SC, Centinari M, Hafner BD, Goebel M, Bauerle T, Kim YM, Nicora CD, Anderton CR, Eissenstat DM, Bell TH. Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites. Plant Cell Environ 2023; 46:3919-3932. [PMID: 37675977 DOI: 10.1111/pce.14705] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/12/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.
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Affiliation(s)
- William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Caylon F Yates
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Lily Cao
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sean O'Rourke-Ibach
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Suzanne M Fleishman
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michela Centinari
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Benjamin D Hafner
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Marc Goebel
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Taryn Bauerle
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - David M Eissenstat
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in International Agriculture and Development, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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7
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Bhattacharjee A, Velickovic D, Richardson JA, Couvillion SP, Vandergrift GW, Qafoku O, Taylor MJ, Jansson JK, Hofmockel K, Anderton CR. Fungal organic acid uptake of mineral-derived K is dependent on distance from carbon hotspot. mBio 2023; 14:e0095623. [PMID: 37655873 PMCID: PMC10653886 DOI: 10.1128/mbio.00956-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/20/2023] [Indexed: 09/02/2023] Open
Abstract
IMPORTANCE Fungal species are foundational members of soil ecosystems with vital contributions that support interspecies resource translocation. The minute details of these biogeochemical processes are poorly investigated. Here, we addressed this knowledge gap by probing fungal growth in a novel mineral-doped soil micromodel platform using spatially-resolved imaging methodologies. We found that fungi uptake K from K-rich minerals using organic acids exuded in a distance-dependent manner from a carbon-rich hotspot. While identification of specific mechanisms within soil remains challenging, our findings demonstrate the significance of reduced complexity platforms such as the mineral-doped micromodel in probing biogeochemical processes. These findings provide visualization into hyphal uptake and transport of mineral-derived nutrients in a resource-limited environment.
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Affiliation(s)
- Arunima Bhattacharjee
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Dusan Velickovic
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jocelyn A. Richardson
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Sneha P. Couvillion
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Gregory W. Vandergrift
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Odeta Qafoku
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Michael J. Taylor
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Janet K. Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kirsten Hofmockel
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
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Sharma K, Zhang G, Hansen J, Bjornstad P, Lee HJ, Menon R, Hejazi L, Liu JJ, Franzone A, Looker HC, Choi BY, Fernandez R, Venkatachalam MA, Kugathasan L, Sridhar VS, Natarajan L, Zhang J, Sharma VS, Kwan B, Waikar SS, Himmelfarb J, Tuttle KR, Kestenbaum B, Fuhrer T, Feldman HI, de Boer IH, Tucci FC, Sedor J, Heerspink HL, Schaub J, Otto EA, Hodgin JB, Kretzler M, Anderton CR, Alexandrov T, Cherney D, Lim SC, Nelson RG, Gelfond J, Iyengar R. Endogenous adenine mediates kidney injury in diabetic models and predicts diabetic kidney disease in patients. J Clin Invest 2023; 133:e170341. [PMID: 37616058 PMCID: PMC10575723 DOI: 10.1172/jci170341] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
Diabetic kidney disease (DKD) can lead to end-stage kidney disease (ESKD) and mortality; however, few mechanistic biomarkers are available for high-risk patients, especially those without macroalbuminuria. Urine from participants with diabetes from the Chronic Renal Insufficiency Cohort (CRIC) study, the Singapore Study of Macro-angiopathy and Micro-vascular Reactivity in Type 2 Diabetes (SMART2D), and the American Indian Study determined whether urine adenine/creatinine ratio (UAdCR) could be a mechanistic biomarker for ESKD. ESKD and mortality were associated with the highest UAdCR tertile in the CRIC study and SMART2D. ESKD was associated with the highest UAdCR tertile in patients without macroalbuminuria in the CRIC study, SMART2D, and the American Indian study. Empagliflozin lowered UAdCR in nonmacroalbuminuric participants. Spatial metabolomics localized adenine to kidney pathology, and single-cell transcriptomics identified ribonucleoprotein biogenesis as a top pathway in proximal tubules of patients without macroalbuminuria, implicating mTOR. Adenine stimulated matrix in tubular cells via mTOR and stimulated mTOR in mouse kidneys. A specific inhibitor of adenine production was found to reduce kidney hypertrophy and kidney injury in diabetic mice. We propose that endogenous adenine may be a causative factor in DKD.
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Affiliation(s)
- Kumar Sharma
- Center for Precision Medicine and
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Guanshi Zhang
- Center for Precision Medicine and
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Jens Hansen
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Petter Bjornstad
- Division of Nephrology, Department of Medicine and Section of Endocrinology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hak Joo Lee
- Center for Precision Medicine and
- Division of Nephrology, Department of Medicine, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Rajasree Menon
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Leila Hejazi
- Center for Precision Medicine and
- SygnaMap Inc., San Antonio, Texas, USA
| | - Jian-Jun Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
| | | | - Helen C. Looker
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Byeong Yeob Choi
- Center for Precision Medicine and
- Department of Population Health Sciences and
| | | | - Manjeri A. Venkatachalam
- Center for Precision Medicine and
- Department of Pathology, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Luxcia Kugathasan
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada. Department of Physiology and Cardiovascular Sciences Collaborative Specialization, University of Toronto, Toronto, Canada
| | - Vikas S. Sridhar
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada. Department of Physiology and Cardiovascular Sciences Collaborative Specialization, University of Toronto, Toronto, Canada
| | - Loki Natarajan
- Herbert Wertheim School of Public Health and
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Jing Zhang
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Varun S. Sharma
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Brian Kwan
- Department of Health Science, California State University, Long Beach, Long Beach, California, USA
| | - Sushrut S. Waikar
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University, Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Jonathan Himmelfarb
- Department of Medicine, Division of Nephrology, Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Katherine R. Tuttle
- Department of Medicine, Division of Nephrology, Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Bryan Kestenbaum
- Department of Medicine, Division of Nephrology, Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Harold I. Feldman
- Center for Clinical Epidemiology and Biostatistics and Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
- Patient-Centered Outcomes Research Institute, Washington, DC, USA
| | - Ian H. de Boer
- Department of Medicine, Division of Nephrology, Kidney Research Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Hiddo Lambers Heerspink
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, Groningen, Netherlands
- The George Institute for Global Health, Sydney, Australia
| | - Jennifer Schaub
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Edgar A. Otto
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jeffrey B. Hodgin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Christopher R. Anderton
- Center for Precision Medicine and
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - David Cherney
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, Ontario, Canada. Department of Physiology and Cardiovascular Sciences Collaborative Specialization, University of Toronto, Toronto, Canada
| | - Su Chi Lim
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
- Diabetes Center, Admiralty Medical Center, Khoo Teck Puat Hospital, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Robert G. Nelson
- Chronic Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, Arizona, USA
| | - Jonathan Gelfond
- Center for Precision Medicine and
- Department of Population Health Sciences and
| | - Ravi Iyengar
- Department of Pharmacological Sciences and Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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9
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Yannarell SM, Beaudoin ES, Talley HS, Schoenborn AA, Orr G, Anderton CR, Chrisler WB, Shank EA. Extensive cellular multi-tasking within Bacillus subtilis biofilms. mSystems 2023; 8:e0089122. [PMID: 37527273 PMCID: PMC10469600 DOI: 10.1128/msystems.00891-22] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/08/2023] [Indexed: 08/03/2023] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells "multi-task," simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cellular phenotypes in B. subtilis biofilms. IMPORTANCE Many microbes differentiate, expressing diverse phenotypes to ensure their survival in various environments. However, studies on phenotypic differentiation have typically examined only a few phenotypes at one time, thus limiting our knowledge about the extent of differentiation and phenotypic overlap in the population. We investigated the spatial organization and gene expression relationships for genes important in B. subtilis biofilms. In doing so, we mapped spatial gene expression patterns and expanded the number of cell populations described in the B. subtilis literature. It is likely that other bacteria also display complex differentiation patterns within their biofilms. Studying the extent of cellular differentiation in other microbes may be important when designing therapies for disease-causing bacteria, where studying only a single phenotype may be masking underlying phenotypic differentiation relevant to infection outcomes.
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Affiliation(s)
- Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Eric S. Beaudoin
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Hunter S. Talley
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - William B. Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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10
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Zemaitis KJ, Lin VS, Ahkami AH, Winkler TE, Anderton CR, Veličković D. Expanded Coverage of Phytocompounds by Mass Spectrometry Imaging Using On-Tissue Chemical Derivatization by 4-APEBA. Anal Chem 2023; 95:12701-12709. [PMID: 37594382 DOI: 10.1021/acs.analchem.3c01345] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Probing the entirety of any species metabolome is an analytical grand challenge, especially on a cellular scale. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a common spatial metabolomics assay, but this technique has limited molecular coverage for several reasons. To expand the application space of spatial metabolomics, we developed an on-tissue chemical derivatization (OTCD) workflow using 4-APEBA for the confident identification of several dozen elusive phytocompounds. Overall, this new OTCD method enabled the annotation of roughly 280 metabolites, with only a 10% overlap in metabolic coverage when compared to analog negative ion mode MALDI-MSI on serial sections. We demonstrate that 4-APEBA outperforms other derivatization agents by providing: (1) broad specificity toward carbonyls, (2) low background, and (3) introduction of bromine isotopes. Notably, the latter two attributes also facilitate more confidence in our bioinformatics for data processing. The workflow detailed here trailblazes a path toward spatial hormonomics within plant samples, enhancing the detection of carboxylates, aldehydes, and plausibly other carbonyls. As such, several phytohormones, which have various roles within stress responses and cellular communication, can now be spatially profiled, as demonstrated in poplar root and soybean root nodule.
