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For: Neumann EK, Patterson NH, Rivera ES, Allen JL, Brewer M, deCaestecker MP, Caprioli RM, Fogo AB, Spraggins JM. Highly multiplexed immunofluorescence of the human kidney using co-detection by indexing. Kidney Int 2022;101:137-143. [PMID: 34619231 PMCID: PMC8741652 DOI: 10.1016/j.kint.2021.08.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 01/03/2023]
Number Cited by Other Article(s)
1
Gorman BL, Shafer CC, Ragi N, Sharma K, Neumann EK, Anderton CR. Imaging and spatially resolved mass spectrometry applications in nephrology. Nat Rev Nephrol 2025;21:399-416. [PMID: 40148534 DOI: 10.1038/s41581-025-00946-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2025] [Indexed: 03/29/2025]
2
Kirchgaessner R, Watson C, Creason A, Keutler K, Goecks J. Imputing single-cell protein abundance in multiplex tissue imaging. Nat Commun 2025;16:4747. [PMID: 40404617 PMCID: PMC12098973 DOI: 10.1038/s41467-025-59788-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/06/2025] [Indexed: 05/24/2025]  Open
3
Veličković D, Purkerson J, Bhotika H, Huyck H, Clair G, Pryhuber GS, Anderton C. Integrating N-glycan and CODEX imaging reveal cell-specific protein glycosylation in healthy human lung. Mol Omics 2025. [PMID: 40392055 PMCID: PMC12090982 DOI: 10.1039/d4mo00230j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 05/11/2025] [Indexed: 05/22/2025]
4
Lee Y, Lee M, Shin Y, Kim K, Kim T. Spatial Omics in Clinical Research: A Comprehensive Review of Technologies and Guidelines for Applications. Int J Mol Sci 2025;26:3949. [PMID: 40362187 PMCID: PMC12071594 DOI: 10.3390/ijms26093949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2025] [Revised: 04/17/2025] [Accepted: 04/17/2025] [Indexed: 05/15/2025]  Open
5
Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Veličković M, Williams SM, Moore RJ, Bramer LM, Veličković D, Zhu Y, Zhou M, Paša-Tolić L. Spatial top-down proteomics for the functional characterization of human kidney. Clin Proteomics 2025;22:9. [PMID: 40045235 PMCID: PMC11881370 DOI: 10.1186/s12014-025-09531-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 09/04/2024] [Indexed: 03/09/2025]  Open
6
Whittle JR, Kriel J, Fatunla OE, Lu T, Moffet JJD, Spiteri M, Best SA, Freytag S. Spatial omics shed light on the tumour organisation of glioblastoma. Semin Cell Dev Biol 2025;167:1-9. [PMID: 39787997 DOI: 10.1016/j.semcdb.2024.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 10/23/2024] [Accepted: 12/30/2024] [Indexed: 01/12/2025]
7
Esselman AB, Moser FA, Tideman LEM, Migas LG, Djambazova KV, Colley ME, Pingry EL, Patterson NH, Farrow MA, Yang H, Fogo AB, de Caestecker M, Van de Plas R, Spraggins JM. In situ molecular profiles of glomerular cells by integrated imaging mass spectrometry and multiplexed immunofluorescence microscopy. Kidney Int 2025;107:332-337. [PMID: 39571907 DOI: 10.1016/j.kint.2024.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 09/13/2024] [Accepted: 11/11/2024] [Indexed: 12/07/2024]
8
Vanderschoot KA, Bender KJ, De Caro CM, Steineman KA, Neumann EK. Multimodal Mass Spectrometry Imaging in Atlas Building: A Review. Semin Nephrol 2024;44:151578. [PMID: 40246671 DOI: 10.1016/j.semnephrol.2025.151578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2025]
9
Tasca P, van den Berg BM, Rabelink TJ, Wang G, Heijs B, van Kooten C, de Vries APJ, Kers J. Application of spatial-omics to the classification of kidney biopsy samples in transplantation. Nat Rev Nephrol 2024;20:755-766. [PMID: 38965417 DOI: 10.1038/s41581-024-00861-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2024] [Indexed: 07/06/2024]
