Single Cell Metabolomics: A Future Tool to Unmask Cellular Heterogeneity and Virus-Host Interaction in Context of Emerging Viral Diseases

Kumar, Rajesh; Ghosh, Mayukh; Kumar, Sandeep; Prasad, Minakshi

doi:10.3389/fmicb.2020.01152

Cited by 44 publications

(26 citation statements)

References 139 publications

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“…These studies have also revealed lipid signaling between beige adipocytes and resident macrophages that regulates the thermogenic response [ 84 , 87 ]. The advent of single cell metabolomics coupled with cell sorting will enable the exploration of the lipid composition of individual subtypes of beige adipocytes [ 88 ].…”

Section: Perspectivesmentioning

confidence: 99%

Mitochondrial Lipid Signaling and Adaptive Thermogenesis

et al. 2021

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Thermogenesis is an energy demanding process by which endotherms produce heat to maintain their body temperature in response to cold exposure. Mitochondria in the brown and beige adipocytes play a key role in thermogenesis, as the site for uncoupling protein 1 (UCP1), which allows for the diffusion of protons through the mitochondrial inner membrane to produce heat. To support this energy demanding process, the mitochondria in brown and beige adipocytes increase oxidation of glucose, amino acids, and lipids. This review article explores the various mitochondria-produced and processed lipids that regulate thermogenesis including cardiolipins, free fatty acids, and acylcarnitines. These lipids play a number of roles in thermogenic adipose tissue including structural support of UCP1, transcriptional regulation, fuel source, and activation of cell signaling cascades.

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Section: Perspectivesmentioning

confidence: 99%

Mitochondrial Lipid Signaling and Adaptive Thermogenesis

et al. 2021

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“…New technologies are emerging, such as a simultaneous high-throughput method for the measurement of chromatin accessibility and mRNA counts (SHARE-seq) in single cells [ 131 ], expansion sequencing (ExSeq) for spatially accurate in situ RNA sequencing of thousands of genes in intact tissue [ 132 , 133 , 134 ], and improved in vitro lung models for respiratory viruses [ 135 , 136 ]. Progress is also being made in multi-omics analyses of single cells [ 137 ], as well as single-cell metabolomics profiling [ 138 ].…”

Section: Discussionmentioning

confidence: 99%

Virus Infection Variability by Single-Cell Profiling

Suomalainen

Greber

2021

Viruses

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Cell-to-cell variability of infection has long been known, yet it has remained one of the least understood phenomena in infection research. It impacts on disease onset and development, yet only recently underlying mechanisms have been studied in clonal cell cultures by single-virion immunofluorescence microscopy and flow cytometry. In this review, we showcase how single-cell RNA sequencing (scRNA-seq), single-molecule RNA-fluorescence in situ hybridization (FISH), and copper(I)-catalyzed azide-alkyne cycloaddition (click) with alkynyl-tagged viral genomes dissect infection variability in human and mouse cells. We show how the combined use of scRNA-FISH and click-chemistry reveals highly variable onsets of adenoviral gene expression, and how single live cell plaques reveal lytic and nonlytic adenovirus transmissions. The review highlights how scRNA-seq profiling and scRNA-FISH of coxsackie, influenza, dengue, zika, and herpes simplex virus infections uncover transcriptional variability, and how the host interferon response tunes influenza and sendai virus infections. We introduce the concept of “cell state” in infection variability, and conclude with advances by single-cell simultaneous measurements of chromatin accessibility and mRNA counts at high-throughput. Such technology will further dissect the sequence of events in virus infection and pathology, and better characterize the genetic and genomic stability of viruses, cell autonomous innate immune responses, and mechanisms of tissue injury.

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“…We refer the reader to one of the many readily available review articles focusing on the various -omics approaches. [283][284][285][286] We conclude this section by providing perspectives on how hydrogel encapsulation may be able to benefit single-cell analyses.…”

Section: Single-cell -Omicsmentioning

confidence: 99%

Single‐Cell Microgels for Diagnostics and Therapeutics

Dubay

Urban

Darling

2021

Adv Funct Materials

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Cell encapsulation within hydrogel droplets is transforming what is feasible in multiple fields of biomedical science such as tissue engineering and regenerative medicine, in vitro modeling, and cell-based therapies. Recent advances have allowed researchers to miniaturize material encapsulation complexes down to single-cell scales, where each complex, termed a singlecell microgel, contains only one cell surrounded by a hydrogel matrix while remaining <100 μm in size. With this achievement, studies requiring singlecell resolution are now possible, similar to those done using liquid droplet encapsulation. Of particular note, applications involving long-term in vitro cultures, modular bioinks, high-throughput screenings, and formation of 3D cellular microenvironments can be tuned independently to suit the needs of individual cells and experimental goals. In this progress report, an overview of established materials and techniques used to fabricate single-cell microgels, as well as insight into potential alternatives is provided. This focused review is concluded by discussing applications that have already benefited from single-cell microgel technologies, as well as prospective applications on the cusp of achieving important new capabilities.

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Single Cell Metabolomics: A Future Tool to Unmask Cellular Heterogeneity and Virus-Host Interaction in Context of Emerging Viral Diseases

Cited by 44 publications

References 139 publications

Mitochondrial Lipid Signaling and Adaptive Thermogenesis

Mitochondrial Lipid Signaling and Adaptive Thermogenesis

Virus Infection Variability by Single-Cell Profiling

Single‐Cell Microgels for Diagnostics and Therapeutics

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