Using Imaging Mass Cytometry to Define Cell Identities and Interactions in Human Tissues

Overview

Journal Front Physiol

Date 2022 Jan 10

PMID 35002783

Authors

Vijayakumar R Kakade

Marlene Weiss

Lloyd G Cantley

Affiliations

Soon will be listed here.

Abstract

In the evolving landscape of highly multiplexed imaging techniques that can be applied to study complex cellular microenvironments, this review characterizes the use of imaging mass cytometry (IMC) to study the human kidney. We provide technical details for antibody validation, cell segmentation, and data analysis specifically tailored to human kidney samples, and elaborate on phenotyping of kidney cell types and novel insights that IMC can provide regarding pathophysiological processes in the injured or diseased kidney. This review will provide the reader with the necessary background to understand both the power and the limitations of IMC and thus support better perception of how IMC analysis can improve our understanding of human disease pathogenesis and can be integrated with other technologies such as single cell sequencing and proteomics to provide spatial context to cellular data.

Citing Articles

Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements.

Sarkar S, Zheng X, Clair G, Kwon Y, You Y, Swensen A Trends Mol Med. 2024; 30(12):1137-1151.

PMID: 39152082 PMC: 11631641. DOI: 10.1016/j.molmed.2024.07.009.

Suborgan Level Quantitation of Proteins in Tissues Delivered by Polymeric Nanocarriers.

Agrohia D, Goswami R, Jantarat T, Cicek Y, Thongsukh K, Jeon T ACS Nano. 2024; 18(26):16808-16818.

PMID: 38870478 PMC: 11497159. DOI: 10.1021/acsnano.4c02344.

Development of a high dimensional imaging mass cytometry panel to investigate spatial organization of tissue microenvironment in formalin-fixed archival clinical tissues.

Tornaas S, Kleftogiannis D, Fromreide S, Smeland H, Aarstad H, Vintermyr O Heliyon. 2024; 10(10):e31191.

PMID: 38803925 PMC: 11128903. DOI: 10.1016/j.heliyon.2024.e31191.

Single nuclei transcriptomics delineates complex immune and kidney cell interactions contributing to kidney allograft fibrosis.

McDaniels J, Shetty A, Kuscu C, Kuscu C, Bardhi E, Rousselle T Kidney Int. 2023; 103(6):1077-1092.

PMID: 36863444 PMC: 10200746. DOI: 10.1016/j.kint.2023.02.018.

Navigating the cellular landscape in tissue: Recent advances in defining the pathogenesis of human disease.

Chen H, Palendira U, Feng C Comput Struct Biotechnol J. 2022; 20:5256-5263.

PMID: 36212528 PMC: 9519395. DOI: 10.1016/j.csbj.2022.09.005.

References

Rost S, Giltnane J, Bordeaux J, Hitzman C, Koeppen H, Liu S . Multiplexed ion beam imaging analysis for quantitation of protein expression in cancer tissue sections. Lab Invest. 2017; 97(8):992-1003. DOI: 10.1038/labinvest.2017.50. View

Singh N, Avigan Z, Kliegel J, Shuch B, Montgomery R, Moeckel G . Development of a 2-dimensional atlas of the human kidney with imaging mass cytometry. JCI Insight. 2019; 4(12). PMC: 6629112. DOI: 10.1172/jci.insight.129477. View

Berg S, Kutra D, Kroeger T, Straehle C, Kausler B, Haubold C . ilastik: interactive machine learning for (bio)image analysis. Nat Methods. 2019; 16(12):1226-1232. DOI: 10.1038/s41592-019-0582-9. View

Melms J, Biermann J, Huang H, Wang Y, Nair A, Tagore S . A molecular single-cell lung atlas of lethal COVID-19. Nature. 2021; 595(7865):114-119. PMC: 8814825. DOI: 10.1038/s41586-021-03569-1. View

Schulz D, Zanotelli V, Fischer J, Schapiro D, Engler S, Lun X . Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry. Cell Syst. 2018; 6(1):25-36.e5. PMC: 5791659. DOI: 10.1016/j.cels.2017.12.001. View

McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini B, Karhohs K . CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 2018; 16(7):e2005970. PMC: 6029841. DOI: 10.1371/journal.pbio.2005970. View

