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Chen X, Ma Y, Shi Y, Fu Y, Nan M, Ren Q, Gao J. Population-Level Cell Trajectory Inference Based on Gaussian Distributions. Biomolecules 2024; 14:1396. [PMID: 39595573 PMCID: PMC11592043 DOI: 10.3390/biom14111396] [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: 10/09/2024] [Revised: 10/29/2024] [Accepted: 10/30/2024] [Indexed: 11/28/2024] Open
Abstract
In the past decade, inferring developmental trajectories from single-cell data has become a significant challenge in bioinformatics. RNA velocity, with its incorporation of directional dynamics, has significantly advanced the study of single-cell trajectories. However, as single-cell RNA sequencing technology evolves, it generates complex, high-dimensional data with high noise levels. Existing trajectory inference methods, which overlook cell distribution characteristics, may perform inadequately under such conditions. To address this, we introduce CPvGTI, a Gaussian distribution-based trajectory inference method. CPvGTI utilizes a Gaussian mixture model, optimized by the Expectation-Maximization algorithm, to construct new cell populations in the original data space. By integrating RNA velocity, CPvGTI employs Gaussian Process Regression to analyze the differentiation trajectories of these cell populations. To evaluate the performance of CPvGTI, we assess CPvGTI's performance against several state-of-the-art methods using four structurally diverse simulated datasets and four real datasets. The simulation studies indicate that CPvGTI excels in pseudo-time prediction and structural reconstruction compared to existing methods. Furthermore, the discovery of new branch trajectories in human forebrain and mouse hematopoiesis datasets confirms CPvGTI's superior performance.
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Affiliation(s)
| | | | | | | | | | | | - Jie Gao
- School of Science, Jiangnan University, Wuxi 214122, China; (X.C.); (Y.M.); (Y.S.); (Y.F.); (M.N.); (Q.R.)
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2
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Molecular Mechanisms and Health Benefits of Ghrelin: A Narrative Review. Nutrients 2022; 14:nu14194191. [PMID: 36235843 PMCID: PMC9572668 DOI: 10.3390/nu14194191] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/26/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022] Open
Abstract
Ghrelin, an endogenous brain-gut peptide, is secreted in large quantities, mainly from the stomach, in humans and rodents. It can perform the biological function of activating the growth hormone secretagogue receptor (GHSR). Since its discovery in 1999, ample research has focused on promoting its effects on the human appetite and pleasure-reward eating. Extensive, in-depth studies have shown that ghrelin is widely secreted and distributed in tissues. Its role in neurohumoral regulation, such as metabolic homeostasis, inflammation, cardiovascular regulation, anxiety and depression, and advanced cancer cachexia, has attracted increasing attention. However, the effects and regulatory mechanisms of ghrelin on obesity, gastrointestinal (GI) inflammation, cardiovascular disease, stress regulation, cachexia treatment, and the prognosis of advanced cancer have not been fully summarized. This review summarizes ghrelin's numerous effects in participating in a variety of biochemical pathways and the clinical significance of ghrelin in the regulation of the homeostasis of organisms. In addition, potential mechanisms are also introduced.
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Protective and Healing Effects of Ghrelin and Risk of Cancer in the Digestive System. Int J Mol Sci 2021; 22:ijms221910571. [PMID: 34638910 PMCID: PMC8509076 DOI: 10.3390/ijms221910571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 01/19/2023] Open
Abstract
Ghrelin is an endogenous ligand for the ghrelin receptor, previously known as the growth hormone secretagogue receptor. This hormone is mainly produced by endocrine cells present in the gastric mucosa. The ghrelin-producing cells are also present in other organs of the body, mainly in the digestive system, but in much smaller amount. Ghrelin exhibits a broad spectrum of physiological effects, such as stimulation of growth hormone secretion, gastric secretion, gastrointestinal motility, and food intake, as well as regulation of glucose homeostasis and bone formation, and inhibition of inflammatory processes. This review summarizes the recent findings concerning animal and human data showing protective and therapeutic effects of ghrelin in the gut, and also presents the role of growth hormone and insulin-like growth factor-1 in these effects. In addition, the current data on the possible influence of ghrelin on the carcinogenesis, its importance in predicting the risk of developing gastrointestinal malignances, as well as the potential usefulness of ghrelin in the treatment of cancer, have been presented.