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Affiliation(s)
- Kevin J Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vivian S Lin
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Amir H Ahkami
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tanya E Winkler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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11
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Vandergrift GW, Zemaitis KJ, Veličković D, Lukowski JK, Paša-Tolić L, Anderton CR, Kew W. Experimental Assessment of Mammalian Lipidome Complexity Using Multimodal 21 T FTICR Mass Spectrometry Imaging. Anal Chem 2023. [PMID: 37427698 DOI: 10.1021/acs.analchem.3c00518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Herein, we assess the complementarity and complexity of data that can be detected within mammalian lipidome mass spectrometry imaging (MSI) via matrix-assisted laser desorption ionization (MALDI) and nanospray desorption electrospray ionization (nano-DESI). We do so by employing 21 T Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) with absorption mode FT processing in both cases, allowing unmatched mass resolving power per unit time (≥613k at m/z 760, 1.536 s transients). While our results demonstrated that molecular coverage and dynamic range capabilities were greater in MALDI analysis, nano-DESI provided superior mass error, and all annotations for both modes had sub-ppm error. Taken together, these experiments highlight the coverage of 1676 lipids and serve as a functional guide for expected lipidome complexity within nano-DESI-MSI and MALDI-MSI. To further assess the lipidome complexity, mass splits (i.e., the difference in mass between neighboring peaks) within single pixels were collated across all pixels from each respective MSI experiment. The spatial localization of these mass splits was powerful in informing whether the observed mass splits were biological or artificial (e.g., matrix related). Mass splits down to 2.4 mDa were observed (i.e., sodium adduct ambiguity) in each experiment, and both modalities highlighted comparable degrees of lipidome complexity. Further, we highlight the persistence of certain mass splits (e.g., 8.9 mDa; double bond ambiguity) independent of ionization biases. We also evaluate the need for ultrahigh mass resolving power for mass splits ≤4.6 mDa (potassium adduct ambiguity) at m/z > 1000, which may only be resolved by advanced FTICR-MS instrumentation.
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Affiliation(s)
- Gregory W Vandergrift
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kevin J Zemaitis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jessica K Lukowski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - William Kew
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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12
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Knizner KT, Kibbe RR, Garrard KP, Nuñez JR, Anderton CR, Muddiman DC. On the importance of color in mass spectrometry imaging. J Mass Spectrom 2022; 57:e4898. [PMID: 36463891 PMCID: PMC9944061 DOI: 10.1002/jms.4898] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 05/12/2023]
Abstract
Mass spectrometry imaging (MSI) data visualization relies on heatmaps to show the spatial distribution and measured abundances of molecules within a sample. Nonuniform color gradients such as jet are still commonly used to visualize MSI data, increasing the probability of data misinterpretation and false conclusions. Also, the use of nonuniform color gradients and the combination of hues used in common colormaps make it challenging for people with color vision deficiencies (CVDs) to visualize and accurately interpret data. Here we present best practices for choosing a colormap to accurately display MSI data, improve readability, and accommodate all CVDs. We also provide other resources on the misuse of color in the scientific field and resources on scientifically derived colormaps presented herein.
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Affiliation(s)
- Kevan T. Knizner
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Russell R. Kibbe
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Kenneth P. Garrard
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNorth CarolinaUSA
- Precision Engineering ConsortiumNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Jamie R. Nuñez
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Christopher R. Anderton
- Earth and Biological Sciences DirectoratePacific Northwest National LaboratoryRichlandWashingtonUSA
| | - David C. Muddiman
- FTMS Laboratory for Human Health Research, Department of ChemistryNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Molecular Education, Technology and Research Innovation Center (METRIC)North Carolina State UniversityRaleighNorth CarolinaUSA
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13
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Lukowski JK, Olson H, Velickovic M, Wang J, Kyle JE, Kim YM, Williams SM, Zhu Y, Huyck HL, McGraw MD, Poole C, Rogers L, Misra R, Alexandrov T, Ansong C, Pryhuber GS, Clair G, Adkins JN, Carson JP, Anderton CR. An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue. Front Mol Biosci 2022; 9:1022775. [PMID: 36465564 PMCID: PMC9709465 DOI: 10.3389/fmolb.2022.1022775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/02/2022] [Indexed: 04/23/2024] Open
Abstract
Human disease states are biomolecularly multifaceted and can span across phenotypic states, therefore it is important to understand diseases on all levels, across cell types, and within and across microanatomical tissue compartments. To obtain an accurate and representative view of the molecular landscape within human lungs, this fragile tissue must be inflated and embedded to maintain spatial fidelity of the location of molecules and minimize molecular degradation for molecular imaging experiments. Here, we evaluated agarose inflation and carboxymethyl cellulose embedding media and determined effective tissue preparation protocols for performing bulk and spatial mass spectrometry-based omics measurements. Mass spectrometry imaging methods were optimized to boost the number of annotatable molecules in agarose inflated lung samples. This optimized protocol permitted the observation of unique lipid distributions within several airway regions in the lung tissue block. Laser capture microdissection of these airway regions followed by high-resolution proteomic analysis allowed us to begin linking the lipidome with the proteome in a spatially resolved manner, where we observed proteins with high abundance specifically localized to the airway regions. We also compared our mass spectrometry results to lung tissue samples preserved using two other inflation/embedding media, but we identified several pitfalls with the sample preparation steps using this preservation method. Overall, we demonstrated the versatility of the inflation method, and we can start to reveal how the metabolome, lipidome, and proteome are connected spatially in human lungs and across disease states through a variety of different experiments.
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Affiliation(s)
| | - Heather Olson
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Marija Velickovic
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Juan Wang
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Jennifer E. Kyle
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Young-Mo Kim
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Sarah M. Williams
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Ying Zhu
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Heidi L. Huyck
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Matthew D. McGraw
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Cory Poole
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Lisa Rogers
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Ravi Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Charles Ansong
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, United States
| | - Geremy Clair
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - Joshua N. Adkins
- Pacific Northwest National Laboratory (PNNL), Richland, WA, United States
| | - James P. Carson
- Texas Advanced Computing Center (TACC), University of Texas at Austin, Austin, TX, United States
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14
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Veličković D, Sharma K, Alexandrov T, Hodgin JB, Anderton CR. Controlled Humidity Levels for Fine Spatial Detail Information in Enzyme-Assisted N-Glycan MALDI MSI. J Am Soc Mass Spectrom 2022; 33:1577-1580. [PMID: 35802124 DOI: 10.1021/jasms.2c00120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Investigation of the spatial distribution of N-glycans in tissue specimens has emerged as a powerful tool in clinical research, in part, because altered N-glycans are often a hallmark of disease progression. Mass spectrometry imaging of N-glycans relies on peptide N-glycanase spraying and tissue incubation for efficient in situ release of N-glycans from their carrier proteins. Unstandardized and uncontrolled incubation steps often cause significant delocalization of released N-glycans, resulting in the inability to link given N-glycan composition to a specific microanatomical region in the tissue. Herein, we optimized the incubation step to provide accurate and sensitive MALDI-MSI of N-glycans. Specifically, we tested saturated solutions of various salts that maintain constant relative humidity in the incubation chamber. We showed that the best performance was achieved using a saturated solution of KNO3 that maintains an 89% RH. Under these conditions, near maximal sensitivity was achieved with the minutest ion delocalization, which we demonstrated at a 35 μm spatial resolution, where we observed six distinct spatial patterns that colocalize to distinct microanatomical compartments in a kidney nephrectomy tissue section.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78229, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jeffrey B Hodgin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109 United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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15
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Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU. A reference tissue atlas for the human kidney. Sci Adv 2022; 8:eabn4965. [PMID: 35675394 PMCID: PMC9176741 DOI: 10.1126/sciadv.abn4965] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/20/2022] [Indexed: 05/08/2023]
Abstract
Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways, and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 adult subjects. We use single-cell/nucleus transcriptomics, subsegmental laser microdissection transcriptomics and proteomics, near-single-cell proteomics, 3D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways, and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites, and pathways. They further show that messenger RNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for the classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.
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Affiliation(s)
- Jens Hansen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rachel Sealfon
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | - Rajasree Menon
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | - Blue B. Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Becky Steck
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kavya Anjani
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Samir Parikh
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Tara K. Sigdel
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Guanshi Zhang
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | | | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Dejan Dobi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Priyanka Rashmi
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Edgar A. Otto
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Miguel Rivera
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Michael P. Rose
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Christopher R. Anderton
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - John P. Shapiro
- Ohio State University College of Medicine, Columbus, OH, USA
| | - Annapurna Pamreddy
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Seth Winfree
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yuguang Xiong
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yongqun He
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Ian H. de Boer
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | | | | | - Abhijit S. Naik
- University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Kumar Sharma
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
| | - Minnie M. Sarwal
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jonathan Himmelfarb
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
| | - Brad Rovin
- Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Zoltan Laszik
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | | | - M. Todd Valerius
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Sanjay Jain
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
| | - Lisa M. Satlin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olga G. Troyanskaya
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
| | | | - Ravi Iyengar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kidney Precision Medicine Project
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Princeton University, Princeton, NJ, USA
- Flatiron Institute, New York, NY, USA
- University of Michigan School of Medicine, Ann Arbor, MI, USA
- Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- University of California San Francisco School of Medicine, San Francisco, CA, USA
- Ohio State University College of Medicine, Columbus, OH, USA
- University of Texas–Health San Antonio School of Medicine, San Antonio, TX, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
- European Molecular Biology Laboratory, Heidelberg, Germany
- Schools of Medicine and Public Health, University of Washington, Seattle, WA, USA
- Duke University School of Medicine, Durham, NC, USA
- Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA, USA
- Washington University in Saint Louis School of Medicine, St. Louis, MS, USA
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16
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Vandergrift GW, Kew W, Lukowski JK, Bhattacharjee A, Liyu AV, Shank EA, Paša-Tolić L, Prabhakaran V, Anderton CR. Imaging and Direct Sampling Capabilities of Nanospray Desorption Electrospray Ionization with Absorption-Mode 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2022; 94:3629-3636. [PMID: 35167251 DOI: 10.1021/acs.analchem.1c05216] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nanospray desorption electrospray ionization mass spectrometry, a powerful ambient sampling and imaging technique, is herein coupled as an isolated source with 21 Tesla (21T) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). Absorption-mode data, enabled by an external data acquisition system, is applied for improved mass resolution, accuracy, and dynamic range without compromising spectral acquisition rates. Isotopic fine structure (IFS) information is obtained from the ambient sampling of living Bacillus and Fusarium species, allowing for high confidence in molecular annotations with a resolution >830 k (at m/z 825). Tandem mass spectrometry experiments for biological samples are shown to retain the IFS in addition to gained fragmentation information, providing a further degree of annotation confidence from ambient analyses. Rat brain was imaged by nanospray desorption electrospray ionization (nano-DESI) 21T FTICR MS in ∼5 h using 768 ms transients, producing over 800 molecular annotations using the METASPACE platform and low-parts-per-billion mass accuracy at a spatial resolution of ∼25 × 180 μm. Finally, nano-DESI 21T FTICR MS imaging is demonstrated to reveal images corresponding to the IFS, as well as hundreds of additional molecular features (including demonstrated differences as low as 8.96 mDa) that are otherwise undetected by a more conventional imaging methodology.
