Zhou Yunlai single cell world 2022-02-10 14:01
Rat, cow, tiger, rabbit, dragon, snake, horse, sheep, monkey, chicken, dog, pig. We are born with a certain kind of connection with nature. One is in the sky and the other is in the ground. The ones in the sky are the constellations, and the ones on the ground are the zodiac signs. Therefore, when we hear them, there is always an inexplicable intimacy.
When it comes to the twelve zodiac signs, we are all familiar with them. With the development of life sciences, they are no longer ancient reflections, but reflect human health at some level, or the relationship between human beings and nature.
Today, let's take a look at the zodiac from a single-cell perspective, and see how similar we are to them and how close our relationship is at the cellular level.
Shuai Ma, Shuhui Sun, Lingling Geng, Moshi Song, et al. Caloric Restriction Reprograms the Single-Cell Transcriptional Landscape of Rattus Norvegicus Aging, Cell, 2020
Single-cell RNA sequencing (scRNA-seq) technology promises to reshape current cell type classification systems. However, a transcriptome-based single-cell map has not yet reached complex mammalian systems. Here, we developed Microwell-seq, a high-volume, low-cost scRNA-seq platform using simple, inexpensive equipment. Using Microwell-seq technology, we analyzed more than 400,000 single cells covering all major mouse organs and constructed a basic protocol for a mouse cell atlas (MCA).
Jia-Jin Wu, Senlin Zhu, Fengfei Gu, Teresa G. Valencak, Jian-Xin Liu, Hui-Zeng Sun, Cross-tissue single-cell transcriptomic landscape reveals the key cell subtypes and their potential roles in the nutrient absorption and metabolism in dairy cattle, Journal of Advanced Research, 2021
Dairy cows are an important ruminant and play a vital role in meeting the worldwide demand for high-quality animal protein production. The complex biological processes that convert human indigestible biomass into highly digestible and nutritious milk are coordinated by various tissues. However, insufficient understanding of the cellular composition and function of key metabolic tissues has hindered improvements in livestock health and performance.
Chen, D., Sun, J., Zhu, J. et al. Single cell atlas for 11 non-model mammals, reptiles and birds. Nat Commun 12, 7083 (2021). https://doi.org/10.1038/ s41467-021-27162-2
Availability of viral infectious agents is a prerequisite for cross-species transmission of SARS-CoV-2. Large-scale single-cell screening of animal cells can reveal expression patterns of viral genes in different hosts. However, this exploration of SARS-CoV-2 is still limited. The authors performed single-nucleus RNA sequencing on 11 non-model species, including pets (cats, dogs, hamsters, and lizards), domestic animals (goats and rabbits), poultry (ducks and pigeons), and wild animals (pangolins, tigers, and deer) , The co-expression of ACE2 and TMPRSS2 was also studied. Furthermore, cross-species analysis of the lung cell maps of the mammals, reptiles and birds studied revealed core developmental programs, key connectomes and conserved regulatory circuits among these evolutionarily distant species.
Liang, D., Xue, J., Geng, L. et al. Cellular and molecular landscape of mammalian sinoatrial node revealed by single-cell RNA sequencing. Nat Commun 12, 287 (2021).
Rabbit is one of the important model animals, especially in antibody research. In this paper, the author compares the SAN gene expression patterns of mice and rabbits. 343 SAN cells were isolated from 6 adult rabbits and subjected to scRNA-seq to detect gene expression of cell clusters. The identification of different cell populations in rabbit SANs mainly used the same criteria as in mice. Three groups of clusters were found in rabbit SAN cells, and three types of cells were studied in detail.
Not sequenced due to being imaginary
Post Y, Puschhof J, Beumer J, Kerkkamp HM, de Bakker MAG, Clevers H. Snake Venom Gland Organoids. Cell. 2020 Jan 23;180(2):233-247.e21. doi: 10.1016/j.cell.2019.11 .038. PMID: 31978343
If you're still asking if snakes can be single-cell sequenced, others have done single-cell sequencing of snake organoids. The authors established long-expanded venom gland organs from several species of snakes. The newly assembled cape coral snake transcriptome shows that the organ expresses high levels of toxin transcripts. Single-cell RNA sequencing of organoids and primary tissues identified distinct venom-expressing cell types, as well as proliferating cells expressing homologues of known mammalian stem cell markers. Regional heterogeneity in the expression of individual venom components is maintained in organoid cultures.
