A human adipose tissue cell-type transcriptome atlas

Norreen-Thorsen, M; Struck, E; Öling, S; Zwahlén, Martin; Feilitzen, Kalle von; Odeberg, Jacob; Lindskog, Cecilia; Pontén, Fredrik; Uhlén, Mathias; Dusart, Philip; Butler, Lynn M.

doi:10.1016/j.celrep.2022.111046

Cited by 42 publications

(46 citation statements)

References 97 publications

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“…Yet another recent section addresses Adipose tissues. 78 In addition to the updates to the HPA database, the HPA workflow and antibodies have been utilized for several major research studies, including several projects linked to the COVID-19 pandemics 79−82 and efforts for advanced imaging. One example is 3D imaging of sympathetic innervations, leading to further understanding of nonalcoholic fatty liver disease.…”

Section: ■ Highlights From the Antibody Pillar/human Protein Atlasmentioning

confidence: 99%

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

et al. 2022

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The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".

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Section: ■ Highlights From the Antibody Pillar/human Protein Atlasmentioning

confidence: 99%

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

et al. 2022

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“…Differences between this study and previous studies could have arisen due to the fact that a greater number of healthy nuclei was analysed in our study or due to the differences in transcriptomics methods (single cell vs single nucleus approaches). While single cell transcriptomics generally capture more RNA per cell, including stable transcripts in the cytoplasm that might not be present in the nucleus, single nucleus transcriptomics enables the capture of a wider variety of cells, including cells that are hard to capture with single cell techniques due to the buoyancy or larger size of cells[26, 27].…”

Section: Discussionmentioning

confidence: 99%

Single nucleus and spatial transcriptomic profiling of human healthy hamstring tendon

Mimpen

Ramos‐Mucci

Paul

et al. 2022

Preprint

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The molecular and cellular basis of health in human tendons remains poorly understood. Amongst human tendons, the hamstrings are the least likely to be injured or degenerate, providing a prototypic healthy tendon reference. The aim of this study was to define the transcriptome and location of all cell types in healthy hamstring tendon. We profiled the transcriptomes of 10,533 nuclei from 4 healthy donors using single-nucleus RNA sequencing (snRNA-seq) and identified 12 distinct cell types. We confirmed the presence of two fibroblast cell types, endothelial cells, mural cells, and immune cells, and revealed the presence of cell types previously unreported for tendon sites, including different skeletal muscle cell types, satellite cells, adipocytes, and nerve cells, which are undefined nervous system cells. Location of these cell types within tendon was defined using spatial transcriptomics and imaging, and transcriptional networks and cell-cell interactions were identified. We demonstrate that fibroblasts have a high number of potential cell-cell interactions, are present throughout the whole tendon tissue, and play an important role in the production and organisation of extracellular matrix, thus confirming their role as key regulators of hamstring tendon tissue homeostasis. Overall, our findings highlight the highly complex cellular networks underpinning tendon function and underpins the importance of fibroblasts as key regulators of hamstring tendon tissue homeostasis.

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“…To identify stomach cell type-enriched transcriptome profiles, we conducted an analysis based on our previously developed method (Butler et al, 2016;Dusart et al, 2019;Norreen-Thorsen et al, 2022), using human stomach bulk RNAseq data (N=359) from Genotype-Tissue Expression (GTEx) portal V8 (https://gtexportal.org) (Consortium, 2015). Each sample was unfractionated and thus contained a mix of cell types (Figure 1 A.i), which contribute differing proportions of transcripts that are measured by RNAseq (Figure 1 A.ii).…”

Section: Cell Type Reference Transcripts Correlate Across Unfractiona...mentioning

confidence: 99%

A human stomach cell type transcriptome atlas

Öling

Thorsen

Zwahlén

et al. 2023

Preprint

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The identification of cell type-specific genes and their modification under different conditions is central to our understanding of human health and disease. The stomach, a hollow organ in the upper gastrointestinal tract, provides an acidic environment that contributes to microbial defence and facilitates the activity of secreted digestive enzymes to process food and nutrients into chyme. In contrast to other sections of the gastrointestinal tract, detailed descriptions of cell type gene enrichment profiles in the stomach are absent from the major single cell sequencing-based atlases. Here, we use an integrative correlation analysis method to predict human stomach cell type transcriptome signatures using unfractionated stomach RNAseq data from 359 individuals. We profile parietal, chief, gastric mucous, gastric enteroendocrine, mitotic, endothelial, fibroblast, macrophage, neutrophil, T-cell and plasma cells, identifying over 1600 cell type-enriched genes. We uncover the cell type expression profile of several non-coding genes strongly associated with the progression of gastric cancer and, using a sex-based subset analysis, uncover a panel of male-only chief cell-enriched genes. This study provides a roadmap to further understand human stomach biology.

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A human adipose tissue cell-type transcriptome atlas

Cited by 42 publications

References 97 publications

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Single nucleus and spatial transcriptomic profiling of human healthy hamstring tendon

A human stomach cell type transcriptome atlas

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