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Affiliation(s)
- Gregory W Vandergrift
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - William Kew
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jessica K Lukowski
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Arunima Bhattacharjee
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Elizabeth A Shank
- University of Massachusetts Chan Medical School, Worcester, Massachusetts 01655, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Venkateshkumar Prabhakaran
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,The Gene & Linda Voil and School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99164, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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17
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Chandler CE, Anderton CR, Scott AJ, Charkoftaki G, Angel PM, Drake RR. Review of the Third Conference of the Imaging Mass Spectrometry Society (IMSS 3): Accounts of a Hybrid Virtual and In-Person Meeting and the State and Future of the Field. J Am Soc Mass Spectrom 2022; 33:238-241. [PMID: 35005981 DOI: 10.1021/jasms.1c00348] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The third annual conference of the Imaging Mass Spectrometry Society (IMSS3) was held October 3-6, 2021 in a hybrid format that included virtual and in-person attendance (Colorado Springs, CO). Here, we highlight many of the methods and applications presented, the state of the field, and some insights into the emerging areas in the field of imaging mass spectrometry. We also reflect upon the processes behind planning a hybrid conference and discuss the successes and challenges of the event in retrospect.
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Affiliation(s)
- Courtney E Chandler
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland─Baltimore, Baltimore, Maryland 21201, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Alison J Scott
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland─Baltimore, Baltimore, Maryland 21201, United States
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Maastricht University, Maastricht 6229 ER, Netherlands
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut 06520, United States
| | - Peggi M Angel
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence for Clinical Glycomics, Charleston, South Carolina 29425, United States
| | - Richard R Drake
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics, Bruker-MUSC Center of Excellence for Clinical Glycomics, Charleston, South Carolina 29425, United States
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18
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Honeker LK, Hildebrand GA, Fudyma JD, Daber LE, Hoyt D, Flowers SE, Gil-Loaiza J, Kübert A, Bamberger I, Anderton CR, Cliff J, Leichty S, AminiTabrizi R, Kreuzwieser J, Shi L, Bai X, Velickovic D, Dippold MA, Ladd SN, Werner C, Meredith LK, Tfaily MM. Elucidating Drought-Tolerance Mechanisms in Plant Roots through 1H NMR Metabolomics in Parallel with MALDI-MS, and NanoSIMS Imaging Techniques. Environ Sci Technol 2022; 56:2021-2032. [PMID: 35048708 DOI: 10.1021/acs.est.1c06772] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As direct mediators between plants and soil, roots play an important role in metabolic responses to environmental stresses such as drought, yet these responses are vastly uncharacterized on a plant-specific level, especially for co-occurring species. Here, we aim to examine the effects of drought on root metabolic profiles and carbon allocation pathways of three tropical rainforest species by combining cutting-edge metabolomic and imaging technologies in an in situ position-specific 13C-pyruvate root-labeling experiment. Further, washed (rhizosphere-depleted) and unwashed roots were examined to test the impact of microbial presence on root metabolic pathways. Drought had a species-specific impact on the metabolic profiles and spatial distribution in Piper sp. and Hibiscus rosa sinensis roots, signifying different defense mechanisms; Piper sp. enhanced root structural defense via recalcitrant compounds including lignin, while H. rosa sinensis enhanced biochemical defense via secretion of antioxidants and fatty acids. In contrast, Clitoria fairchildiana, a legume tree, was not influenced as much by drought but rather by rhizosphere presence where carbohydrate storage was enhanced, indicating a close association with symbiotic microbes. This study demonstrates how multiple techniques can be combined to identify how plants cope with drought through different drought-tolerance strategies and the consequences of such changes on below-ground organic matter composition.
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Affiliation(s)
- Linnea K Honeker
- BIO5 Institute, The University of Arizona, 1657 East Helen Street., Tucson, Arizona 85719, United States
- Biosphere 2, University of Arizona, 32540 South Biosphere Road, Oracle, Arizona 85739, United States
| | - Gina A Hildebrand
- Department of Environmental Science, University of Arizona, 1177 East Fourth Street, Tucson, Arizona 85721, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 East Fourth Street, Tucson, Arizona 85721, United States
| | - L Erik Daber
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - David Hoyt
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Sarah E Flowers
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, 1064 East Lowell Sreet, Tucson, Arizona 85721, United States
| | - Angelika Kübert
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Ines Bamberger
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Christopher R Anderton
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - John Cliff
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Sarah Leichty
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Roya AminiTabrizi
- Department of Environmental Science, University of Arizona, 1177 East Fourth Street, Tucson, Arizona 85721, United States
| | - Jürgen Kreuzwieser
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Lingling Shi
- Biogeochemistry of Agroecosystems, Department of Crop Science, Georg August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Xuejuan Bai
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, 712100 Shaanxi, China
| | - Dusan Velickovic
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Michaela A Dippold
- Biogeochemistry of Agroecosystems, Department of Crop Science, Georg August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - S Nemiah Ladd
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Christiane Werner
- Chair of Ecosystem Physiology, Georges-Köhler-Allee 53/54, University of Freiburg, 79110 Freiburg, Germany
| | - Laura K Meredith
- BIO5 Institute, The University of Arizona, 1657 East Helen Street., Tucson, Arizona 85719, United States
- Biosphere 2, University of Arizona, 32540 South Biosphere Road, Oracle, Arizona 85739, United States
- School of Natural Resources and the Environment, University of Arizona, 1064 East Lowell Sreet, Tucson, Arizona 85721, United States
| | - Malak M Tfaily
- BIO5 Institute, The University of Arizona, 1657 East Helen Street., Tucson, Arizona 85719, United States
- Department of Environmental Science, University of Arizona, 1177 East Fourth Street, Tucson, Arizona 85721, United States
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354, United States
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19
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Samarah LZ, Vertes A, Anderton CR. Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures. Methods Mol Biol 2022; 2437:61-75. [PMID: 34902140 DOI: 10.1007/978-1-0716-2030-4_4] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Metabolomic measurements can provide functional readouts of cellular states and phenotypes. Here, we present a protocol for single-cell metabolomics that permits direct untargeted detection of a broad number of metabolites under ambient conditions, without the need for sample processing, and with high confidence in the discovery and identification of the molecular formulas for detected metabolites. This protocol describes combining fiber-based laser ablation electrospray ionization (f-LAESI) with a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T-FTICR-MS) to obtain high confidence molecular formula information about detected metabolites. The f-LAESI source utilizes mid-infrared laser ablation through a sharp optical fiber tip, affording direct ambient analysis of cells without the need for sample processing. Using the 21T-FTICR-MS as a mass analyzer enabled measurement of the isotopic fine structure (IFS) for numerous metabolites simultaneously from single cells, and the IFSs were in turn computationally processed to rapidly determine the corresponding elemental compositions. This metabolomics technique complements other single cell omics measurement methods, helping to resolve complex molecular interactions that take place within cells unattainable from single cell transcriptomic and proteomics methods.
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Affiliation(s)
- Laith Z Samarah
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Akos Vertes
- Department of Chemistry, George Washington University, Washington, DC, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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20
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Veličković D, Bečejac T, Mamedov S, Sharma K, Ambalavanan N, Alexandrov T, Anderton CR. Rapid Automated Annotation and Analysis of N-Glycan Mass Spectrometry Imaging Data Sets Using NGlycDB in METASPACE. Anal Chem 2021; 93:13421-13425. [PMID: 34581565 DOI: 10.1021/acs.analchem.1c02347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Imaging N-glycan spatial distribution in tissues using mass spectrometry imaging (MSI) is emerging as a promising tool in biological and clinical applications. However, there is currently no high-throughput tool for visualization and molecular annotation of N-glycans in MSI data, which significantly slows down data processing and hampers the applicability of this approach. Here, we present how METASPACE, an open-source cloud engine for molecular annotation of MSI data, can be used to automatically annotate, visualize, analyze, and interpret high-resolution mass spectrometry-based spatial N-glycomics data. METASPACE is an emerging tool in spatial metabolomics, but the lack of compatible glycan databases has limited its application for comprehensive N-glycan annotations from MSI data sets. We created NGlycDB, a public database of N-glycans, by adapting available glycan databases. We demonstrate the applicability of NGlycDB in METASPACE by analyzing MALDI-MSI data from formalin-fixed paraffin-embedded (FFPE) human kidney and mouse lung tissue sections. We added NGlycDB to METASPACE for public use, thus, facilitating applications of MSI in glycobiology.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tamara Bečejac
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sergii Mamedov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78229, United States
| | - Namasivayam Ambalavanan
- Department of Pediatrics, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78229, United States
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21
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Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SSC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY. Vision, challenges and opportunities for a Plant Cell Atlas. eLife 2021; 10:e66877. [PMID: 34491200 PMCID: PMC8423441 DOI: 10.7554/elife.66877] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 01/25/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.
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Affiliation(s)
- Suryatapa Ghosh Jha
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Alexander T Borowsky
- Department of Botany and Plant Sciences, University of California, RiversideRiversideUnited States
| | - Benjamin J Cole
- Joint Genome Institute, Lawrence Berkeley National LaboratoryWalnut CreekUnited States
| | - Noah Fahlgren
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Andrew Farmer
- National Center for Genome ResourcesSanta FeUnited States
| | | | - Purva Karia
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincolnUnited States
| | - Nicholas J Provart
- Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Selena L Rice
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Maite Saura-Sanchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos AiresBuenos AiresArgentina
| | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Amir H Ahkami
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Steven P Briggs
- Department of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | | | | | - Luigi F Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico IINapoliItaly
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Plant Biology, Carnegie Institution for ScienceTübingenGermany
| | | | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universitaet zu BerlinBerlinGermany
| | - Dae Kwan Ko
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Sagar Kumar
- Department of Plant Breeding & Genetics, Mata Gujri College, Fatehgarh Sahib, Punjabi UniversityPatialaIndia
| | - Andrey V Malkovskiy
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-LincolnMadisonUnited States
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-MadisonMadisonUnited States
| | - Gergo Palfalvi
- Division of Evolutionary Biology, National Institute for Basic BiologyOkazakiJapan
| | - Elsa H Quezada-Rodríguez
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de MéxicoLeónMexico
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhianaIndia
| | - R Glen Uhrig
- Department of Science, University of AlbertaEdmontonCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Klaas Van Wijk
- School of Integrated Plant Science, Plant Biology Section, Cornell UniversityIthacaUnited States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia TechBlacksburgUnited States
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
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22
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Taylor MJ, Liyu A, Vertes A, Anderton CR. Ambient Single-Cell Analysis and Native Tissue Imaging Using Laser-Ablation Electrospray Ionization Mass Spectrometry with Increased Spatial Resolution. J Am Soc Mass Spectrom 2021; 32:2490-2494. [PMID: 34374553 DOI: 10.1021/jasms.1c00149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Laser-ablation electrospray ionization mass spectrometry (LAESI-MS) is an emerging method that has the potential to transform the field of metabolomics. This is in part due to LAESI-MS being an ambient ionization method that requires minimal sample preparation and uses (endogenous) water for in situ analysis. This application note details the employment of the "LAESI microscope" source to perform spatially resolved MS analysis of cells and MS imaging (MSI) of tissues at high spatial resolution. This source configuration utilizes a long-working-distance reflective objective that permits both visualization of the sample and a smaller LAESI laser beam profile than conventional LAESI setups. Here, we analyzed 200 single cells of Allium cepa (red onion) and imaged Fittonia argyroneura (nerve plant) in high spatial resolution using this source coupled to a Fourier transform mass spectrometer for high-mass-resolution and high-mass-accuracy metabolomics.
