Single-Cell Transcriptome Profiling

Shapira, Guy; Shomron, Noam

doi:10.1007/978-1-0716-1103-6_16

Cited by 3 publications

(3 citation statements)

References 17 publications

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“…30 RNA sequencing has emerged as a powerful technique to interpret the molecular mechanisms of drugs. 31 HCA analysis revealed that the samples could be grouped into four categories based on transcriptome alterations, suggesting differential gene expression profiles among these groups. To investigate the latent regulatory mechanisms in the livers of NAFLD mice following different interventions, we selected 489 shared DEGs for GO and KEGG pathway analyses.…”

Section: ■ Discussionmentioning

confidence: 99%

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Liposome-Based Silibinin for Mitigating Nonalcoholic Fatty Liver Disease: Dual Effects via Parenteral and Intestinal Routes

Yan,

Zheng,

Wang

et al. 2023

ACS Pharmacol. Transl. Sci.

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Section: ■ Discussionmentioning

confidence: 99%

“…RNA sequencing has emerged as a powerful technique to interpret the molecular mechanisms of drugs . HCA analysis revealed that the samples could be grouped into four categories based on transcriptome alterations, suggesting differential gene expression profiles among these groups.…”

Section: Discussionmentioning

confidence: 99%

Liposome-Based Silibinin for Mitigating Nonalcoholic Fatty Liver Disease: Dual Effects via Parenteral and Intestinal Routes

Yan,

Zheng,

Wang

et al. 2023

ACS Pharmacol. Transl. Sci.

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“…In particular, WGS provides a uniform amplification process for assessing genomic sequences in target cells using an exon-trapping method ( 10 ). WTS is aimed at all transcripts and is especially suitable for GeneScan assessment of stem cells and early embryonic cells with high heterogeneity ( 11 ). Alternatively, epigenetic sequencing can be used to elucidate the unfolding roles of DNA methylation, histone modification and structural and regulatory chromatin loops in transcriptional heterogeneity ( 12 ).…”

Section: Overview Of Single-cell Sequencingmentioning

confidence: 99%

The Single-Cell Sequencing: A Dazzling Light Shining on the Dark Corner of Cancer

et al. 2021

Front. Oncol.

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Tumorigenesis refers to the process of clonal dysplasia that occurs due to the collapse of normal growth regulation in cells caused by the action of various carcinogenic factors. These “successful” tumor cells pass on the genetic templates to their generations in evolutionary terms, but they also constantly adapt to ever-changing host environments. A unique peculiarity known as intratumor heterogeneity (ITH) is extensively involved in tumor development, metastasis, chemoresistance, and immune escape. An understanding of ITH is urgently required to identify the diversity and complexity of the tumor microenvironment (TME), but achieving this understanding has been a challenge. Single-cell sequencing (SCS) is a powerful tool that can gauge the distribution of genomic sequences in a single cell and the genetic variability among tumor cells, which can improve the understanding of ITH. SCS provides fundamental ideas about existing diversity in specific TMEs, thus improving cancer diagnosis and prognosis prediction, as well as improving the monitoring of therapeutic response. Herein, we will discuss advances in SCS and review SCS application in tumors based on current evidence.

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Spatial metabolomics reveals glycogen as an actionable target for pulmonary fibrosis

et al. 2023

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Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high-dimensionality reduction/spatial clustering and histopathological annotation of matrix assisted laser desorption/ionization imaging datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesize that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed blunted N-linked glycan levels and nearly 90% reduction in endpoint fibrosis when compared to WT animals. Collectively, we provide conclusive evidence that lysosomal utilization of glycogen is required for pulmonary fibrosis progression. In summary, our study provides a roadmap to leverage spatial metabolomics to understand foundational biology in pulmonary diseases.

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Single-Cell Transcriptome Profiling

Cited by 3 publications

References 17 publications

Liposome-Based Silibinin for Mitigating Nonalcoholic Fatty Liver Disease: Dual Effects via Parenteral and Intestinal Routes

Liposome-Based Silibinin for Mitigating Nonalcoholic Fatty Liver Disease: Dual Effects via Parenteral and Intestinal Routes

The Single-Cell Sequencing: A Dazzling Light Shining on the Dark Corner of Cancer

Spatial metabolomics reveals glycogen as an actionable target for pulmonary fibrosis

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