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Lopes MG, Recktenwald SM, Simionato G, Eichler H, Wagner C, Quint S, Kaestner L. Big Data in Transfusion Medicine and Artificial Intelligence Analysis for Red Blood Cell Quality Control. Transfus Med Hemother 2023; 50:163-173. [PMID: 37408647 PMCID: PMC10319094 DOI: 10.1159/000530458] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/27/2023] [Indexed: 07/07/2023] Open
Abstract
Background "Artificial intelligence" and "big data" increasingly take the step from just being interesting concepts to being relevant or even part of our lives. This general statement holds also true for transfusion medicine. Besides all advancements in transfusion medicine, there is not yet an established red blood cell quality measure, which is generally applied. Summary We highlight the usefulness of big data in transfusion medicine. Furthermore, we emphasize in the example of quality control of red blood cell units the application of artificial intelligence. Key Messages A variety of concepts making use of big data and artificial intelligence are readily available but still await to be implemented into any clinical routine. For the quality control of red blood cell units, clinical validation is still required.
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Affiliation(s)
- Marcelle G.M. Lopes
- Experimental Physics, Saarland University, Saarbrücken, Germany
- Cysmic GmbH, Saarbrücken, Germany
| | | | - Greta Simionato
- Experimental Physics, Saarland University, Saarbrücken, Germany
- Institute for Clinical and Experimental Surgery, Saarland University, Saarbrücken, Germany
| | - Hermann Eichler
- Institute of Clinical Hemostaseology and Transfusion Medicine, Saarland University, Saarbrücken, Germany
| | - Christian Wagner
- Experimental Physics, Saarland University, Saarbrücken, Germany
- Physics and Materials Science Research Unit, University of Luxembourg, Luxembourg City, Luxembourg
| | | | - Lars Kaestner
- Experimental Physics, Saarland University, Saarbrücken, Germany
- Theoretical Medicine and Biosciences, Saarland University, Saarbrücken, Germany
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Ma J, Tran G, Wan AMD, Young EWK, Kumacheva E, Iscove NN, Zandstra PW. Microdroplet-based one-step RT-PCR for ultrahigh throughput single-cell multiplex gene expression analysis and rare cell detection. Sci Rep 2021; 11:6777. [PMID: 33762663 PMCID: PMC7990930 DOI: 10.1038/s41598-021-86087-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023] Open
Abstract
Gene expression analysis of individual cells enables characterization of heterogeneous and rare cell populations, yet widespread implementation of existing single-cell gene analysis techniques has been hindered due to limitations in scale, ease, and cost. Here, we present a novel microdroplet-based, one-step reverse-transcriptase polymerase chain reaction (RT-PCR) platform and demonstrate the detection of three targets simultaneously in over 100,000 single cells in a single experiment with a rapid read-out. Our customized reagent cocktail incorporates the bacteriophage T7 gene 2.5 protein to overcome cell lysate-mediated inhibition and allows for one-step RT-PCR of single cells encapsulated in nanoliter droplets. Fluorescent signals indicative of gene expressions are analyzed using a probabilistic deconvolution method to account for ambient RNA and cell doublets and produce single-cell gene signature profiles, as well as predict cell frequencies within heterogeneous samples. We also developed a simulation model to guide experimental design and optimize the accuracy and precision of the assay. Using mixtures of in vitro transcripts and murine cell lines, we demonstrated the detection of single RNA molecules and rare cell populations at a frequency of 0.1%. This low cost, sensitive, and adaptable technique will provide an accessible platform for high throughput single-cell analysis and enable a wide range of research and clinical applications.
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Affiliation(s)
- Jennifer Ma
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Gary Tran
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alwin M D Wan
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
| | - Edmond W K Young
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
| | - Eugenia Kumacheva
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Norman N Iscove
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Sturgess KHM, Calero-Nieto FJ, Göttgens B, Wilson NK. Single-Cell Analysis of Hematopoietic Stem Cells. Methods Mol Biol 2021; 2308:301-337. [PMID: 34057731 DOI: 10.1007/978-1-0716-1425-9_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The study of hematopoiesis has been revolutionized in recent years by the application of single-cell RNA sequencing technologies. The technique coupled with rapidly developing bioinformatic analysis has provided great insight into the cell type compositions of many populations previously defined by their cell surface phenotype. Moreover, transcriptomic information enables the identification of individual molecules and pathways which define novel cell populations and their transitions including cell lineage decisions. Combining single-cell transcriptional profiling with molecular perturbations allows functional analysis of individual factors in gene regulatory networks and better understanding of the earliest stages of malignant transformation. In this chapter we describe a comprehensive protocol for scRNA-Seq analysis of the mouse bone marrow, using both plate-based (low throughput) and droplet-based (high throughput) methods. The protocol includes instructions for sample preparation, an antibody panel for flow cytometric purification of hematopoietic progenitors with index sorting for plate-based analysis or in bulk for droplet-based methods. The plate-based protocol described in this chapter is a combination of the Smart-Seq2 and mcSCRB-Seq protocols, optimized in our laboratory. It utilizes off-the-shelf reagents for cDNA preparation, is amenable to automation using a liquid handler, and takes 4 days from preparation of the cells for sorting to producing a sequencing-ready library. The droplet-based method (using for instance the 10× Genomics platform) relies on the manufacturer's user guide and commercial reagents, and takes 3 days from isolation of the cells to the production of a library ready for sequencing.