Zhang W, Parikh C . Biomarkers of Acute and Chronic Kidney Disease. Annu Rev Physiol. 2019; 81:309-333. PMC: 7879424. DOI: 10.1146/annurev-physiol-020518-114605. View

Garcia-Melchor E, Cafaro G, MacDonald L, Crowe L, Sood S, McLean M . Novel self-amplificatory loop between T cells and tenocytes as a driver of chronicity in tendon disease. Ann Rheum Dis. 2021; 80(8):1075-1085. PMC: 8292554. DOI: 10.1136/annrheumdis-2020-219335. View

Wu H, Malone A, Donnelly E, Kirita Y, Uchimura K, Ramakrishnan S . Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response. J Am Soc Nephrol. 2018; 29(8):2069-2080. PMC: 6065085. DOI: 10.1681/ASN.2018020125. View

10.

Wang C, Xu J, Wang S, Pan S, Zhang J, Han Y . Imaging Mass Cytometric Analysis of Postmortem Tissues Reveals Dysregulated Immune Cell and Cytokine Responses in Multiple Organs of COVID-19 Patients. Front Microbiol. 2021; 11:600989. PMC: 7785801. DOI: 10.3389/fmicb.2020.600989. View

11.

Kretzler M, Cohen C, Doran P, Henger A, Madden S, Grone E . Repuncturing the renal biopsy: strategies for molecular diagnosis in nephrology. J Am Soc Nephrol. 2002; 13(7):1961-72. DOI: 10.1097/01.asn.0000020390.29418.70. View

12.

Bodenmiller B . Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications. Cell Syst. 2016; 2(4):225-38. DOI: 10.1016/j.cels.2016.03.008. View

13.

Baharlou H, Canete N, Cunningham A, Harman A, Patrick E . Mass Cytometry Imaging for the Study of Human Diseases-Applications and Data Analysis Strategies. Front Immunol. 2019; 10:2657. PMC: 6868098. DOI: 10.3389/fimmu.2019.02657. View

14.

Lake B, Chen S, Hoshi M, Plongthongkum N, Salamon D, Knoten A . A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys. Nat Commun. 2019; 10(1):2832. PMC: 6597610. DOI: 10.1038/s41467-019-10861-2. View

15.

Guo N, van Unen V, Ijsselsteijn M, Ouboter L, van der Meulen A, Chuva de Sousa Lopes S . A 34-Marker Panel for Imaging Mass Cytometric Analysis of Human Snap-Frozen Tissue. Front Immunol. 2020; 11:1466. PMC: 7381123. DOI: 10.3389/fimmu.2020.01466. View

16.

Lehmann M, Allers K, Heldt C, Meinhardt J, Schmidt F, Rodriguez-Sillke Y . Human small intestinal infection by SARS-CoV-2 is characterized by a mucosal infiltration with activated CD8 T cells. Mucosal Immunol. 2021; 14(6):1381-1392. PMC: 8379580. DOI: 10.1038/s41385-021-00437-z. View

17.

Avigan Z, Singh N, Kliegel J, Weiss M, Moeckel G, Cantley L . Tubular Cell Dropout in Preimplantation Deceased Donor Biopsies as a Predictor of Delayed Graft Function. Transplant Direct. 2021; 7(7):e716. PMC: 8384397. DOI: 10.1097/TXD.0000000000001168. View

18.

Damond N, Engler S, Zanotelli V, Schapiro D, Wasserfall C, Kusmartseva I . A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry. Cell Metab. 2019; 29(3):755-768.e5. PMC: 6821395. DOI: 10.1016/j.cmet.2018.11.014. View

19.

Hartmann F, Bendall S . Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nat Rev Rheumatol. 2020; 16(2):87-99. PMC: 7232872. DOI: 10.1038/s41584-019-0338-z. View

20.

Wang Y, Traum D, Schug J, Gao L, Liu C, Atkinson M . Multiplexed In Situ Imaging Mass Cytometry Analysis of the Human Endocrine Pancreas and Immune System in Type 1 Diabetes. Cell Metab. 2019; 29(3):769-783.e4. PMC: 6436557. DOI: 10.1016/j.cmet.2019.01.003. View