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Detection of Lipase Activity in Cells by a Fluorescent Probe Based on Formation of Self-Assembled Micelles. iScience 2020; 23:101294. [PMID: 32623339 PMCID: PMC7334599 DOI: 10.1016/j.isci.2020.101294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 05/25/2020] [Accepted: 06/15/2020] [Indexed: 01/26/2023] Open
Abstract
Reliable and sensitive detection of lipase activity is essential for the early diagnosis and monitoring of acute pancreatitis or progression of digestive diseases. However, the available fluorescent probes for detection of lipase activity are only implemented in a hexane-water two-phase system due to the nature of heterogeneous catalysis of lipase, thus limiting their applications in direct imaging of lipase activity in living cells and tissues. Here we designed and synthesized a "turn on" fluorescent probe CPP based on self-assembled micelles for hydrolysis of lipase. The CPP probe exhibits high selectivity and excellent sensitivity for the detection of lipase in such a homogeneous system and is successfully applied for monitoring lipase activity in pancreatic AR42J cells, tissues, and serums. Taken together, the fluorescent CPP probe not only provides a tool for diagnostic potential in pancreatic disease but also demonstrates an application potential for micelle self-assembly-based development of biological probes.
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Stempniewicz A, Ceranowicz P, Warzecha Z. Potential Therapeutic Effects of Gut Hormones, Ghrelin and Obestatin in Oral Mucositis. Int J Mol Sci 2019; 20:ijms20071534. [PMID: 30934722 PMCID: PMC6479885 DOI: 10.3390/ijms20071534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 12/16/2022] Open
Abstract
Chemotherapy and/or head and neck radiotherapy are frequently associated with oral mucositis. Oral pain, odynophagia and dysphagia, opioid use, weight loss, dehydration, systemic infection, hospitalization and introduction of a feeding tube should be mentioned as the main determinated effect of oral mucositis. Oral mucositis leads to a decreased quality of life and an increase in treatment costs. Moreover, oral mucositis is a life-threatening disease. In addition to its own direct life-threatening consequences, it can also lead to a reduced survival due to the discontinuation or dose reduction of anti-neoplasm therapy. There are numerous strategies for the prevention or treatment of oral mucositis; however, their effectiveness is limited and does not correspond to expectations. This review is focused on the ghrelin and obestatin as potentially useful candidates for the prevention and treatment of chemo- or/and radiotherapy-induced oral mucositis.
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Affiliation(s)
- Agnieszka Stempniewicz
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Grzegórzecka 16 St., 31-531 Krakow, Poland.
| | - Piotr Ceranowicz
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Grzegórzecka 16 St., 31-531 Krakow, Poland.
| | - Zygmunt Warzecha
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Grzegórzecka 16 St., 31-531 Krakow, Poland.
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Konarska K, Cieszkowski J, Warzecha Z, Ceranowicz P, Chmura A, Kuśnierz-Cabala B, Gałązka K, Kowalczyk P, Miskiewicz A, Konturek TJ, Pędziwiatr M, Dembiński A. Treatment with Obestatin-A Ghrelin Gene-Encoded Peptide-Reduces the Severity of Experimental Colitis Evoked by Trinitrobenzene Sulfonic Acid. Int J Mol Sci 2018; 19:ijms19061643. [PMID: 29865176 PMCID: PMC6032262 DOI: 10.3390/ijms19061643] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 02/06/2023] Open
Abstract
Obestatin is a 23-amino acid peptide derived from proghrelin, a common prohormone for ghrelin and obestatin. Previous studies showed that obestatin exhibited some protective and therapeutic effects in the gut. The aim of our presented study was to examine the effect of treatment with obestatin on trinitrobenzene sulfonic acid (TNBS)-induced colitis. In rats anesthetized with ketamine, colitis was induced through intrarectal administration of 25 mg of 2,4,6-trinitrobenzene sulfonic acid (TNBS). Obestatin was administered intraperitoneally at doses of 4, 8, or 16 nmol/kg, twice per day for four consecutive days. The first dose of obestatin was given one day before the induction of colitis, and the last one was given two days after administration of TNBS. Fourteen days after the induction of colitis, rats were anesthetized again with ketamine, and the severity of colitis was determined. The administration of obestatin had no effect on the parameters tested in rats without the induction of colitis. In rats with colitis, administration of obestatin at doses of 8 or 16 nmol/kg reduced the area of colonic damage, and improved mucosal blood flow in the colon. These effects were accompanied by a reduction in the colitis-evoked increase in the level of blood leukocytes, and mucosal concentration of pro-inflammatory interleukin-1β. Moreover, obestatin administered at doses of 8 or 16 nmol/kg reduced histological signs of colonic damage. The administration of obestatin at a dose of 4 nmol/kg failed to significantly affect the parameters tested. Overall, treatment with obestatin reduced the severity of TNBS-induced colitis in rats. This effect was associated with an improvement in mucosal blood flow in the colon, and a decrease in local and systemic inflammatory processes.
