Single-cell omics: A new direction for functional genetic research in human diseases and animal models

Kong, Siyuan; Li, Rongrong; Tian, Yunhan; Zhang, Yaqiu; Lu, Yuhui; Ou, Qiaoer; Gao, Peiwen; Li, Kui; Zhang, Yubo

doi:10.3389/fgene.2022.1100016

Cited by 16 publications

(9 citation statements)

References 206 publications

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“…( B ) Cell classification and 2D embedding from a PBMC sample of 10,000 input cells prepared with RevGel-seq were downsampled by raw read subsampling at a depth of 20,000 raw reads per cell on average. Post-processing was performed using Seurat 21 and automated cell classification was performed using the SingleR 22 algorithm based on the reference dataset MonacoImmuneData 23 . Unassigned cells had classification uncertainties that were considered too high according to the pruneScores method with default parameters.…”

Section: Resultsmentioning

confidence: 99%

“…Other investigations have focused on specific organs, often in relation to pathologies 16 , especially cancer, immunotherapy, and cardiovascular diseases 17 – 19 . Research has focused as well on development 20 , 21 , various forms of multiomics 22 , and spatial transcriptomics 23 . In addition, applications to plants are emerging 24 , highlighting single-nucleus (snRNA-seq) approaches 25 .…”

Section: Introductionmentioning

confidence: 99%

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RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

Komatsu¹,

Cico²,

Poncin³

et al. 2023

Sci Rep

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Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology optimized for samples of fresh cells. Complexes of one cell paired with one barcoded bead are stabilized by a chemical linker and dispersed in a hydrogel in the liquid state. Upon gelation on ice the complexes are immobilized and physically separated without requiring nanowells or droplets. Cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcoded beads for further processing with reverse transcription and preparation for cDNA sequencing. As a proof of concept, analysis of PBMC using RevGel-seq achieves results similar to microfluidic-based technologies when using the same original sample and the same data analysis software. In addition, a clinically relevant application of RevGel-seq is presented for pancreatic islet cells. Furthermore, characterizations carried out on cardiomyocytes demonstrate that the hydrogel technology readily accommodates very large cells. Standard analyses are in the 10,000-input cell range with the current gelation device, in order to satisfy common requirements for single-cell research. A convenient stopping point after two hours has been established by freezing at the cell lysis step, with full preservation of gene expression profiles. Overall, our results show that RevGel-seq represents an accessible and efficient instrument-free alternative, enabling flexibility in terms of experimental design and timing of sample processing, while providing broad coverage of cell types.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

Komatsu¹,

Cico²,

Poncin³

et al. 2023

Sci Rep

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“…Single-cell multi-omic technologies allow to sequence DNA, to obtain the RNA transcriptome and detect epigenomic events simultaneously within the same cell at low cost and high throughput. Single-cell proteomics and metabolomics profiling are possible too, although a concurrent multi-omic profiling combining these omics with DNA or RNA related omics is not yet available [ 75 ]. However, single-cell multi-omic technologies need development in epilepsy to understand genotype–phenotype interactions in single cells.…”

Section: Towards the Futurementioning

confidence: 99%

Steps to Improve Precision Medicine in Epilepsy

Balestrini,

Mei,

Sisodiya

et al. 2023

Mol Diagn Ther

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Precision medicine is an old concept, but it is not widely applied across human health conditions as yet. Numerous attempts have been made to apply precision medicine in epilepsy, this has been based on a better understanding of aetiological mechanisms and deconstructing disease into multiple biological subsets. The scope of precision medicine is to provide effective strategies for treating individual patients with specific agent(s) that are likely to work best based on the causal biological make-up. We provide an overview of the main applications of precision medicine in epilepsy, including the current limitations and pitfalls, and propose potential strategies for implementation and to achieve a higher rate of success in patient care. Such strategies include establishing a definition of precision medicine and its outcomes; learning from past experiences, from failures and from other fields (e.g. oncology); using appropriate precision medicine strategies (e.g. drug repurposing versus traditional drug discovery process); and using adequate methods to assess efficacy (e.g. randomised controlled trials versus alternative trial designs). Although the progress of diagnostic techniques now allows comprehensive characterisation of each individual epilepsy condition from a molecular, biological, structural and clinical perspective, there remain challenges in the integration of individual data in clinical practice to achieve effective applications of precision medicine in this domain.

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“…Hence, the main branches of omics techniques are known as genomics, epigenomics, transcriptomics, proteomics and metabolomics. The most advanced omics techniques include single cell omics and spatial omics, which allows to investigate the molecular events occurring at single cell resolution and to retain the spatial information [35,36]. There are also other advanced and upcoming sequencing-based omics, such as epitranscriptomics, epiproteomics and interactomics (DNA-RNA, RNA-RNA, RNA-protein, protein-protein, protein-metabolite), which give detailed information on the complex interactions and dynamics of regulation in a biological system [34].…”

Section: Introduction To Omics: Principles and Advancementsmentioning

confidence: 99%

Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome and Transcriptome in Health and Disease

Tisi,

Palaniappan,

Maccarrone

2023

Preprint

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Advanced genomics, transcriptomics and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids, and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research, the principles of genomics, transcriptomics and epigenomics, alongside their most advanced technologies (like single cell omics and spatial omics), which allows to investigate the molecular events that occur at single cell resolution retaining the spatial information.

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Single-cell omics: A new direction for functional genetic research in human diseases and animal models

Cited by 16 publications

References 206 publications

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding

Steps to Improve Precision Medicine in Epilepsy

Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome and Transcriptome in Health and Disease

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