10
Gorman BL, Lukowski JK. Spatial Metabolomics and Lipidomics in Kidney Disease. Semin Nephrol 2024;44:151582. [PMID: 40234137 DOI: 10.1016/j.semnephrol.2025.151582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
11
Kaur H, Heiser CN, McKinley ET, Ventura-Antunes L, Harris CR, Roland JT, Farrow MA, Selden HJ, Pingry EL, Moore JF, Ehrlich LIR, Shrubsole MJ, Spraggins JM, Coffey RJ, Lau KS, Vandekar SN. Consensus tissue domain detection in spatial omics data using multiplex image labeling with regional morphology (MILWRM). Commun Biol 2024;7:1295. [PMID: 39478141 PMCID: PMC11525554 DOI: 10.1038/s42003-024-06281-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/02/2024] [Indexed: 11/02/2024]  Open
12
Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y. Proteome-Scale Tissue Mapping Using Mass Spectrometry Based on Label-Free and Multiplexed Workflows. Mol Cell Proteomics 2024;23:100841. [PMID: 39307423 PMCID: PMC11541776 DOI: 10.1016/j.mcpro.2024.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 08/19/2024] [Accepted: 08/23/2024] [Indexed: 09/25/2024]  Open
13
Kondo A, McGrady M, Nallapothula D, Ali H, Trevino AE, Lam A, Preska R, D'Angio HB, Wu Z, Lopez LN, Badhesha HK, Vargas CR, Ramesh A, Wiegley N, Han SS, Dall'Era M, Jen KY, Mayer AT, Afkarian M. Spatial proteomics of human diabetic kidney disease, from health to class III. Diabetologia 2024;67:1962-1979. [PMID: 39037603 DOI: 10.1007/s00125-024-06210-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/30/2024] [Indexed: 07/23/2024]
14
Kirchgaessner R, Watson C, Creason A, Keutler K, Goecks J. Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.05.570058. [PMID: 38106203 PMCID: PMC10723289 DOI: 10.1101/2023.12.05.570058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
15
Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y. Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583367. [PMID: 38496682 PMCID: PMC10942300 DOI: 10.1101/2024.03.04.583367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
16
Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Veličković M, Williams SM, Moore RJ, Bramer LM, Veličković D, Zhu Y, Zhou M, Paša-Tolić L. Spatial top-down proteomics for the functional characterization of human kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580062. [PMID: 38405958 PMCID: PMC10888776 DOI: 10.1101/2024.02.13.580062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
17
Brewer M, Migas LG, Clouthier KA, Allen JL, Anderson DM, Pingry E, Farrow M, Quardokus EM, Spraggins JM, Van de Plas R, de Caestecker MP. Validation of an organ mapping antibody panel for cyclical immunofluorescence microscopy on normal human kidneys. Am J Physiol Renal Physiol 2024;327:F91-F102. [PMID: 38721662 PMCID: PMC11390132 DOI: 10.1152/ajprenal.00426.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 06/21/2024]  Open
18
Asowata EO, Romoli S, Sargeant R, Tan JY, Hoffmann S, Huang MM, Mahbubani KT, Krause FN, Jachimowicz D, Agren R, Koulman A, Jenkins B, Musial B, Griffin JL, Soderberg M, Ling S, Hansen PBL, Saeb-Parsy K, Woollard KJ. Multi-omics and imaging mass cytometry characterization of human kidneys to identify pathways and phenotypes associated with impaired kidney function. Kidney Int 2024;106:85-97. [PMID: 38431215 DOI: 10.1016/j.kint.2024.01.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
19
Kozakowski N. The histomorphology of the senescent kidney - the clinical relevance of specimen and biopsy findings in the elderly native kidneys. Curr Opin Urol 2024;34:170-175. [PMID: 38410848 DOI: 10.1097/mou.0000000000001164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