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Affiliation(s)
- Michael J Taylor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Andrey Liyu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, D.C. 20052, United States
| | - Christopher R Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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23
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Birer-Williams CMC, Chu RK, Anderton CR, Wright ES. SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions. mSystems 2021; 6:e0090221. [PMID: 34427520 PMCID: PMC8422993 DOI: 10.1128/msystems.00902-21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 11/20/2022] Open
Abstract
Communication within the microbiome occurs through an immense diversity of small molecules. Capturing these microbial interactions is a significant challenge due to the complexity of the exometabolome and its sensitivity to environmental stimuli. Traditional methods for acquiring exometabolomic data from interacting microorganisms are limited by their low throughput or lack of sampling depth. To address this challenge, we introduce subtapping (short for substrate tapping), a technique for tapping into extracellular metabolites that are being transferred through the growth substrate during coculture. High-throughput subtapping is made possible by a new coculturing platform, named SubTap, that we engineered to resemble a 96-well plate. The three-dimensional (3D) printed SubTap platform captures the exometabolome in an agar compartment that connects physically separated growth chambers, which permits cell growth without competition for space. We show how SubTap facilitates replicable and quick detection of exometabolites via direct infusion mass spectrometry analysis. Using bacterial isolates from the soil, we apply SubTap to characterize the effects of growth medium, growth duration, and mixed versus unmixed coculturing on the exometabolome. Finally, we demonstrate SubTap's versatility by interrogating microbial interactions in multicultures with up to four strains. IMPORTANCE Improvements in experimental techniques and instrumentation have led to the discovery that the microbiome plays an essential role in human and environmental health. Nevertheless, there remain major impediments to conducting large-scale interrogations of the microbiome in a high-throughput manner, particularly in the field of exometabolomics. Existing methods to coculture microorganisms and interrogate their interactions are labor-intensive and low throughput. This inspired us to develop a solution for coculturing that was (i) open source, (ii) inexpensive, (iii) scalable, (iv) customizable, and (v) compatible with existing mass spectrometry instrumentation. Here, we present SubTap-a 3D printed coculturing platform that permits tapping directly into the growth substrate between physically separated, but interconnected, growth compartments. SubTap allows multiculture (with up to four distinct growth compartments) in spatially mixed or unmixed configurations and enables repeatable results with mass spectrometry, as shown by our validation with known compounds and cultures of one to four organisms.
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Affiliation(s)
- Caroline M. C. Birer-Williams
- Biomolécules et Biotechnologies Végétales (BBV) EA 2106, Université de Tours, Tours, France
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Erik S. Wright
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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24
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Taylor M, Lukowski JK, Anderton CR. Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics. J Am Soc Mass Spectrom 2021; 32:872-894. [PMID: 33656885 PMCID: PMC8033567 DOI: 10.1021/jasms.0c00439] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.
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Affiliation(s)
- Michael
J. Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jessica K. Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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25
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Veličković D, Chu RK, Henkel C, Nyhuis A, Tao N, Kyle JE, Adkins JN, Anderton CR, Paurus V, Bloodsworth K, Bramer LM, Cornett DS, Curtis WR, Burnum‐Johnson KE. Preserved and variable spatial-chemical changes of lipids across tomato leaves in response to central vein wounding reveals potential origin of linolenic acid in signal transduction cascade. Plant Environ Interact 2021; 2:28-35. [PMID: 37283847 PMCID: PMC10168036 DOI: 10.1002/pei3.10038] [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: 10/14/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/08/2023]
Abstract
Membrane lipids serve as substrates for the generation of numerous signaling lipids when plants are exposed to environmental stresses, and jasmonic acid, an oxidized product of 18-carbon unsaturated fatty acids (e.g., linolenic acid), has been recognized as the essential signal in wound-induced gene expression. Yet, the contribution of individual membrane lipids in linolenic acid generation is ill-defined. In this work, we performed spatial lipidomic experiments to track lipid changes that occur locally at the sight of leaf injury to better understand the potential origin of linolenic and linoleic acids from individual membrane lipids. The central veins of tomato leaflets were crushed using surgical forceps, leaves were cryosectioned and analyzed by two orthogonal matrix-assisted laser desorption/ionization mass spectrometry imaging platforms for insight into lipid spatial distribution. Significant changes in lipid composition are only observed 30 min after wounding, while after 60 min lipidome homeostasis has been re-established. Phosphatidylcholines exhibit a variable pattern of spatial behavior in individual plants. Among lysolipids, lysophosphatidylcholines strongly co-localize with the injured zone of wounded leaflets, while, for example, lysophosphatidylglycerol (LPG) (16:1) accumulated preferentially toward the apex in the injured zone of wounded leaflets. In contrast, two other LPGs (LPG [18:3] and LPG [18:2]) are depleted in the injured zone. Our high-resolution co-localization imaging analyses suggest that linolenic acids are predominantly released from PCs with 16_18 fatty acid composition along the entire leaf, while it seems that in the apex zone PG (16:1_18:3) significantly contributes to the linolenic acid pool. These results also indicate distinct localization and/or substrate preferences of phospholipase isoforms in leaf tissue.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | - Rosalie K. Chu
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | | | | | | | - Jennifer E. Kyle
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Joshua N. Adkins
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Christopher R. Anderton
- Environmental Molecular Sciences LaboratoryPacific Northwest National LaboratoryRichlandWAUSA
| | - Vanessa Paurus
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Kent Bloodsworth
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Lisa M. Bramer
- Computing & Analytics DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | | | - Wayne R. Curtis
- Department of Chemical EngineeringThe Pennsylvania State UniversityUniversity ParkPAUSA
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26
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El-Achkar TM, Eadon MT, Menon R, Lake BB, Sigdel TK, Alexandrov T, Parikh S, Zhang G, Dobi D, Dunn KW, Otto EA, Anderton CR, Carson JM, Luo J, Park C, Hamidi H, Zhou J, Hoover P, Schroeder A, Joanes M, Azeloglu EU, Sealfon R, Winfree S, Steck B, He Y, D’Agati V, Iyengar R, Troyanskaya OG, Barisoni L, Gaut J, Zhang K, Laszik Z, Rovin BH, Dagher PC, Sharma K, Sarwal MM, Hodgin JB, Alpers CE, Kretzler M, Jain S. A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project. Physiol Genomics 2021; 53:1-11. [PMID: 33197228 PMCID: PMC7847045 DOI: 10.1152/physiolgenomics.00104.2020] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. We describe a "follow the tissue" pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.
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Affiliation(s)
| | | | - Rajasree Menon
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Blue B. Lake
- 3Jacobs School of Engineering, University of California, San Diego, California
| | - Tara K. Sigdel
- 4University of California San Francisco School of Medicine, San Francisco, California
| | | | - Samir Parikh
- 6Ohio State University College of Medicine, Columbus, Ohio
| | - Guanshi Zhang
- 7UT-Health San Antonio School of Medicine, San Antonio, Texas
| | - Dejan Dobi
- 4University of California San Francisco School of Medicine, San Francisco, California
| | - Kenneth W. Dunn
- 1Indiana University School of Medicine, Indianapolis, Indiana
| | - Edgar A. Otto
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Christopher R. Anderton
- 7UT-Health San Antonio School of Medicine, San Antonio, Texas,8Pacific Northwest National Laboratory, Richland, Washington
| | - Jonas M. Carson
- 9Schools of Medicine and Public Health, University of Washington, Seattle, Washington
| | - Jinghui Luo
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Chris Park
- 9Schools of Medicine and Public Health, University of Washington, Seattle, Washington
| | - Habib Hamidi
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Jian Zhou
- 12Princeton University, Princeton, New Jersey,14Columbia University School of Medicine, New York City, New York
| | - Paul Hoover
- 10Harvard University School of Medicine, Boston Massachusetts
| | - Andrew Schroeder
- 4University of California San Francisco School of Medicine, San Francisco, California
| | - Marianinha Joanes
- 4University of California San Francisco School of Medicine, San Francisco, California
| | | | - Rachel Sealfon
- 12Princeton University, Princeton, New Jersey,14Columbia University School of Medicine, New York City, New York
| | - Seth Winfree
- 1Indiana University School of Medicine, Indianapolis, Indiana
| | - Becky Steck
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Yongqun He
- 2University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Vivette D’Agati
- 14Columbia University School of Medicine, New York City, New York
| | - Ravi Iyengar
- 11Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Olga G. Troyanskaya
- 12Princeton University, Princeton, New Jersey,14Columbia University School of Medicine, New York City, New York
| | - Laura Barisoni
- 15Duke University School of Medicine, Durham, North Carolina
| | - Joseph Gaut
- 16Washington University in Saint Louis School of Medicine, St. Louis, Missouri
| | - Kun Zhang
- 3Jacobs School of Engineering, University of California, San Diego, California
| | - Zoltan Laszik
- 4University of California San Francisco School of Medicine, San Francisco, California
| | - Brad H. Rovin
- 6Ohio State University College of Medicine, Columbus, Ohio
| | | | - Kumar Sharma
- 7UT-Health San Antonio School of Medicine, San Antonio, Texas
| | - Minnie M. Sarwal
- 4University of California San Francisco School of Medicine, San Francisco, California
| | | | - Charles E. Alpers
- 9Schools of Medicine and Public Health, University of Washington, Seattle, Washington
| | | | - Sanjay Jain
- 16Washington University in Saint Louis School of Medicine, St. Louis, Missouri
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27
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Lukowski JK, Pamreddy A, Velickovic D, Zhang G, Pasa-Tolic L, Alexandrov T, Sharma K, Anderton CR. Storage Conditions of Human Kidney Tissue Sections Affect Spatial Lipidomics Analysis Reproducibility. J Am Soc Mass Spectrom 2020; 31:2538-2546. [PMID: 32897710 PMCID: PMC8162764 DOI: 10.1021/jasms.0c00256] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Lipids often are labile, unstable, and tend to degrade overtime, so it is of the upmost importance to study these molecules in their most native state. We sought to understand the optimal storage conditions for spatial lipidomic analysis of human kidney tissue sections. Specifically, we evaluated human kidney tissue sections on several different days throughout the span of a week using our established protocol for elucidating lipids using high mass resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). We studied kidney tissue sections stored under five different conditions: open stored at -80 °C, vacuumed sealed and stored at -80 °C, with matrix preapplied before storage at -80 °C, under a nitrogen atmosphere and stored at -80 °C, and at room temperature in a desiccator. Results were compared to data obtained from kidney tissue sections that were prepared and analyzed immediately after cryosectioning. Data was processed using METASPACE. After a week of storage, the sections stored at room temperature showed the largest amount of lipid degradation, while sections stored under nitrogen and at -80 °C retained the greatest number of overlapping annotations in relation to freshly cut tissue. Overall, we found that molecular degradation of the tissue sections was unavoidable over time, regardless of storage conditions, but storing tissue sections in an inert gas at low temperatures can curtail molecular degradation within tissue sections.
