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Srivastava J, Ovcharenko I. Regulatory Plasticity of the Human Genome. Mol Biol Evol 2025; 42:msaf050. [PMID: 40056383 PMCID: PMC11934273 DOI: 10.1093/molbev/msaf050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 01/13/2025] [Accepted: 01/27/2025] [Indexed: 03/10/2025] Open
Abstract
Evolutionary turnover in noncoding regions has driven phenotypic divergence during past speciation events and continues to facilitate environmental adaptation through variants. We used a deep learning model to identify the substrates of regulatory turnover using genome-wide mutations mimicking three evolutionary pathways: recent history (human-chimp substitutions), modern population (human population variation), and mutational susceptibility (random mutations). We observed enhancer turnover in approximately 6% of the whole genome, with more than 80% of the novel activity arising from repurposing of enhancers between cell types. Frequency of turnover in a cell type is remarkably similar across the three pathways, despite only ∼19% overlap in the source regions. The majority of turnover loci were found to be localized within 100 kb of a gene, with the highest turnover occurring near neurodevelopmental genes including CNTNAP2, NPAS3, and AUTS2. Flanking enhancers of these genes undergo high turnover irrespective of the mutational model pathway, suggesting a high plasticity in neurocognitive evolution. Based on susceptibility to random mutations, these enhancers were identified as vulnerable by nature and feature a higher abundance of cell type-specific transcription factor binding sites. Our findings suggest that enhancer repurposing within vulnerable loci drives regulatory innovation while keeping the core regulatory networks intact.
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Affiliation(s)
- Jaya Srivastava
- Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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Wu Q, Yang D, Liu C, Xu T. Alcohol Plus Additional Risk Factors: Rodent Model of Liver Injury. Semin Liver Dis 2025; 45:81-98. [PMID: 39719149 DOI: 10.1055/a-2490-4278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2024]
Abstract
Alcohol-associated liver disease (ALD), primarily caused by chronic excessive alcohol consumption, is a leading cause of chronic liver disease worldwide. ALD includes alcohol-associated steatotic liver, alcohol-associated hepatitis (AH), fibrosis, cirrhosis, and can even progress to hepatocellular carcinoma (HCC). Existing research indicates that the risk factors of ALD are quite numerous. In addition to drinking patterns, factors such as aldehyde dehydrogenase 2 (ALDH2) deficiency, smoking, medication administration, high-fat diet (HFD), hepatitis virus infection, and disruption of circadian rhythms can also increase susceptibility to ALD. However, there is limited understanding regarding the exacerbation of liver injury by alcohol plus additional risk factors. This review presents rodent models of EtOH + "X," which simulate the synergistic effects of alcohol and additional risk factors in causing liver injury. These models offer a further exploration of the interactions between alcohol and additional risk factors, advancing the simulation of human ALD and providing a more reliable platform for studying disease mechanisms and exploring therapeutic interventions. We summarize the modeling methods, relevant indicators of liver injury, and focus on the targets of the synergistic effects as well as the associated mechanisms.
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Affiliation(s)
- Qixiang Wu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, P.R. China
- Institute for Liver Diseases of Anhui Medical University, Hefei, Anhui, P.R. China
| | - Dashuai Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, P.R. China
- Institute for Liver Diseases of Anhui Medical University, Hefei, Anhui, P.R. China
| | - Chixiang Liu
- Department of Blood Transfusion, Southern Medical University, Nanfang Hospital, Guangzhou, P.R. China
- School of Laboratory and Biotechnology, Institute of Antibody Engineering, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, Anhui Medical University, Hefei, Anhui, P.R. China
- Institute for Liver Diseases of Anhui Medical University, Hefei, Anhui, P.R. China
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Emmanuel NS, Yusuf T, Bako IG, Malgwi IS, Eze ED, Ali Z, Aliyu M. Hematological changes, oxidative stress assessment, and dysregulation of aquaporin-3 channel, prolactin, and oxytocin receptors in kidneys of lactating Wistar rats treated with monosodium glutamate. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:6213-6229. [PMID: 38446217 DOI: 10.1007/s00210-024-03008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
High consumption of locally produced delicacies could expose nursing mothers to high monosodium glutamate (MSG) levels, frequently used as a necessary condiment in low-income countries. Thus, this study evaluated some novel preliminary changes in renal hormonal receptors, the aquaporin-3 channel, oxidative stress markers, and hematological indices induced by monosodium glutamate in lactating rats. Post-parturition, twenty-four (24) lactating Wistar rats were divided into four (4) groups of six rats each (n = 6). Oral administration of distilled water and MSG started three (3) days postpartum as follows: group 1: distilled water (1 ml/kg BW), group 2: MSG (925 mg/kg BW), group 3: MSG (1850 mg/kg BW), and group 4: MSG (3700 mg/kg BW). At the end of the experiment, which lasted fourteen (14) days, animals were sacrificed and samples of blood and tissues were obtained for biochemical analysis. MSG administration significantly (p < 0.05) increased ROS and MDA, with a significant (p < 0.05) decrease in kidney antioxidants. Serum creatinine, total, conjugated, and unconjugated bilirubin significantly (p < 0.05) increased with MSG administration. The prolactin receptor was significantly reduced (p < 0.05), while the oxytocin receptor and aquaporin-3 channel were significantly (p < 0.05) increased in the MSG-administered groups. There were significant (p < 0.05) changes in the hematological indices of the MSG-administered animals. Thus, the findings of this study suggest that high MSG consumption causes hematological alterations and may alter renal function via increased ROS production and dysregulation of the AQP-3 channel, prolactin, and oxytocin receptors in the kidneys of lactating Wistar rats.
