Approaching Mass Cytometry Translational Studies by Experimental and Data Curation Settings

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2024 Mar 25

PMID 38526795

Authors

Paulina Rybakowska

Marta E Alarcon-Riquelme

Concepcion Maranon

Affiliations

Soon will be listed here.

Abstract

Clinical studies are conducted to better understand the pathological mechanism of diseases and to find biomarkers associated with disease activity, drug response, or outcome prediction. Mass cytometry (MC) is a high-throughput single-cell technology that measures hundreds of cells per second with more than 40 markers per cell. Thus, it is a suitable tool for immune monitoring and biomarker discovery studies. Working in translational and clinical settings requires a careful experimental design to minimize, monitor, and correct the variations introduced during sample collection, preparation, acquisition, and analysis. In this review, we will focus on these important aspects of MC-related experiments and data curation in the context of translational clinical research projects.

Citing Articles

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Liu P, Pan Y, Chang H, Wang W, Fang Y, Xue X Brief Bioinform. 2024; 26(1).

PMID: 39656848 PMC: 11630031. DOI: 10.1093/bib/bbae633.

References

Oliveira J, Fleisher T . Molecular- and flow cytometry-based diagnosis of primary immunodeficiency disorders. Curr Allergy Asthma Rep. 2010; 10(6):460-7. DOI: 10.1007/s11882-010-0137-8. View

Shah N, Bhojwani D, August K, Baruchel A, Bertrand Y, Boklan J . Results from an international phase 2 study of the anti-CD22 immunotoxin moxetumomab pasudotox in relapsed or refractory childhood B-lineage acute lymphoblastic leukemia. Pediatr Blood Cancer. 2020; 67(5):e28112. PMC: 7485266. DOI: 10.1002/pbc.28112. View

Haddad R, Concha-Benavente F, Blumenschein Jr G, Fayette J, Guigay J, Colevas A . Nivolumab treatment beyond RECIST-defined progression in recurrent or metastatic squamous cell carcinoma of the head and neck in CheckMate 141: A subgroup analysis of a randomized phase 3 clinical trial. Cancer. 2019; 125(18):3208-3218. PMC: 6771504. DOI: 10.1002/cncr.32190. View

Hartmann F, Bernard-Valnet R, Queriault C, Mrdjen D, Weber L, Galli E . High-dimensional single-cell analysis reveals the immune signature of narcolepsy. J Exp Med. 2016; 213(12):2621-2633. PMC: 5110028. DOI: 10.1084/jem.20160897. View

Frei A, Bava F, Zunder E, Hsieh E, Chen S, Nolan G . Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods. 2016; 13(3):269-75. PMC: 4767631. DOI: 10.1038/nmeth.3742. View

Behbehani G, Bendall S, Clutter M, Fantl W, Nolan G . Single-cell mass cytometry adapted to measurements of the cell cycle. Cytometry A. 2012; 81(7):552-66. PMC: 3667754. DOI: 10.1002/cyto.a.22075. View

Cheung P, Vallania F, Warsinske H, Donato M, Schaffert S, Chang S . Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging. Cell. 2018; 173(6):1385-1397.e14. PMC: 5984186. DOI: 10.1016/j.cell.2018.03.079. View

Hartmann F, Mrdjen D, McCaffrey E, Glass D, Greenwald N, Bharadwaj A . Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol. 2020; 39(2):186-197. PMC: 7878201. DOI: 10.1038/s41587-020-0651-8. View

Levine L, Hiam-Galvez K, Marquez D, Tenvooren I, Madden M, Contreras D . Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8 T cells during the primary immune response. Immunity. 2021; 54(4):829-844.e5. PMC: 8046726. DOI: 10.1016/j.immuni.2021.02.018. View

10.

Koladiya A, Davis K . Advances in Clinical Mass Cytometry. Clin Lab Med. 2023; 43(3):507-519. DOI: 10.1016/j.cll.2023.05.004. View

11.

Iyer A, Hamers A, Pillai A . CyTOF for the Masses. Front Immunol. 2022; 13:815828. PMC: 9047695. DOI: 10.3389/fimmu.2022.815828. View

12.

Rahman A, Tordesillas L, Berin M . Heparin reduces nonspecific eosinophil staining artifacts in mass cytometry experiments. Cytometry A. 2016; 89(6):601-7. PMC: 4919163. DOI: 10.1002/cyto.a.22826. View

13.

Olsen L, Leipold M, Pedersen C, Maecker H . The anatomy of single cell mass cytometry data. Cytometry A. 2018; 95(2):156-172. DOI: 10.1002/cyto.a.23621. View

14.

Tricot S, Meyrand M, Sammicheli C, Elhmouzi-Younes J, Corneau A, Bertholet S . Evaluating the efficiency of isotope transmission for improved panel design and a comparison of the detection sensitivities of mass cytometer instruments. Cytometry A. 2015; 87(4):357-68. DOI: 10.1002/cyto.a.22648. View

15.

Takahashi C, Au-Yeung A, Fuh F, Ramirez-Montagut T, Bolen C, Mathews W . Mass cytometry panel optimization through the designed distribution of signal interference. Cytometry A. 2016; 91(1):39-47. DOI: 10.1002/cyto.a.22977. View

16.

Bendall S, Nolan G, Roederer M, Chattopadhyay P . A deep profiler's guide to cytometry. Trends Immunol. 2012; 33(7):323-32. PMC: 3383392. DOI: 10.1016/j.it.2012.02.010. View

17.

Lee B, Kelly G, Bradford S, Davila M, Guo X, Amir E . A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer. Cytometry A. 2019; 95(9):1019-1030. PMC: 6750971. DOI: 10.1002/cyto.a.23866. View

18.

Rybakowska P, Van Gassen S, Quintelier K, Saeys Y, Alarcon-Riquelme M, Maranon C . Data processing workflow for large-scale immune monitoring studies by mass cytometry. Comput Struct Biotechnol J. 2021; 19:3160-3175. PMC: 8188119. DOI: 10.1016/j.csbj.2021.05.032. View

19.

Das M . Multicenter Studies: Relevance, Design and Implementation. Indian Pediatr. 2022; 59(7):571-579. View

20.

Leipold M, Obermoser G, Fenwick C, Kleinstuber K, Rashidi N, McNevin J . Comparison of CyTOF assays across sites: Results of a six-center pilot study. J Immunol Methods. 2017; 453:37-43. PMC: 5805584. DOI: 10.1016/j.jim.2017.11.008. View