Harman, RM, Patel, RS, Fan, JC et al. Single-cell RNA sequencing of equine mesenchymal stromal cells from primary donor-matched tissue sources reveals functional heterogeneity in immune modulation and cell motility. Stem Cell Res Ther 11, 524 (2020 ).
The efficacy of mesenchymal stromal cell (MSC) therapy is thought to depend on the inherent heterogeneity of MSC cultures isolated from different tissue sources and individual MSCs isolated from the same tissue source, neither of which is clear. To investigate this, we used MSC cultures isolated from horses. The horse is considered a physiologically relevant large animal model suitable for translational mesenchymal stem cell research.
Yang H, Ma J, Wan Z, Wang Q, Wang Z, Zhao J, Wang F, Zhang Y. Characterization of sheep spermatogenesis through single-cell RNA sequencing. FASEB J. 2021 Feb;35(2):e21187. doi: 10.1096/fj.202001035RRR. Epub 2020 Nov 16. PMID: 33197070.
The researchers collected scRNA-seq data from adult sheep testes (11 772 cells) to identify all known germ cells (including primary spermatocytes early, anaphase primary spermatocytes, spermatids, elongated spermatids, spermatids), somatic cells (Sertoli's cells and Leydig cells). Functional enrichment analysis showed that pathways such as cell cycle, gametogenesis, protein processing, and mRNA surveillance were significantly enriched in testicular germ cell types, among which the ribosomal pathway was significantly enriched.
Ma, S., Sun, S., Li, J. et al. Single-cell transcriptomic atlas of primate cardiopulmonary aging. Cell Res 31, 415–432 (2021). https://doi.org/10.1038/s41422- 020-00412-6
Aging is a major risk factor for many diseases, especially among the highly prevalent cardiopulmonary comorbidities and infectious diseases including coronavirus disease 2019 (COVID-19). Therefore, there is an urgent need to address the cellular and molecular mechanisms associated with aging in higher mammals. We created mononuclear/cellular transcriptome maps of the lungs, hearts, and arteries of young and old nonhuman primates, the target tissues of SARS-CoV-2. Analysis of cell-type-specific senescence-associated transcriptional changes revealed impaired systemic inflammation and viral defense.
Mantri, M., Scuderi, GJ, Abedini-Nassab, R. et al. Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis. Nat Commun 12, 1771 (2021). https://doi .org/10.1038/s41467-021-21892-z
In this study, we combined single-cell transcriptomics and spatial transcriptomics with data integration algorithms to study the development of chicken hearts from early to late stages of the four-chambered heart. Spatial localization of cardiac lineage differentiation transitions defines transcriptional differences between epicardial lineage epithelial and mesenchymal cells.
Fastrès A, Pirottin D, Fievez L, Tutunaru AC, Bolen G, Merveille AC, Marichal T, Desmet CJ, Bureau F and Clercx C (2020) Identification of Pro-Fibrotic Macrophage Populations by Single-Cell Transcriptomic Analysis in West Highland White Terriers Affected With Canine Idiopathic Pulmonary Fibrosis. Front. Immunol. 11:611749. doi: 10.3389/fimmu.2020.611749
In dogs, scRNA-seq was recently validated for detection of cell populations in bronchoalveolar lavage fluid (BALF) from healthy dogs. We used scRNA-seq to characterize disease-associated heterogeneity within macrophage/monocyte (Ma/Mo) cell populations in BALF from five CIPF-affected WHWTs compared to three healthy WHWTs. Gene set enrichment analysis was also used to assess the profibrotic capacity of the Ma/Mo population. Five Ma/Mo clusters were identified.
Jianbo Li, Ligang Wang, Dawei Yu, Junfeng Hao, Longchao Zhang, Adeniyi C. Adeolag,Single-cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-genesis in Pigs,Genomics, Proteomics & Bioinformatics, 2021
The development of the thoracolumbar vertebrae (TLV) and rib primordium (RP) is a coevolutionary feature of vertebrates, although organism-wide analysis of the expression dynamics of TLV and RP-related genes is currently lacking. Here, we investigated the single-cell transcriptome of thoracic (TV), lumbar (LV), and RP cells from porcine embryos at 27 days post-fertilization (dpf) and identified 6 cell types with distinct gene expression signatures.