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Burclaff J, Bliton RJ, Breau KA, Ok MT, Gomez-Martinez I, Ranek JS, Bhatt AP, Purvis JE, Woosley JT, Magness ST. A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics. Cell Mol Gastroenterol Hepatol 2022; 13:1554-1589. [PMID: 35176508 PMCID: PMC9043569 DOI: 10.1016/j.jcmgh.2022.02.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS Single-cell transcriptomics offer unprecedented resolution of tissue function at the cellular level, yet studies analyzing healthy adult human small intestine and colon are sparse. Here, we present single-cell transcriptomics covering the duodenum, jejunum, ileum, and ascending, transverse, and descending colon from 3 human beings. METHODS A total of 12,590 single epithelial cells from 3 independently processed organ donors were evaluated for organ-specific lineage biomarkers, differentially regulated genes, receptors, and drug targets. Analyses focused on intrinsic cell properties and their capacity for response to extrinsic signals along the gut axis across different human beings. RESULTS Cells were assigned to 25 epithelial lineage clusters. Multiple accepted intestinal stem cell markers do not specifically mark all human intestinal stem cells. Lysozyme expression is not unique to human Paneth cells, and Paneth cells lack expression of expected niche factors. Bestrophin 4 (BEST4)+ cells express Neuropeptide Y (NPY) and show maturational differences between the small intestine and colon. Tuft cells possess a broad ability to interact with the innate and adaptive immune systems through previously unreported receptors. Some classes of mucins, hormones, cell junctions, and nutrient absorption genes show unappreciated regional expression differences across lineages. The differential expression of receptors and drug targets across lineages show biological variation and the potential for variegated responses. CONCLUSIONS Our study identifies novel lineage marker genes, covers regional differences, shows important differences between mouse and human gut epithelium, and reveals insight into how the epithelium responds to the environment and drugs. This comprehensive cell atlas of the healthy adult human intestinal epithelium resolves likely functional differences across anatomic regions along the gastrointestinal tract and advances our understanding of human intestinal physiology.
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Affiliation(s)
- Joseph Burclaff
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - R Jarrett Bliton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Meryem T Ok
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Ismael Gomez-Martinez
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jolene S Ranek
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Aadra P Bhatt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeremy E Purvis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John T Woosley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Scott T Magness
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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Gomes JR, Freitas JR, Grassiolli S. Effects of Physical Exercise on the Intestinal Mucosa of Rats Submitted to a Hypothalamic Obesity Condition. Anat Rec (Hoboken) 2016; 299:1389-96. [PMID: 27488821 DOI: 10.1002/ar.23453] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/17/2016] [Accepted: 03/25/2016] [Indexed: 11/08/2022]
Abstract
The small intestine plays a role in obesity as well as in satiation. However, the effect of physical exercise on the morphology and function of the small intestine during obesity has not been reported to date. This study aimed to evaluate the effects of physical exercise on morphological aspects of the rat small intestine during hypothalamic monosodium glutamate (MSG)-induced obesity. The rats were divided into four groups: Sedentary (S), Monosodium Glutamate (MSG), Exercised (E), and Exercised Monosodium Glutamate (EMSG). The MSG and EMSG groups received a daily injection of monosodium glutamate (4 g/kg) during the 5 first days after birth. The S and E groups were considered as control groups and received injections of saline. At weaning, at 21 days after birth, the EMSG and E groups were submitted to swimming practice 3 times a week until the 90th day, when all groups were sacrificed and the parameters studied recorded. Exercise significantly reduced fat deposits and the Lee Index in MSG-treated animals, and also reduced the thickness of the intestinal wall, the number of goblet cells and intestinal alkaline phosphatase activity. However, physical activity alone increased the thickness and height of villi, and the depth of the crypts. In conclusion, regular physical exercise may alter the morphology or/and functions of the small intestine, reducing the prejudicial effects of hypothalamic obesity. Anat Rec, 299:1389-1396, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- J R Gomes
- Departamento de Biologia Estrutural Molecular e Genetica, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brasil, Avenida Carlos Cavalcanti, 4748, Ponta Grossa, PR, CEP 84030-900, Brazil.
| | - J R Freitas
- Departamento de Biologia Estrutural Molecular e Genetica, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brasil, Avenida Carlos Cavalcanti, 4748, Ponta Grossa, PR, CEP 84030-900, Brazil
| | - S Grassiolli
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná -Campus de Cascavel, Rua Universitária, 2069, Bairro: Jardim Universitário, CEP 85819-110, Cascavel, PR, Brazil
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Soares MADM, Okada MA, Ayub CLSC, Gomes JR. Effects of fasting at different stages of lighting regimen on the proliferation of jejunal epithelial cells during rat pup weaning. Anat Rec (Hoboken) 2009; 292:955-9. [PMID: 19548307 DOI: 10.1002/ar.20926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The lifespan of intestinal epithelial cells is predetermined by the process of cell proliferation that occurs constantly in the crypt. The control of this process involves some endogenous factors, such as hormones, as well as exogenous factors, like food and natural light variations. These last two exogenous factors seem to be the major modulators of the cell proliferation process. Fasting treatment was conducted to assess the role of food and its effect on the metaphase index (MI) of the intestinal epithelium at different times and periods (light and dark) of the day. The effects of short- (5 hr) and long-term (25 hr) fasting on the MI in the jejunal epithelium of young rats were investigated at 09:00 h, 15:00 hr, 21:00 hr, and 02:00 hr using the arrested metaphases method. The present study demonstrates that 5 hr and 25 hr of fasting treatment decrease the MI at 09:00 hr. It was observed from MI analysis that there is an interaction between the fed/fasted status of the animal and the different times of the day. This result suggests that during the transition from youth to adulthood, the control of MI by the light/dark cycle seems to be more pronounced as compared with control by food intake at some periods of the day, although at other times food had a greater impact on the MI.