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Affiliation(s)
- Katherine H M Sturgess
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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Sommarin MNE, Warfvinge R, Safi F, Karlsson G. A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations. J Vis Exp 2018. [PMID: 30417863 DOI: 10.3791/57831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Immunophenotypic characterization and molecular analysis have long been used to delineate heterogeneity and define distinct cell populations. FACS is inherently a single-cell assay, however prior to molecular analysis, the target cells are often prospectively isolated in bulk, thereby losing single-cell resolution. Single-cell gene expression analysis provides a means to understand molecular differences between individual cells in heterogeneous cell populations. In bulk cell analysis an overrepresentation of a distinct cell type results in biases and occlusions of signals from rare cells with biological importance. By utilizing FACS index sorting coupled to single-cell gene expression analysis, populations can be investigated without the loss of single-cell resolution while cells with intermediate cell surface marker expression are also captured, enabling evaluation of the relevance of continuous surface marker expression. Here, we describe an approach that combines single-cell reverse transcription quantitative PCR (RT-qPCR) and FACS index sorting to simultaneously characterize the molecular and immunophenotypic heterogeneity within cell populations. In contrast to single-cell RNA sequencing methods, the use of qPCR with specific target amplification allows for robust measurements of low-abundance transcripts with fewer dropouts, while it is not confounded by issues related to cell-to-cell variations in read depth. Moreover, by directly index-sorting single-cells into lysis buffer this method, allows for cDNA synthesis and specific target pre-amplification to be performed in one step as well as for correlation of subsequently derived molecular signatures with cell surface marker expression. The described approach has been developed to investigate hematopoietic single-cells, but have also been used successfully on other cell types. In conclusion, the approach described herein allows for sensitive measurement of mRNA expression for a panel of pre-selected genes with the possibility to develop protocols for subsequent prospective isolation of molecularly distinct subpopulations.
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Affiliation(s)
| | - Rebecca Warfvinge
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University
| | - Fatemeh Safi
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University
| | - Göran Karlsson
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University;
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Phetsouphanh C, Zaunders JJ, Kelleher AD. Detecting Antigen-Specific T Cell Responses: From Bulk Populations to Single Cells. Int J Mol Sci 2015; 16:18878-93. [PMID: 26274954 PMCID: PMC4581277 DOI: 10.3390/ijms160818878] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 12/18/2022] Open
Abstract
A new generation of sensitive T cell-based assays facilitates the direct quantitation and characterization of antigen-specific T cell responses. Single-cell analyses have focused on measuring the quality and breadth of a response. Accumulating data from these studies demonstrate that there is considerable, previously-unrecognized, heterogeneity. Standard assays, such as the ICS, are often insufficient for characterization of rare subsets of cells. Enhanced flow cytometry with imaging capabilities enables the determination of cell morphology, as well as the spatial localization of the protein molecules within a single cell. Advances in both microfluidics and digital PCR have improved the efficiency of single-cell sorting and allowed multiplexed gene detection at the single-cell level. Delving further into the transcriptome of single-cells using RNA-seq is likely to reveal the fine-specificity of cellular events such as alternative splicing (i.e., splice variants) and allele-specific expression, and will also define the roles of new genes. Finally, detailed analysis of clonally related antigen-specific T cells using single-cell TCR RNA-seq will provide information on pathways of differentiation of memory T cells. With these state of the art technologies the transcriptomics and genomics of Ag-specific T cells can be more definitively elucidated.
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Affiliation(s)
| | - John James Zaunders
- Kirby Institute, University of New South Wales, 2031 Sydney, Australia.
- Centre for Applied Medical Research, St. Vincent's Hospital, 2010 Sydney, Australia.
| | - Anthony Dominic Kelleher
- Kirby Institute, University of New South Wales, 2031 Sydney, Australia.
- Centre for Applied Medical Research, St. Vincent's Hospital, 2010 Sydney, Australia.