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Affiliation(s)
- Katarzyna Konarska
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Jakub Cieszkowski
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Zygmunt Warzecha
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Piotr Ceranowicz
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Anna Chmura
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Beata Kuśnierz-Cabala
- Department of Clinical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, 31-501 Cracow, Poland.
| | - Krystyna Gałązka
- Department of Pathomorphology, Faculty of Medicine, Jagiellonian University Medical College, 31-531 Cracow, Poland.
| | - Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, 05-110 Jablonna, Poland.
| | - Andrzej Miskiewicz
- Department of Periodontology and Oral Diseases, Medical University of Warsaw, 00-246 Warsaw, Poland.
| | - Thomas Jan Konturek
- Department of Medicine, St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA 02135, USA.
| | - Michał Pędziwiatr
- Second Department of General Surgery, Faculty of Medicine, Jagiellonian University Medical College, 31-501 Cracow, Poland.
| | - Artur Dembiński
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 31-531 Cracow, Poland.
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Jeong YK, Kim H. A Mini-Review on the Effect of Docosahexaenoic Acid (DHA) on Cerulein-Induced and Hypertriglyceridemic Acute Pancreatitis. Int J Mol Sci 2017; 18:ijms18112239. [PMID: 29068376 PMCID: PMC5713209 DOI: 10.3390/ijms18112239] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 12/17/2022] Open
Abstract
Acute pancreatitis refers to the sudden inflammation of the pancreas. It is associated with premature activation and release of digestive enzymes into the pancreatic interstitium and systemic circulation, resulting in pancreatic tissue autodigestion and multiple organ dysfunction, as well as with increased cytokine production, ultimately leading to deleterious local and systemic effects. Although mechanisms involved in pathogenesis of acute pancreatitis have not been completely elucidated, oxidative stress is regarded as a major risk factor. In human acute pancreatitis, lipid peroxide levels in pancreatic tissues increase. Docosahexaenoic acid (DHA), an omega-3 polyunsaturated fatty acid (C22:6n-3), exerts anti-inflammatory and antioxidant effects on various cells. Previous studies have shown that DHA activates peroxisome proliferator-activated receptor-γ and induces catalase, which inhibits oxidative stress-mediated inflammatory signaling required for cytokine expression in experimental acute pancreatitis using cerulein. Cerulein, a cholecystokinin analog, induces intra-acinar activation of trypsinogen in the pancreas, which results in human acute pancreatitis-like symptoms. Therefore, DHA supplementation may be beneficial for preventing or inhibiting acute pancreatitis development. Since DHA reduces serum triglyceride levels, addition of DHA to lipid-lowering drugs like statins has been investigated to reduce hypertriglyceridemic acute pancreatitis. However, high DHA concentrations increase cytosolic Ca2+, which activates protein kinase C and may induce hyperlipidemic acute pancreatitis. In this review, effect of DHA on cerulein-induced and hypertriglyceridemic acute pancreatitis has been discussed. The relation of high concentration of DHA to hyperlipidemic acute pancreatitis has been included.
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Affiliation(s)
- Yoo Kyung Jeong
- Department of Food and Nutrition, Brian Korea 21 PLUS Project, College of Human Ecology, Yonsei University, Seoul 03722, Korea.
| | - Hyeyoung Kim
- Department of Food and Nutrition, Brian Korea 21 PLUS Project, College of Human Ecology, Yonsei University, Seoul 03722, Korea.