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Affiliation(s)
- Jessica K Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Annapurna Pamreddy
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78284, United States
| | - Dusan Velickovic
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Guanshi Zhang
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78284, United States
- Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, Texas 78284, United States
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78284, United States
- Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, Texas 78284, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington99352, United States
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health, San Antonio, Texas 78284, United States
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28
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Zegeye EK, Sadler NC, Lomas GX, Attah IK, Jansson JK, Hofmockel KS, Anderton CR, Wright AT. Activity-Based Protein Profiling of Chitin Catabolism. Chembiochem 2020; 22:717-723. [PMID: 33049124 DOI: 10.1002/cbic.202000616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/12/2020] [Indexed: 01/09/2023]
Abstract
The microbial catabolism of chitin, an abundant and ubiquitous environmental organic polymer, is a fundamental cog in terrestrial and aquatic carbon and nitrogen cycles. Despite the importance of this critical bio-geochemical function, there is a limited understanding of the synergy between the various hydrolytic and accessory enzymes involved in chitin catabolism. To address this deficit, we synthesized activity-based probes (ABPs) designed to target active chitinolytic enzymes by modifying the chitin subunits N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. We demonstrate the utility of these ABPs in determining the synergy between various enzymes involved in chitin catabolism. The strategy can be used to gain molecular-level insights that can be used to better understand microbial roles in soil bio-geochemical cycling in the face of a changing climate.
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Affiliation(s)
- Elias K Zegeye
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Natalie C Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Gerard X Lomas
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Isaac K Attah
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
| | - Kirsten S Hofmockel
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
- Department of Ecology, Evolution and Organismal Biology Iowa State University, 251 Bessey Hall, Ames, Iowa (USA) 50011
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA
| | - Aaron T Wright
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, 1505 NE Stadium Way, Pullman, WA 99164, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Box 999, Richland, WA 99354, USA
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29
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Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y. Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. Nat Rev Nephrol 2020; 16:686-696. [PMID: 32939051 PMCID: PMC8012202 DOI: 10.1038/s41581-020-00335-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2020] [Indexed: 12/29/2022]
Abstract
An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medicine Project are working towards this goal through the collection and integration of large, disparate clinical, biological and imaging data from patients with kidney disease. Ontologies are powerful tools that facilitate these efforts by enabling researchers to organize and make sense of different data elements and the relationships between them. Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinical, imaging and biopsy data from diverse sources must be combined to define a patient's phenotype. The development of two new ontologies - the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation - will support the creation of the Kidney Tissue Atlas, which aims to provide a comprehensive molecular, cellular and anatomical map of the kidney. These ontologies will improve the annotation of kidney-relevant data, and eventually lead to new definitions of kidney disease in support of precision medicine.
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Affiliation(s)
- Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lucy L Wang
- Allen Institute for Artificial Intelligence, Seattle, WA, USA
| | - Jennifer Schaub
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John F O'Toole
- Department of Nephrology and Hypertension, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Becky Steck
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Frederick Dowd
- UW Medicine Research IT, University of Washington, Seattle, WA, USA
| | - Jens Hansen
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Barisoni
- Division of AI/Computational Pathology, Department of Pathology, and Division of Nephrology, Department of Medicine, Duke University, Durham, NC, USA
| | - Sanjay Jain
- Division of Nephrology, School of Medicine, Washington University in St. Louis, St Louis, MO, USA
| | - Ian H de Boer
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - M Todd Valerius
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sushrut S Waikar
- Section of Nephrology, Boston University Medical Center, Boston, MA, USA
| | - Christopher Park
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Cleveland, OH, USA
| | - Theodore Alexandrov
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Christian Stoeckert
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Philadelphia, PA, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Alexander D Diehl
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa Haendel
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - Ravi Iyengar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthias Kretzler
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sean Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
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30
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Agtuca BJ, Stopka SA, Evans S, Samarah L, Liu Y, Xu D, Stacey MG, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. Metabolomic profiling of wild-type and mutant soybean root nodules using laser-ablation electrospray ionization mass spectrometry reveals altered metabolism. Plant J 2020; 103:1937-1958. [PMID: 32410239 DOI: 10.1111/tpj.14815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 05/18/2023]
Abstract
The establishment of the nitrogen-fixing symbiosis between soybean and Bradyrhizobium japonicum is a complex process. To document the changes in plant metabolism as a result of symbiosis, we utilized laser ablation electrospray ionization-mass spectrometry (LAESI-MS) for in situ metabolic profiling of wild-type nodules, nodules infected with a B. japonicum nifH mutant unable to fix nitrogen, nodules doubly infected by both strains, and nodules formed on plants mutated in the stearoyl-acyl carrier protein desaturase (sacpd-c) gene, which were previously shown to have an altered nodule ultrastructure. The results showed that the relative abundance of fatty acids, purines, and lipids was significantly changed in response to the symbiosis. The nifH mutant nodules had elevated levels of jasmonic acid, correlating with signs of nitrogen deprivation. Nodules resulting from the mixed inoculant displayed similar, overlapping metabolic distributions within the sectors of effective (fix+ ) and ineffective (nifH mutant, fix- ) endosymbionts. These data are inconsistent with the notion that plant sanctioning is cell autonomous. Nodules lacking sacpd-c displayed an elevation of soyasaponins and organic acids in the central necrotic regions. The present study demonstrates the utility of LAESI-MS for high-throughput screening of plant phenotypes. Overall, nodules disrupted in the symbiosis were elevated in metabolites related to plant defense.
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Affiliation(s)
- Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Sterling Evans
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Laith Samarah
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Yang Liu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Minviluz G Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
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31
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Lee JY, Sadler NC, Egbert RG, Anderton CR, Hofmockel KS, Jansson JK, Song HS. Deep learning predicts microbial interactions from self-organized spatiotemporal patterns. Comput Struct Biotechnol J 2020; 18:1259-1269. [PMID: 32612750 PMCID: PMC7298420 DOI: 10.1016/j.csbj.2020.05.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised deep learning as a new tool for network inference. An agent-based model was used to simulate the spatiotemporal evolution of two interacting organisms under diverse growth and interaction scenarios, the data of which was subsequently used to train deep neural networks. For small-size domains (100 µm × 100 µm) over which interaction coefficients are assumed to be invariant, we obtained fairly accurate predictions, as indicated by an average R2 value of 0.84. In application to relatively larger domains (450 µm × 450 µm) where interaction coefficients are varying in space, deep learning models correctly predicted spatial distributions of interaction coefficients without any additional training. Lastly, we evaluated our model against real biological data obtained using Pseudomonas fluorescens and Escherichia coli co-cultures treated with polymeric chitin or N-acetylglucosamine, the hydrolysis product of chitin. While P. fluorescens can utilize both substrates for growth, E. coli lacked the ability to degrade chitin. Consistent with our expectations, our model predicted context-dependent interactions across two substrates, i.e., degrader-cheater relationship on chitin polymers and competition on monomers. The combined use of the agent-based model and machine learning algorithm successfully demonstrates how to infer microbial interactions from spatially distributed data, presenting itself as a useful tool for the analysis of more complex microbial community interactions.
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Affiliation(s)
- Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Natalie C. Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G. Egbert
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kirsten S. Hofmockel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Janet K. Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hyun-Seob Song
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
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32
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Samarah LZ, Khattar R, Tran TH, Stopka SA, Brantner CA, Parlanti P, Veličković D, Shaw JB, Agtuca BJ, Stacey G, Paša-Tolić L, Tolić N, Anderton CR, Vertes A. Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations. Anal Chem 2020; 92:7289-7298. [PMID: 32314907 DOI: 10.1021/acs.analchem.0c00936] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Characterization of the metabolic heterogeneity in cell populations requires the analysis of single cells. Most current methods in single-cell analysis rely on cell manipulation, potentially altering the abundance of metabolites in individual cells. A small sample volume and the chemical diversity of metabolites are additional challenges in single-cell metabolomics. Here, we describe the combination of fiber-based laser ablation electrospray ionization (f-LAESI) with 21 T Fourier transform ion cyclotron resonance mass spectrometry (21TFTICR-MS) for in situ single-cell metabolic profiling in plant tissue. Single plant cells infected by bacteria were selected and sampled directly from the tissue without cell manipulation through mid-infrared ablation with a fine optical fiber tip for ionization by f-LAESI. Ultrahigh performance 21T-FTICR-MS enabled the simultaneous capture of isotopic fine structures (IFSs) for 47 known and 11 unknown compounds, thus elucidating their elemental compositions from single cells and providing information on metabolic heterogeneity in the cell population.