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Pina C, Teles J, Fugazza C, May G, Wang D, Guo Y, Soneji S, Brown J, Edén P, Ohlsson M, Peterson C, Enver T. Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis. Cell Rep 2015; 11:1503-10. [PMID: 26051941 PMCID: PMC4528262 DOI: 10.1016/j.celrep.2015.05.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 04/02/2015] [Accepted: 05/10/2015] [Indexed: 10/29/2022] Open
Abstract
We explore cell heterogeneity during spontaneous and transcription-factor-driven commitment for network inference in hematopoiesis. Since individual genes display discrete OFF states or a distribution of ON levels, we compute and combine pairwise gene associations from binary and continuous components of gene expression in single cells. Ddit3 emerges as a regulatory node with positive linkage to erythroid regulators and negative association with myeloid determinants. Ddit3 loss impairs erythroid colony output from multipotent cells, while forcing Ddit3 in granulo-monocytic progenitors (GMPs) enhances self-renewal and impedes differentiation. Network analysis of Ddit3-transduced GMPs reveals uncoupling of myeloid networks and strengthening of erythroid linkages. RNA sequencing suggests that Ddit3 acts through development or stabilization of a precursor upstream of GMPs with inherent Meg-E potential. The enrichment of Gata2 target genes in Ddit3-dependent transcriptional responses suggests that Ddit3 functions in an erythroid transcriptional network nucleated by Gata2.
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Affiliation(s)
- Cristina Pina
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK
| | - José Teles
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK; Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, 223 62 Lund, Sweden
| | - Cristina Fugazza
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK
| | - Gillian May
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK
| | - Dapeng Wang
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK
| | - Yanping Guo
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK
| | - Shamit Soneji
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK
| | - John Brown
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK
| | - Patrik Edén
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, 223 62 Lund, Sweden
| | - Mattias Ohlsson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, 223 62 Lund, Sweden
| | - Carsten Peterson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, 223 62 Lund, Sweden
| | - Tariq Enver
- Stem Cell Laboratory, UCL Cancer Institute, University College London, London W1CE 6BT, UK.
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Ruden DM, Cingolani PE, Sen A, Qu W, Wang L, Senut MC, Garfinkel MD, Sollars VE, Lu X. Epigenetics as an answer to Darwin's "special difficulty," Part 2: natural selection of metastable epialleles in honeybee castes. Front Genet 2015; 6:60. [PMID: 25759717 PMCID: PMC4338822 DOI: 10.3389/fgene.2015.00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/08/2015] [Indexed: 11/15/2022] Open
Abstract
In a recent perspective in this journal, Herb (2014) discussed how epigenetics is a possible mechanism to circumvent Charles Darwin's "special difficulty" in using natural selection to explain the existence of the sterile-fertile dimorphism in eusocial insects. Darwin's classic book "On the Origin of Species by Means of Natural Selection" explains how natural selection of the fittest individuals in a population can allow a species to adapt to a novel or changing environment. However, in bees and other eusocial insects, such as ants and termites, there exist two or more castes of genetically similar females, from fertile queens to multiple sub-castes of sterile workers, with vastly different phenotypes, lifespans, and behaviors. This necessitates the selection of groups (or kin) rather than individuals in the evolution of honeybee hives, but group and kin selection theories of evolution are controversial and mechanistically uncertain. Also, group selection would seem to be prohibitively inefficient because the effective population size of a colony is reduced from thousands to a single breeding queen. In this follow-up perspective, we elaborate on possible mechanisms for how a combination of both epigenetics, specifically, the selection of metastable epialleles, and genetics, the selection of mutations generated by the selected metastable epialleles, allows for a combined means for selection amongst the fertile members of a species to increase colony fitness. This "intra-caste evolution" hypothesis is a variation of the epigenetic directed genetic error hypothesis, which proposes that selected metastable epialleles increase genetic variability by directing mutations specifically to the epialleles. Natural selection of random metastable epialleles followed by a second round of natural selection of random mutations generated by the metastable epialleles would allow a way around the small effective population size of eusocial insects.
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Affiliation(s)
- Douglas M. Ruden
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development and Center for Urban Responses to Environmental Stressors, Institute of Environmental Health Sciences, Wayne State UniversityDetroit, MI, USA
| | - Pablo E. Cingolani
- School of Computer Science and Genome Quebec Innovation Centre, McGill UniversityMontreal, QC, Canada
| | - Arko Sen
- Department of Pharmacology, Wayne State UniversityDetroit, MI, USA
| | - Wen Qu
- Department of Pharmacology, Wayne State UniversityDetroit, MI, USA
| | - Luan Wang
- Institute of Environmental Health Sciences, Wayne State UniversityDetroit, MI, USA
| | - Marie-Claude Senut
- Institute of Environmental Health Sciences, Wayne State UniversityDetroit, MI, USA
| | - Mark D. Garfinkel
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Vincent E. Sollars
- Department of Biochemistry and Microbiology, Joan C. Edwards School of Medicine, Marshall UniversityHuntington, WV, USA
| | - Xiangyi Lu
- Institute of Environmental Health Sciences, Wayne State UniversityDetroit, MI, USA
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