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Shadan FF. Circadian tempo: A paradigm for genome stability? Med Hypotheses 2007; 68:883-91. [PMID: 17092657 DOI: 10.1016/j.mehy.2006.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 07/25/2006] [Accepted: 08/11/2006] [Indexed: 11/16/2022]
Abstract
Circadian clocks are molecular time-keeping systems that underlie daily biological rhythms in anticipation of the changing light and dark cycles. These clocks mediate daily rhythms in physiology and behavior that are thought to confer an adaptive advantage for organisms. It is hypothesized that cell cycle checkpoints are gated to an intrinsic circadian clock to protect DNA from diurnal exposure to mutagens (e.g.; UV radiation peaks with daylight and dissolved genotoxins that fluctuate with feeding periods). It is proposed that DNA replication arrest in response to genotoxic stress is a likely basis for the evolution of circadian-gated DNA replication. This protective mechanism is highly conserved and can be traced along the evolutionary time-line to the early prokaryotes, unicellular eukaryotes and viruses. Peak DNA repair capacity is normally synchronous to the crest of mutagenic stress as they oscillate with respect to time. Mutator phenotypes with increased vulnerability to genotoxic stress may therefore develop when the circadian pattern of cell cycle control, DNA repair or apoptotic response are phase-shifted relative to the rhythm of mutagenic stress. The accumulating mutations would lead to accelerated aging, genome instability and neoplasia. The proposed model delineates areas of research with potentially profound implications for carcinogenesis.
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Affiliation(s)
- Farhad F Shadan
- The Scripps Research Institute and Scripps Clinic, La Jolla, CA 92037, USA.
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Grandi D, Schunack W, Morini G. Epithelial cell proliferation is promoted by the histamine H3 receptor agonist (R)-α-methylhistamine throughout the rat gastrointestinal tract. Eur J Pharmacol 2006; 538:141-7. [PMID: 16682020 DOI: 10.1016/j.ejphar.2006.03.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 03/15/2006] [Accepted: 03/16/2006] [Indexed: 01/08/2023]
Abstract
The temporal effect of (R)-alpha-methylhistamine on epithelial cell proliferation throughout the rat gastrointestinal tract was investigated. (R)-alpha-methylhistamine was administered at 100 mg/kg orally and the rats were sacrificed 1, 24, 48, 72 and 144 h later. All the animals received 5-bromo-2'-deoxyuridine, (BrdU), 200 mg/kg i.p., 2 h before sacrifice. Gastrointestinal tissue was processed for histology and immunohistochemistry. (R)-alpha-methylhistamine caused a progressive increase in mucosal thickness of gastric fundus, distal small intestine and distal colon. Statistically significant differences from control values were found between 48 and 72 h after (R)-alpha-methylhistamine. (R)-alpha-methylhistamine significantly increased the number of BrdU-positive cells in the gastric fundus and antrum, intermediate and distal small intestine and distal colon. Peak effects were observed between 1 and 24 h after (R)-alpha-methylhistamine administration. Proliferating cell number and mucosal thickness were comparable to those of control rats at 144 h. (R)-alpha-methylhistamine exerts a long lasting growth-promoting effect on the stomach, distal small intestine and distal colon. Present data support a role of histamine H(3) receptors in the normal regulation of cell cycle in epithelial tissue.
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Affiliation(s)
- Daniela Grandi
- Department of Human Anatomy, Pharmacology and Forensic Medicine, University of Parma, 43100 Parma, Italy
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Gomes JR, Pereira AAM, Barth L, Silva JS, Leite ML, Wille ACM, Soares MAM. Circadian variation of the cell proliferation in the jejunal epithelium of rats at weaning phase. Cell Prolif 2005; 38:147-52. [PMID: 15985059 PMCID: PMC6496721 DOI: 10.1111/j.1365-2184.2005.00339.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Circadian variation in cell proliferation of the jejunal epithelium of 18-day-old rats was studied using the 2-h arrested metaphase score and crypt isolation method. A continuous decrease in the arrested metaphases occurred from 07.00 h to 13.00 h. From 17.00 h arrested metaphase values increased and were maintained at the higher level during the dark period as showed by Cosinor analyses (P < 0.05). These results indicate that in the young rat there is already a circadian variation in jejunal epithelial cell proliferation as early as 18 days. We can even suggest that the presence of a circadian rhythm at weaning contributes to the steady state of cell proliferation in the intestinal epithelium observed in adult life.
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Affiliation(s)
- J R Gomes
- Departamento de Biologia Estrutural, Molecular e Genética. Setor de Ciências Biológicas e da Saúde, Universidade Estadual de Ponta Grossa, Paraná, Brazil.
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