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Affiliation(s)
- Laith Z Samarah
- Department of Chemistry, George Washington University, Washington D.C. 20052, United States
| | - Rikkita Khattar
- Department of Chemistry, George Washington University, Washington D.C. 20052, United States
| | - Tina H Tran
- Department of Chemistry, George Washington University, Washington D.C. 20052, United States
| | - Sylwia A Stopka
- Department of Chemistry, George Washington University, Washington D.C. 20052, United States
| | - Christine A Brantner
- Nanofabrication and Imaging Center, George Washington University, Washington D.C. 20052, United States
| | - Paola Parlanti
- Nanofabrication and Imaging Center, George Washington University, Washington D.C. 20052, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Nikola Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Akos Vertes
- Department of Chemistry, George Washington University, Washington D.C. 20052, United States
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33
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Krounbi L, Enders A, Anderton CR, Engelhard MH, Hestrin R, Torres-Rojas D, Dynes JJ, Lehmann J. Sequential Ammonia and Carbon Dioxide Adsorption on Pyrolyzed Biomass to Recover Waste Stream Nutrients. ACS Sustain Chem Eng 2020; 8:7121-7131. [PMID: 32421071 PMCID: PMC7218926 DOI: 10.1021/acssuschemeng.0c01427] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/29/2020] [Indexed: 06/11/2023]
Abstract
The amine-rich surfaces of pyrolyzed human solid waste (py-HSW) can be "primed" or "regenerated" with carbon dioxide (CO2) to enhance their adsorption of ammonia (NH3) for use as a soil amendment. To better understand the mechanism by which CO2 exposure facilitates NH3 adsorption to py-HSW, we artificially enriched a model sorbent, pyrolyzed, oxidized wood (py-ox wood) with amine functional groups through exposure to NH3. We then exposed these N-enriched materials to CO2 and then resorbed NH3. The high heat of CO2 adsorption (Q st) on py-HSW, 49 kJ mol-1, at low surface coverage, 0.4 mmol CO2 g-1, showed that the naturally occurring N compounds in py-HSW have a high affinity for CO2. The Q st of CO2 on py-ox wood also increased after exposure to NH3, reaching 50 kJ mol-1 at 0.7 mmol CO2 g-1, demonstrating that the incorporation of N-rich functional groups by NH3 adsorption is favorable for CO2 uptake. Adsorption kinetics of py-ox wood revealed continued, albeit diminishing NH3 uptake after each CO2 treatment, averaging 5.9 mmol NH3 g-1 for the first NH3 exposure event and 3.5 and 2.9 mmol NH3 g-1 for the second and third; the electrophilic character of CO2 serves as a Lewis acid, enhancing surface affinity for NH3 uptake. Furthermore, penetration of 15NH3 and 13CO2 measured by NanoSIMS reached over 7 μm deep into both materials, explaining the large NH3 capture. We expected similar NH3 uptake in py-HSW sorbed with CO2 and py-ox wood because both materials, py-HSW and py-ox wood sorbed with NH3, had similar N contents and similarly high CO2 uptake. Yet NH3 sorption in py-HSW was unexpectedly low, apparently from potassium (K) bicarbonate precipitation, reducing interactions between NH3 and sorbed CO2; 2-fold greater surface K in py-HSW was detected after exposure to CO2 and NH3 than before gas exposure. We show that amine-rich pyrolyzed waste materials have high CO2 affinity, which facilitates NH3 uptake. However, high ash contents as found in py-HSW hinder this mechanism.
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Affiliation(s)
- Leilah Krounbi
- Soil
and Crop Sciences, College of Agriculture and Life Sciences, Cornell University, 306 Tower Road, Ithaca, New York 14853, United States
| | - Akio Enders
- Soil
and Crop Sciences, College of Agriculture and Life Sciences, Cornell University, 306 Tower Road, Ithaca, New York 14853, United States
| | - Christopher R. Anderton
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Lab, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Mark H. Engelhard
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Lab, 902 Battelle Boulevard, Richland, Washington 99354, United States
| | - Rachel Hestrin
- Soil
and Crop Sciences, College of Agriculture and Life Sciences, Cornell University, 306 Tower Road, Ithaca, New York 14853, United States
| | - Dorisel Torres-Rojas
- Soil
and Crop Sciences, College of Agriculture and Life Sciences, Cornell University, 306 Tower Road, Ithaca, New York 14853, United States
| | - James J. Dynes
- Canadian
Light Source, 44 Innovation Blvd, Saskatoon, SK S7N 2V3, Canada
| | - Johannes Lehmann
- Soil
and Crop Sciences, College of Agriculture and Life Sciences, Cornell University, 306 Tower Road, Ithaca, New York 14853, United States
- Atkinson
Center for a Sustainable Future, Cornell
University, 200 Rice
Hall, Ithaca, New York 14853, United States
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Veličković D, Chu RK, Myers GL, Ahkami AH, Anderton CR. An approach for visualizing the spatial metabolome of an entire plant root system inspired by the Swiss-rolling technique. J Mass Spectrom 2020; 55:e4363. [PMID: 31018010 DOI: 10.1002/jms.4363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 05/11/2023]
Abstract
The spatial configuration and morphology of roots are commonly monitored for a better understanding of plant health and development. However, this approach provides minimal details about the biochemistry regulating the observable traits. Therefore, the ability to metabolically map the entire root structure would be of major value. Here, we developed a sample preparation approach that enables imaging of the entire root within a restricted space (width of microscope slide), which was influenced by the Swiss-rolling technique. We were able to image and confidently identify molecules along the entire root structure from rolled-root tissue sections using multiple spatially resolved mass spectrometry approaches.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Gabriel L Myers
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
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Veličković D, Zhang G, Bezbradica D, Bhattacharjee A, Paša-Tolić L, Sharma K, Alexandrov T, Anderton CR. Response Surface Methodology As a New Approach for Finding Optimal MALDI Matrix Spraying Parameters for Mass Spectrometry Imaging. J Am Soc Mass Spectrom 2020; 31:508-516. [PMID: 32126772 PMCID: PMC7293970 DOI: 10.1021/jasms.9b00074] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Automated spraying devices have become ubiquitous in laboratories employing matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), in part because they permit control of a number of matrix application parameters that can easily be reproduced for intra- and interlaboratory studies. Determining the optimal parameters for MALDI matrix application, such as temperature, flow rate, spraying velocity, number of spraying cycles, and solvent composition for matrix application, is critical for obtaining high-quality MALDI-MSI data. However, there are no established approaches for optimizing these multiple parameters simultaneously. Instead optimization is performed iteratively (i.e., one parameter at a time), which is time-consuming and can lead to overall nonoptimal settings. In this report, we demonstrate the use a novel experimental design and the response surface methodology to optimize five parameters of MALDI matrix application using a robotic sprayer. Thirty-two combinations of MALDI matrix spraying conditions were tested, which allowed us to elucidate relationships between each of the application parameters as determined by MALDI-MS (specifically, using a 15 T Fourier transform ion cyclotron resonance mass spectrometer). As such, we were able to determine the optimal automated spraying parameters that minimized signal delocalization and enabled high MALDI sensitivity. We envision this optimization strategy can be utilized for other matrix application approaches and MALDI-MSI analyses of other molecular classes and tissue types.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Guanshi Zhang
- Center for Renal Precision Medicine, University of Texas Health-San Antonio, San Antonio, Texas 78284, United States
| | - Dejan Bezbradica
- Department of Biochemical Engineering and Biotechnology, Faculty of Technology and Metallurgy, University of Belgrade, Belgrade 11000, Serbia
| | - Arunima Bhattacharjee
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kumar Sharma
- Center for Renal Precision Medicine, University of Texas Health-San Antonio, San Antonio, Texas 78284, United States
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Center for Renal Precision Medicine, University of Texas Health-San Antonio, San Antonio, Texas 78284, United States
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36
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Agtuca BJ, Stopka SA, Tuleski TR, do Amaral FP, Evans S, Liu Y, Xu D, Monteiro RA, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria. Mol Plant Microbe Interact 2020; 33:272-283. [PMID: 31544655 DOI: 10.1094/mpmi-06-19-0174-r] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix+) or a fix- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix- strain, perhaps reflecting a plant defense response.
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Affiliation(s)
- Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Thalita R Tuleski
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - Fernanda P do Amaral
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sterling Evans
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Yang Liu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
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37
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Zhang G, Zhang J, DeHoog RJ, Pennathur S, Anderton CR, Venkatachalam MA, Alexandrov T, Eberlin LS, Sharma K. DESI-MSI and METASPACE indicates lipid abnormalities and altered mitochondrial membrane components in diabetic renal proximal tubules. Metabolomics 2020; 16:11. [PMID: 31925564 PMCID: PMC7301343 DOI: 10.1007/s11306-020-1637-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/04/2020] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Diabetic kidney disease (DKD) is the most prevalent complication in diabetic patients, which contributes to high morbidity and mortality. Urine and plasma metabolomics studies have been demonstrated to provide valuable insights for DKD. However, limited information on spatial distributions of metabolites in kidney tissues have been reported. OBJECTIVES In this work, we employed an ambient desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) coupled to a novel bioinformatics platform (METASPACE) to characterize the metabolome in a mouse model of DKD. METHODS DESI-MSI was performed for spatial untargeted metabolomics analysis in kidneys of mouse models (F1 C57BL/6J-Ins2Akita male mice at 17 weeks of age) of type 1 diabetes (T1D, n = 5) and heathy controls (n = 6). RESULTS Multivariate analyses (i.e., PCA and PLS-DA (a 2000 permutation test: P < 0.001)) showed clearly separated clusters for the two groups of mice on the basis of 878 measured m/z's in kidney cortical tissues. Specifically, mice with T1D had increased relative abundances of pseudouridine, accumulation of free polyunsaturated fatty acids (PUFAs), and decreased relative abundances of cardiolipins in cortical proximal tubules when compared with healthy controls. CONCLUSION Results from the current study support potential key roles of pseudouridine and cardiolipins for maintaining normal RNA structure and normal mitochondrial function, respectively, in cortical proximal tubules with DKD. DESI-MSI technology coupled with METASPACE could serve as powerful new tools to provide insight on fundamental pathways in DKD.
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Affiliation(s)
- Guanshi Zhang
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, TX, USA
| | - Jialing Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Rachel J DeHoog
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Livia S Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Kumar Sharma
- Center for Renal Precision Medicine, Division of Nephrology, Department of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Audie L. Murphy Memorial VA Hospital, South Texas Veterans Health Care System, San Antonio, TX, USA.
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38
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Veličkovic D, Liao HL, Vilgalys R, Chu RK, Anderton CR. Spatiotemporal Transformation in the Alkaloid Profile of Pinus Roots in Response to Mycorrhization. J Nat Prod 2019; 82:1382-1386. [PMID: 31009217 DOI: 10.1021/acs.jnatprod.8b01050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Root alkaloids remain highly unexplored in ectomycorrhizae development studies. By employing ultrahigh mass resolution mass spectrometry imaging techniques, we showed substantial relocation and transformation of piperidine alkaloids in pine root tips in response to Suillus mycorrhization. We imaged, in the time frame of ectomycorrhizae formation, a completely different alkaloid profile in Pinus strobus, where basidiospores of Suillus spraguei induce morphogenesis of symbiotic tissues, than in Pinus taeda, where such interaction fails to induce morphogenesis. On the basis of spatial colocalization studies, we proposed some alternative routes for biosynthesis of these alkaloids that supplement existing literature data.