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Bonior J, Warzecha Z, Ceranowicz P, Gajdosz R, Pierzchalski P, Kot M, Leja-Szpak A, Nawrot-Porąbka K, Link-Lenczowski P, Pędziwiatr M, Olszanecki R, Bartuś K, Trąbka R, Kuśnierz-Cabala B, Dembiński A, Jaworek J. Capsaicin-Sensitive Sensory Nerves Are Necessary for the Protective Effect of Ghrelin in Cerulein-Induced Acute Pancreatitis in Rats. Int J Mol Sci 2017; 18:E1402. [PMID: 28665321 PMCID: PMC5535895 DOI: 10.3390/ijms18071402] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
Ghrelin was shown to exhibit protective and therapeutic effect in the gut. Aim of the study was to investigate the role of sensory nerves (SN) in the protective effect of ghrelin in acute pancreatitis (AP). Studies were performed on male Wistar rats or isolated pancreatic acinar cells. After capsaicin deactivation of sensory nerves (CDSN) or treatment with saline, rats were pretreated intraperitoneally with ghrelin or saline. In those rats, AP was induced by cerulein or pancreases were used for isolation of pancreatic acinar cells. Pancreatic acinar cells were incubated in cerulein-free or cerulein containing solution. In rats with intact SN, pretreatment with ghrelin led to a reversal of the cerulein-induced increase in pancreatic weight, plasma activity of lipase and plasma concentration of tumor necrosis factor-α (TNF-α). These effects were associated with an increase in plasma interleukin-4 concentration and reduction in histological signs of pancreatic damage. CDSN tended to increase the severity of AP and abolished the protective effect of ghrelin. Exposure of pancreatic acinar cells to cerulein led to increase in cellular expression of mRNA for TNF-α and cellular synthesis of this cytokine. Pretreatment with ghrelin reduced this alteration, but this effect was only observed in acinar cells obtained from rats with intact SN. Moreover, CDSN inhibited the cerulein- and ghrelin-induced increase in gene expression and synthesis of heat shock protein 70 (HSP70) in those cells. Ghrelin exhibits the protective effect in cerulein-induced AP on the organ and pancreatic acinar cell level. Sensory nerves ablation abolishes this effect.
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Affiliation(s)
- Joanna Bonior
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, 12 Michałowskiego St., 31-126 Krakow, Poland.
| | - Zygmunt Warzecha
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegórzecka St., 31-531 Krakow, Poland.
| | - Piotr Ceranowicz
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegórzecka St., 31-531 Krakow, Poland.
| | - Ryszard Gajdosz
- Department of Emergency Medical Care, Faculty of Health Sciences, Jagiellonian University Medical College, 12 Michałowskiego St., 31-126 Krakow, Poland.
| | - Piotr Pierzchalski
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, 12 Michałowskiego St., 31-126 Krakow, Poland.
| | - Michalina Kot
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, 12 Michałowskiego St., 31-126 Krakow, Poland.
| | - Anna Leja-Szpak
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, 12 Michałowskiego St., 31-126 Krakow, Poland.
| | - Katarzyna Nawrot-Porąbka
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, 12 Michałowskiego St., 31-126 Krakow, Poland.
| | - Paweł Link-Lenczowski
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, 12 Michałowskiego St., 31-126 Krakow, Poland.
| | - Michał Pędziwiatr
- 2nd Department of Surgery, Faculty of Medicine, Jagiellonian University Medical College, 21 Kopernika St., 31-501 Krakow, Poland.
| | - Rafał Olszanecki
- Department of Pharmacology, Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegórzecka St., 31-531 Krakow, Poland.
| | - Krzysztof Bartuś
- Department of Cardiovascular Surgery and Transplantology, Faculty of Medicine, Jagiellonian University, JP II Hospital, 80 Prądnicka St., 31-202 Krakow, Poland.
| | - Rafał Trąbka
- Department of Rehabilitation, Faculty of Health Sciences, Jagiellonian University Medical College, 3 Koło Strzelnicy St., 30-219 Krakow, Poland.
| | - Beata Kuśnierz-Cabala
- Department of Diagnostics, Chair of Clinical Biochemistry, Faculty of Medicine Jagiellonian University Medical College, 15 A Kopernika St., 31-501 Krakow, Poland.
| | - Artur Dembiński
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegórzecka St., 31-531 Krakow, Poland.
| | - Jolanta Jaworek
- Department of Medical Physiology, Faculty of Health Sciences, Jagiellonian University Medical College, 12 Michałowskiego St., 31-126 Krakow, Poland.
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