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Yan Z, Yang J, Wei WT, Zhou ML, Mo DX, Wan X, Ma R, Wu MM, Huang JH, Liu YJ, Lv FH, Li MH. A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues. Nat Commun 2024; 15:3970. [PMID: 38730227 PMCID: PMC11087590 DOI: 10.1038/s41467-024-48261-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.
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Affiliation(s)
- Ze Yan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wen-Tian Wei
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ming-Liang Zhou
- Sichuan Academy of Grassland Science, Chengdu, 611743, China
| | - Dong-Xin Mo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing Wan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Rui Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mei-Ming Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ya-Jing Liu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feng-Hua Lv
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Ehrmann J, Generaux C, Ostergaard S, Johnson W, Rose A, Mendenhall V. Thoracic Lymph Duct Catheterization with a Venous Shunt in the Nonhuman Primate. J INVEST SURG 2021; 35:502-510. [PMID: 33622163 DOI: 10.1080/08941939.2021.1874081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: Biologic therapeutics constitute up to 30% of all drugs approved from 2010 to 2018 and represent a continuous growing market. In contrast to small molecules, biologic therapeutics (>1 kDa MW) are administered parenterally or intravenously due to poor bioavailability when administered orally. The absorption and disposition of biologics that are administered subcutaneously may be absorbed via lymphatic or blood capillaries. Methods: To understand the absorption and distribution of biotherapeutics via the lymphatic system a surgical model was developed in the cynomolgus macaque (Macaca fascicularis) to allow for frequent and chronic collection of lymph fluid. Additionally, the model allowed for the recirculation of the lymph fluid into the blood stream providing true physiologic redistribution of the biologic drug from the bloodstream back into the lymph. Results: To our knowledge, models of lymphatic duct catheterization with recirculation in the NHP have not been reported. The model consisted of two surgically implanted catheters, one in the thoracic lymph duct and one in the azygous vein. These two catheters were then exteriorized and connected to each other to allow for recirculation of lymph back into the venous blood stream. The exteriorized catheters were protected within the pocket of a jacket. Thirty-one surgical procedures were performed with an overall success rate of 70%. Unsuccessful attempts were related to anatomical differences where the lymphatic duct was either not identifiable (n = 3) or too small to catheterize (n = 6). The patency rate was 90% instrumented animals for at least 24 h, up to 168 h. Conclusion: We present the surgical technique, complications, and refinements which resulted in a reliable and reproducible model in the nonhuman primate for the chronic collection and recirculation of lymphatic fluid.
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Affiliation(s)
- Jon Ehrmann
- Veterinary Sciences, Bristol Myers Squibb, Princeton, NJ, USA
| | - Claudia Generaux
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Nonclinical Research and Development, Princeton, NJ, USA
| | | | - Wendy Johnson
- Veterinary Sciences, Bristol Myers Squibb, Princeton, NJ, USA
| | - Anne Rose
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Nonclinical Research and Development, Princeton, NJ, USA
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Hunka J, Riley JT, Debes GF. Approaches to overcome flow cytometry limitations in the analysis of cells from veterinary relevant species. BMC Vet Res 2020; 16:83. [PMID: 32143631 PMCID: PMC7060616 DOI: 10.1186/s12917-020-02299-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/25/2020] [Indexed: 01/04/2023] Open
Abstract
Background Flow cytometry is a powerful tool for the multiparameter analysis of leukocyte subsets on the single cell level. Recent advances have greatly increased the number of fluorochrome-labeled antibodies in flow cytometry. In particular, an increase in available fluorochromes with distinct excitation and emission spectra combined with novel multicolor flow cytometers with several lasers have enhanced the generation of multidimensional expression data for leukocytes and other cell types. However, these advances have mainly benefited the analysis of human or mouse cell samples given the lack of reagents for most animal species. The flow cytometric analysis of important veterinary, agricultural, wildlife, and other animal species is still hampered by several technical limitations, even though animal species other than the mouse can serve as more accurate models of specific human physiology and diseases. Results Here we present time-tested approaches that our laboratory regularly uses in the multiparameter flow cytometric analysis of ovine leukocytes. The discussed approaches will be applicable to the analysis of cells from most animal species and include direct modification of antibodies by covalent conjugation or Fc-directed labeling (Zenon™ technology), labeled secondary antibodies and other second step reagents, labeled receptor ligands, and antibodies with species cross-reactivity. Conclusions Using refined technical approaches, the number of parameters analyzed by flow cytometry per cell sample can be greatly increased, enabling multidimensional analysis of rare samples and giving critical insight into veterinary and other less commonly analyzed species. By maximizing information from each cell sample, multicolor flow cytometry can reduce the required number of animals used in a study.
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Affiliation(s)
- Julia Hunka
- Department of Microbiology and Immunology, Sidney Kimmel Medical College and Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th Street, Philadelphia, PA, 19107, USA.,Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - John T Riley
- Department of Microbiology and Immunology, Sidney Kimmel Medical College and Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th Street, Philadelphia, PA, 19107, USA
| | - Gudrun F Debes
- Department of Microbiology and Immunology, Sidney Kimmel Medical College and Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 S 10th Street, Philadelphia, PA, 19107, USA.
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Characterisation of ovine lymphatic vessels in fresh specimens. PLoS One 2019; 14:e0209414. [PMID: 30650093 PMCID: PMC6334992 DOI: 10.1371/journal.pone.0209414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 12/05/2018] [Indexed: 12/27/2022] Open
Abstract
Background and aim The development and use of experimental models using lymphatic cannulation techniques have been hampered by the lack of high-quality colour imaging of lymphatic vessels in situ. Most descriptions of lymphatic anatomy in sheep have historically depended on schematic diagrams due to limitations in the ability to publish colour images of the lymphatic vessels with decent resolution. The aim of this work was to encourage more widespread use of the ovine cannulation model by providing clear photographic images identifying the location and anatomical layout of some major lymphatic ducts and their in situ relationship to surrounding tissues. Methods The cadavers of the sheep were collected after they had been euthanized at the end of animal trials not associated with this study. The lymphatics were dissected and exposed to show their appearance in the surrounding tissues and their relationship to other organs. Patent Blue was used to locate lymphatic vessels in exploratory preparations. However, in order to present the natural appearance of the vessels, we used minimal dissection and dye was not used for the photographed examples. Instead, we have indicated the course of the vessels with lines where their position is less clear. Results and conclusion In this paper, we have used sheep specimens as examples to show characteristic images of lymphatic vessels. The images of in situ lymphatics and lymph nodes combined with schematic summaries provide a concise illustration of the lymphatic drainage scheme in sheep.
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