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Affiliation(s)
- Dušan Veličkovic
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Hui-Ling Liao
- Biology Department , Duke University , 130 Science Drive , Durham , North Carolina 27708 , United States
- North Florida Research and Education Center , University of Florida , 155 Research Road , Quincy , Florida 32351 , United States
| | - Rytas Vilgalys
- Biology Department , Duke University , 130 Science Drive , Durham , North Carolina 27708 , United States
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate , Pacific Northwest National Laboratory , 902 Battelle Boulevard , Richland , Washington 99354 , United States
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39
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Stopka SA, Samarah LZ, Shaw JB, Liyu AV, Veličković D, Agtuca BJ, Kukolj C, Koppenaal DW, Stacey G, Paša-Tolić L, Anderton CR, Vertes A. Ambient Metabolic Profiling and Imaging of Biological Samples with Ultrahigh Molecular Resolution Using Laser Ablation Electrospray Ionization 21 Tesla FTICR Mass Spectrometry. Anal Chem 2019; 91:5028-5035. [PMID: 30821434 DOI: 10.1021/acs.analchem.8b05084] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mass spectrometry (MS) is an indispensable analytical tool to capture the array of metabolites within complex biological systems. However, conventional MS-based metabolomic workflows require extensive sample processing and separation resulting in limited throughput and potential alteration of the native molecular states in these systems. Ambient ionization methods, capable of sampling directly from tissues, circumvent some of these issues but require high-performance MS to resolve the molecular complexity within these samples. Here, we demonstrate a unique combination of laser ablation electrospray ionization (LAESI) coupled with a 21 tesla Fourier transform ion cyclotron resonance (21T-FTICR) for direct MS analysis and imaging applications. This analytical platform provides isotopic fine structure information directly from biological tissues, enabling the rapid assignment of molecular formulas and delivering a higher degree of confidence for molecular identification.
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Affiliation(s)
- Sylwia A Stopka
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Laith Z Samarah
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Caroline Kukolj
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center , University of Missouri , Columbia , Missouri 65211 , United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory and Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Akos Vertes
- Department of Chemistry , The George Washington University , Washington , D.C. 20052 , United States
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40
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Angerer TB, Chakravarty N, Taylor MJ, Nicora CD, Graham DJ, Anderton CR, Chudler EH, Gamble LJ. Insights into the histology of planarian flatworm Phagocata gracilis based on location specific, intact lipid information provided by GCIB-ToF-SIMS imaging. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:733-743. [PMID: 30731132 DOI: 10.1016/j.bbalip.2019.01.011] [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: 07/26/2018] [Revised: 11/13/2018] [Accepted: 01/25/2019] [Indexed: 11/17/2022]
Abstract
Planarian flatworms are known as the masters of regeneration, re-growing an entire organism from as little as 1/279th part of their body. While the proteomics of these processes has been studied extensively, the planarian lipodome remains relatively unknown. In this study we investigate the lipid profile of planarian tissue sections with imaging Time-of-Flight - Secondary-Ion-Mass-Spectrometry (ToF-SIMS). ToF-SIMS is a label-free technique capable of gathering intact, location specific lipid information on a cellular scale. Lipid identities are confirmed using LC-MS/MS. Our data shows that different organ structures within planarians have unique lipid profiles. The 22-carbon atom poly unsaturated fatty acids (PUFAs) which occur in unusually high amounts in planarians are found to be mainly located in the testes. Additionally, we observe that planarians contain various odd numbered fatty acid species, that are usually found in bacteria, localized in the reproductive and ectodermal structures of the planarian. An abundance of poorly understood ether fatty acids and ether lipids were found in unique areas in planarians as well as a new, yet unidentified class of potential lipids in planarian intestines. Identifying the location of these lipids in the planarian body provides insights into their bodily functions and, in combination with knowledge about their diet and their genome, enables drawing conclusions about planarian fatty acid processing.
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Affiliation(s)
- Tina B Angerer
- NESACBIO, University of Washington, Seattle, WA, United States of America; Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - Neil Chakravarty
- Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - Michael J Taylor
- NESACBIO, University of Washington, Seattle, WA, United States of America; Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - Carrie D Nicora
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Daniel J Graham
- NESACBIO, University of Washington, Seattle, WA, United States of America; Department of Bioengineering, University of Washington, Seattle, WA, United States of America
| | - Christopher R Anderton
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Eric H Chudler
- Department of Bioengineering, University of Washington, Seattle, WA, United States of America; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, United States of America
| | - Lara J Gamble
- NESACBIO, University of Washington, Seattle, WA, United States of America; Department of Bioengineering, University of Washington, Seattle, WA, United States of America.
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41
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Nagy G, Veličković D, Chu RK, Carrell AA, Weston DJ, Ibrahim YM, Anderton CR, Smith RD. Towards resolving the spatial metabolome with unambiguous molecular annotations in complex biological systems by coupling mass spectrometry imaging with structures for lossless ion manipulations. Chem Commun (Camb) 2019; 55:306-309. [PMID: 30534702 PMCID: PMC6537888 DOI: 10.1039/c8cc07482h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We demonstrate the coupling of liquid extraction surface analysis (LESA) to structures for lossless ion manipulations in conjunction with serpentine ultralong path with extending routing (SLIM SUPER) ion mobility-mass spectrometry (IM-MS) for the unambiguous annotation of important isomeric glycoforms in carbon-fixing communities.
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Affiliation(s)
- Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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42
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Veličković D, Agtuca BJ, Stopka SA, Vertes A, Koppenaal DW, Paša-Tolić L, Stacey G, Anderton CR. Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange. ISME J 2018. [PMID: 29899508 DOI: 10.1038/s41396-018-0188-188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
In this study, the three-dimensional spatial distributions of a number of metabolites involved in regulating symbiosis and biological nitrogen fixation (BNF) within soybean root nodules were revealed using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). While many metabolites exhibited distinct spatial compartmentalization, some metabolites were asymmetrically distributed throughout the nodule (e.g., S-adenosylmethionine). These results establish a more complex metabolic view of plant-bacteria symbiosis (and BNF) within soybean nodules than previously hypothesized. Collectively these findings suggest that spatial perspectives in metabolic regulation should be considered to unravel the overall complexity of interacting organisms, like those relating to associations of nitrogen-fixing bacteria with host plants.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA.
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43
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Veličković D, Agtuca BJ, Stopka SA, Vertes A, Koppenaal DW, Paša-Tolić L, Stacey G, Anderton CR. Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange. ISME J 2018; 12:2335-2338. [PMID: 29899508 PMCID: PMC6092352 DOI: 10.1038/s41396-018-0188-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/02/2018] [Accepted: 02/26/2018] [Indexed: 11/30/2022]
Abstract
In this study, the three-dimensional spatial distributions of a number of metabolites involved in regulating symbiosis and biological nitrogen fixation (BNF) within soybean root nodules were revealed using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). While many metabolites exhibited distinct spatial compartmentalization, some metabolites were asymmetrically distributed throughout the nodule (e.g., S-adenosylmethionine). These results establish a more complex metabolic view of plant-bacteria symbiosis (and BNF) within soybean nodules than previously hypothesized. Collectively these findings suggest that spatial perspectives in metabolic regulation should be considered to unravel the overall complexity of interacting organisms, like those relating to associations of nitrogen-fixing bacteria with host plants.
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Affiliation(s)
- Dušan Veličković
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA.
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44
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Nuñez JR, Anderton CR, Renslow RS. Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data. PLoS One 2018; 13:e0199239. [PMID: 30067751 PMCID: PMC6070163 DOI: 10.1371/journal.pone.0199239] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/04/2018] [Indexed: 11/24/2022] Open
Abstract
Color vision deficiency (CVD) affects more than 4% of the population and leads to a different visual perception of colors. Though this has been known for decades, colormaps with many colors across the visual spectra are often used to represent data, leading to the potential for misinterpretation or difficulty with interpretation by someone with this deficiency. Until the creation of the module presented here, there were no colormaps mathematically optimized for CVD using modern color appearance models. While there have been some attempts to make aesthetically pleasing or subjectively tolerable colormaps for those with CVD, our goal was to make optimized colormaps for the most accurate perception of scientific data by as many viewers as possible. We developed a Python module, cmaputil, to create CVD-optimized colormaps, which imports colormaps and modifies them to be perceptually uniform in CVD-safe colorspace while linearizing and maximizing the brightness range. The module is made available to the science community to enable others to easily create their own CVD-optimized colormaps. Here, we present an example CVD-optimized colormap created with this module that is optimized for viewing by those without a CVD as well as those with red-green colorblindness. This colormap, cividis, enables nearly-identical visual-data interpretation to both groups, is perceptually uniform in hue and brightness, and increases in brightness linearly.
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Affiliation(s)
- Jamie R. Nuñez
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Christopher R. Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Ryan S. Renslow
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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Stopka SA, Khattar R, Agtuca BJ, Anderton CR, Paša-Tolić L, Stacey G, Vertes A. Metabolic Noise and Distinct Subpopulations Observed by Single Cell LAESI Mass Spectrometry of Plant Cells in situ. Front Plant Sci 2018; 9:1646. [PMID: 30498504 PMCID: PMC6250120 DOI: 10.3389/fpls.2018.01646] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/23/2018] [Indexed: 05/18/2023]
Abstract
Phenotypic variations and stochastic expression of transcripts, proteins, and metabolites in biological tissues lead to cellular heterogeneity. As a result, distinct cellular subpopulations emerge. They are characterized by different metabolite expression levels and by associated metabolic noise distributions. To capture these biological variations unperturbed, highly sensitive in situ analytical techniques are needed that can sample tissue embedded single cells with minimum sample preparation. Optical fiber-based laser ablation electrospray ionization mass spectrometry (f-LAESI-MS) is a promising tool for metabolic profiling of single cells under ambient conditions. Integration of this MS-based platform with fluorescence and brightfield microscopy provides the ability to target single cells of specific type and allows for the selection of rare cells, e.g., excretory idioblasts. Analysis of individual Egeria densa leaf blade cells (n = 103) by f-LAESI-MS revealed significant differences between the prespecified subpopulations of epidermal cells (n = 97) and excretory idioblasts (n = 6) that otherwise would have been masked by the population average. Primary metabolites, e.g., malate, aspartate, and ascorbate, as well as several glucosides were detected in higher abundance in the epidermal cells. The idioblasts contained lipids, e.g., PG(16:0/18:2), and triterpene saponins, e.g., medicoside I and azukisaponin I, and their isomers. Metabolic noise for the epidermal cells were compared to results for soybean (Glycine max) root nodule cells (n = 60) infected by rhizobia (Bradyrhizobium japonicum). Whereas some primary metabolites showed lower noise in the latter, both cell types exhibited higher noise for secondary metabolites. Post hoc grouping of epidermal and root nodule cells, based on the abundance distributions for certain metabolites (e.g., malate), enabled the discovery of cellular subpopulations characterized by different mean abundance values, and the magnitudes of the corresponding metabolic noise. Comparison of prespecified populations from epidermal cells of the closely related E. densa (n = 20) and Elodea canadensis (n = 20) revealed significant differences, e.g., higher sugar content in the former and higher levels of ascorbate in the latter, and the presence of species-specific metabolites. These results demonstrate that the f-LAESI-MS single cell analysis platform has the potential to explore cellular heterogeneity and metabolic noise for hundreds of tissue-embedded cells.