20
Alexander MP, Zaidi M, Larson N, Mullan A, Pavelko KD, Stegall MD, Bentall A, Wouters BG, McKee T, Taner T. Exploring the single-cell immune landscape of kidney allograft inflammation using imaging mass cytometry. Am J Transplant 2024;24:549-563. [PMID: 37979921 DOI: 10.1016/j.ajt.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/01/2023] [Accepted: 11/11/2023] [Indexed: 11/20/2023]
21
Abraham MJ, Goncalves C, McCallum P, Gupta V, Preston SEJ, Huang F, Chou H, Gagnon N, Johnson NA, Miller WH, Mann KK, Del Rincon SV. Tunable PhenoCycler imaging of the murine pre-clinical tumour microenvironments. Cell Biosci 2024;14:19. [PMID: 38311785 PMCID: PMC10840224 DOI: 10.1186/s13578-024-01199-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024]  Open
22
Schnuelle P. Renal Biopsy for Diagnosis in Kidney Disease: Indication, Technique, and Safety. J Clin Med 2023;12:6424. [PMID: 37835066 PMCID: PMC10573674 DOI: 10.3390/jcm12196424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]  Open
23
Marshall CR, Farrow MA, Djambazova KV, Spraggins JM. Untangling Alzheimer's disease with spatial multi-omics: a brief review. Front Aging Neurosci 2023;15:1150512. [PMID: 37533766 PMCID: PMC10390637 DOI: 10.3389/fnagi.2023.1150512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/13/2023] [Indexed: 08/04/2023]  Open
24
Border S, Lucarelli N, Eadon MT, El-Achkar TM, Jain S, Sarder P. Computational Pathology Fusing Spatial Technologies. Clin J Am Soc Nephrol 2023;18:675-677. [PMID: 36913267 PMCID: PMC10278855 DOI: 10.2215/cjn.0000000000000146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023]
25
Yang M, Unsihuay D, Hu H, Meke FN, Qu Z, Zhang ZY, Laskin J. Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. Anal Chem 2023;95:5214-5222. [PMID: 36917636 PMCID: PMC11330692 DOI: 10.1021/acs.analchem.2c04795] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
26
Barbetta A, Rocque B, Sarode D, Bartlett JA, Emamaullee J. Revisiting transplant immunology through the lens of single-cell technologies. Semin Immunopathol 2023;45:91-109. [PMID: 35980400 PMCID: PMC9386203 DOI: 10.1007/s00281-022-00958-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/06/2022] [Indexed: 11/03/2022]
27
Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL. Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. SCIENCE ADVANCES 2022;8:eabp9929. [PMID: 35947651 PMCID: PMC9365283 DOI: 10.1126/sciadv.abp9929] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/24/2022] [Indexed: 05/25/2023]
28
Santoriello D, Nasr SH. Novel approaches beyond standard immunofluorescence for kidney biopsies. Curr Opin Nephrol Hypertens 2022;31:221-227. [PMID: 35256574 DOI: 10.1097/mnh.0000000000000783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
29
El-Achkar TM, Winfree S, Talukder N, Barwinska D, Ferkowicz MJ, Al Hasan M. Tissue Cytometry With Machine Learning in Kidney: From Small Specimens to Big Data. Front Physiol 2022;13:832457. [PMID: 35309077 PMCID: PMC8931540 DOI: 10.3389/fphys.2022.832457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/28/2022] [Indexed: 12/19/2022]  Open
30
Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods 2022;19:284-295. [PMID: 34811556 PMCID: PMC9264278 DOI: 10.1038/s41592-021-01316-y] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
31
Kruse ARS, Spraggins JM. Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. Front Physiol 2022;13:837773. [PMID: 35222094 PMCID: PMC8874197 DOI: 10.3389/fphys.2022.837773] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 02/06/2023]  Open
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