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Affiliation(s)
- Sylwia A. Stopka
- Department of Chemistry, The George Washington University, Washington, DC, United States
- *Correspondence: Sylwia A. Stopka, ; orcid.org/0000-0003-3761-6899 Akos Vertes, ; orcid.org/0000-0001-5186-5352
| | - Rikkita Khattar
- Department of Chemistry, The George Washington University, Washington, DC, United States
| | - Beverly J. Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, United States
- *Correspondence: Sylwia A. Stopka, ; orcid.org/0000-0003-3761-6899 Akos Vertes, ; orcid.org/0000-0001-5186-5352
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Veličković D, Chu RK, Carrell AA, Thomas M, Paša-Tolić L, Weston DJ, Anderton CR. Multimodal MSI in Conjunction with Broad Coverage Spatially Resolved MS 2 Increases Confidence in Both Molecular Identification and Localization. Anal Chem 2017; 90:702-707. [PMID: 29210566 DOI: 10.1021/acs.analchem.7b04319] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
One critical aspect of mass spectrometry imaging (MSI) is the need to confidently identify detected analytes. While orthogonal tandem MS (e.g., LC-MS2) experiments from sample extracts can assist in annotating ions, the spatial information about these molecules is lost. Accordingly, this could cause mislead conclusions, especially in cases where isobaric species exhibit different distributions within a sample. In this Technical Note, we employed a multimodal imaging approach, using matrix assisted laser desorption/ionization (MALDI)-MSI and liquid extraction surface analysis (LESA)-MS2I, to confidently annotate and localize a broad range of metabolites involved in a tripartite symbiosis system of moss, cyanobacteria, and fungus. We found that the combination of these two imaging modalities generated very congruent ion images, providing the link between highly accurate structural information onfered by LESA and high spatial resolution attainable by MALDI. These results demonstrate how this combined methodology could be very useful in differentiating metabolite routes in complex systems.
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Affiliation(s)
| | | | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | | | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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Stopka SA, Agtuca BJ, Koppenaal DW, Paša-Tolić L, Stacey G, Vertes A, Anderton CR. Laser-ablation electrospray ionization mass spectrometry with ion mobility separation reveals metabolites in the symbiotic interactions of soybean roots and rhizobia. Plant J 2017; 91:340-354. [PMID: 28394446 DOI: 10.1111/tpj.13569] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 05/18/2023]
Abstract
Technologies enabling in situ metabolic profiling of living plant systems are invaluable for understanding physiological processes and could be used for rapid phenotypic screening (e.g., to produce plants with superior biological nitrogen-fixing ability). The symbiotic interaction between legumes and nitrogen-fixing soil bacteria results in a specialized plant organ (i.e., root nodule) where the exchange of nutrients between host and endosymbiont occurs. Laser-ablation electrospray ionization mass spectrometry (LAESI-MS) is a method that can be performed under ambient conditions requiring minimal sample preparation. Here, we employed LAESI-MS to explore the well characterized symbiosis between soybean (Glycine max L. Merr.) and its compatible symbiont, Bradyrhizobium japonicum. The utilization of ion mobility separation (IMS) improved the molecular coverage, selectivity, and identification of the detected biomolecules. Specifically, incorporation of IMS resulted in an increase of 153 differentially abundant spectral features in the nodule samples. The data presented demonstrate the advantages of using LAESI-IMS-MS for the rapid analysis of intact root nodules, uninfected root segments, and free-living rhizobia. Untargeted pathway analysis revealed several metabolic processes within the nodule (e.g., zeatin, riboflavin, and purine synthesis). Compounds specific to the uninfected root and bacteria were also detected. Lastly, we performed depth profiling of intact nodules to reveal the location of metabolites to the cortex and inside the infected region, and lateral profiling of sectioned nodules confirmed these molecular distributions. Our results established the feasibility of LAESI-IMS-MS for the analysis and spatial mapping of plant tissues, with its specific demonstration to improve our understanding of the soybean-rhizobial symbiosis.
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Affiliation(s)
- Sylwia A Stopka
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, Washington, DC, 20052, USA
| | - Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Akos Vertes
- Department of Chemistry, W. M. Keck Institute for Proteomics Technology and Applications, The George Washington University, Washington, DC, 20052, USA
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA, 99354, USA
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48
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Nguyen SN, Liyu AV, Chu RK, Anderton CR, Laskin J. Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography. Anal Chem 2016; 89:1131-1137. [PMID: 27973782 DOI: 10.1021/acs.analchem.6b03293] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new approach for constant-distance mode mass spectrometry imaging (MSI) of biological samples using nanospray desorption electrospray ionization (nano-DESI) was developed by integrating a shear-force probe with the nano-DESI probe. The technical concept and basic instrumental setup, as well as the general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enabled the constant-distance imaging mode via a computer-controlled closed-feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites, including nonribosomal peptides (surfactin, plipastatin, and iturin) on the surface of living bacterial colonies, ranging in diameter from 10 to 13 mm, with height variations up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Based on this effort, constant-mode nano-DESI MSI proved to be ideally suited for imaging biological samples of complex topography in their native states.
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Affiliation(s)
- Son N Nguyen
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Andrey V Liyu
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Rosalie K Chu
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Christopher R Anderton
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
| | - Julia Laskin
- Physical Sciences Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington, United States
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49
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Renslow RS, Lindemann SR, Cole JK, Zhu Z, Anderton CR. Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis. Biointerphases 2016; 11:02A322. [PMID: 26872582 PMCID: PMC5848783 DOI: 10.1116/1.4941764] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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] [Received: 11/12/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 11/17/2022] Open
Abstract
Elucidating nutrient exchange in microbial communities is an important step in understanding the relationships between microbial systems and global biogeochemical cycles, but these communities are complex and the interspecies interactions that occur within them are not well understood. Phototrophic consortia are useful and relevant experimental systems to investigate such interactions as they are not only prevalent in the environment, but some are cultivable in vitro and amenable to controlled scientific experimentation. Nanoscale secondary ion mass spectrometry (NanoSIMS) is a powerful, high spatial resolution tool capable of visualizing the metabolic activities of single cells within a biofilm, but quantitative analysis of the resulting data has typically been a manual process, resulting in a task that is both laborious and susceptible to human error. Here, the authors describe the creation and application of a semiautomated image-processing pipeline that can analyze NanoSIMS-generated data, applied to phototrophic biofilms as an example. The tool employs an image analysis process, which includes both elemental and morphological segmentation, producing a final segmented image that allows for discrimination between autotrophic and heterotrophic biomass, the detection of individual cyanobacterial filaments and heterotrophic cells, the quantification of isotopic incorporation of individual heterotrophic cells, and calculation of relevant population statistics. The authors demonstrate the functionality of the tool by using it to analyze the uptake of (15)N provided as either nitrate or ammonium through the unicyanobacterial consortium UCC-O and imaged via NanoSIMS. The authors found that the degree of (15)N incorporation by individual cells was highly variable when labeled with (15)NH4 (+), but much more even when biofilms were labeled with (15)NO3 (-). In the (15)NH4 (+)-amended biofilms, the heterotrophic distribution of (15)N incorporation was highly skewed, with a large population showing moderate (15)N incorporation and a small number of organisms displaying very high (15)N uptake. The results showed that analysis of NanoSIMS data can be performed in a way that allows for quantitation of the elemental uptake of individual cells, a technique necessary for advancing research into the metabolic networks that exist within biofilms with statistical analyses that are supported by automated, user-friendly processes.
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Affiliation(s)
- Ryan S Renslow
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Stephen R Lindemann
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Jessica K Cole
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Zihua Zhu
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, Washington 99354
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50
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Proetto MT, Anderton CR, Hu D, Szymanski CJ, Zhu Z, Patterson JP, Kammeyer JK, Nilewski LG, Rush AM, Bell NC, Evans JE, Orr G, Howell SB, Gianneschi NC. Cellular Delivery of Nanoparticles Revealed with Combined Optical and Isotopic Nanoscopy. ACS Nano 2016; 10:4046-54. [PMID: 27022832 PMCID: PMC8459375 DOI: 10.1021/acsnano.5b06477] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Direct polymerization of an oxaliplatin analogue was used to reproducibly generate amphiphiles in one pot, which consistently and spontaneously self-assemble into well-defined nanoparticles (NPs). Despite inefficient drug leakage in cell-free assays, the NPs were observed to be as cytotoxic as free oxaliplatin in cell culture experiments. We investigated this phenomenon by super-resolution fluorescence structured illumination microscopy (SIM) and nanoscale secondary ion mass spectrometry (NanoSIMS). In combination, these techniques revealed NPs are taken up via endocytic pathways before intracellular release of their cytotoxic cargo. As with other drug-carrying nanomaterials, these systems have potential as cellular delivery vehicles. However, high-resolution methods to track nanocarriers and their cargo at the micro- and nanoscale have been underutilized in general, limiting our understanding of their interactions with cells and tissues. We contend this type of combined optical and isotopic imaging strategy represents a powerful and potentially generalizable methodology for cellular tracking of nanocarriers and their cargo.
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Affiliation(s)
- Maria T. Proetto
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Craig J. Szymanski
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Zihua Zhu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Joseph P. Patterson
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Jacquelin K. Kammeyer
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Lizanne G. Nilewski
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Anthony M. Rush
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Nia C. Bell
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - James E. Evans
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Galya Orr
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Stephen B. Howell
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
| | - Nathan C. Gianneschi
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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