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Affiliation(s)
- Nachamada Solomon Emmanuel
- Department of Human Physiology, Faculty of Basic Medical Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Kaduna, Nigeria.
| | - Tanko Yusuf
- Department of Human Physiology, Faculty of Basic Medical Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Kaduna, Nigeria
| | - Ibrahim Gaya Bako
- Department of Human Physiology, Faculty of Basic Medical Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Kaduna, Nigeria
| | - Ibrahim Samaila Malgwi
- Department of Human Physiology, College of Medical Sciences, University of Maiduguri, Maiduguri, Borno, Nigeria
| | - Ejike Daniel Eze
- Department of Physiology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Huye Campus, Huye, Rwanda
| | - Zubairu Ali
- Department of Human Physiology, College of Medical Sciences, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Mohammed Aliyu
- Department of Human Physiology, Faculty of Basic Medical Sciences, College of Medical Sciences, Ahmadu Bello University, Zaria, Kaduna, Nigeria
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Qadir NA, Stachler L, Reddy AD, Diaz-Garcia G, Sottile E. Polysubstance-Induced Hepatotoxicity and the Role of Supportive Management. Cureus 2024; 16:e60649. [PMID: 38899269 PMCID: PMC11185993 DOI: 10.7759/cureus.60649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2024] [Indexed: 06/21/2024] Open
Abstract
With the continued rise of polysubstance use throughout the country, it has been shown to affect a multitude of organ systems. Drug-induced liver injury (DILI) has been widely documented in its association with salicylates or acetaminophen and the utility of using N-acetylcysteine (NAC) for its hepatoprotective effects. However, DILI caused by illicit drug use and guideline-directed management has had little research. We present the case of a 29-year-old female who presented with altered mental status. She was found to have a concomitant liver injury and was treated supportively without the use of NAC, with gradual improvement.
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Affiliation(s)
- Nadim A Qadir
- Internal Medicine, University of Florida College of Medicine - Jacksonville, Jacksonville, USA
| | - Luke Stachler
- Internal Medicine, University of Florida College of Medicine - Jacksonville, Jacksonville, USA
| | - Anvit D Reddy
- Internal Medicine, University of Florida College of Medicine - Jacksonville, Jacksonville, USA
| | - Gerardo Diaz-Garcia
- Internal Medicine, University of Florida College of Medicine - Jacksonville, Jacksonville, USA
| | - Elisa Sottile
- Internal Medicine, University of Florida College of Medicine - Jacksonville, Jacksonville, USA
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Mahdi WA, AlGhamdi SA, Alghamdi AM, Imam SS, Alshehri S, Almaniea MA, Hajjar BM, Al-Abbasi FA, Sayyed N, Kazmi I. Effect of Europinidin against Alcohol-Induced Liver Damage in Rats by Inhibiting the TNF-α/TGF-β/IFN-γ/NF-kB/Caspase-3 Signaling Pathway. ACS OMEGA 2023; 8:22656-22664. [PMID: 37396259 PMCID: PMC10308532 DOI: 10.1021/acsomega.3c01312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/12/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND The effect of europinidin on alcoholic liver damage in rats was examined in this research. METHODS A total of 24 Wistar rats were grouped in the same way into four groups: normal control (normal), ethanol control (EtOH), europinidin low dose (10 mg/kg), and europinidin higher dose (20 mg/kg). The test group rats were orally treated with europinidin-10 and europinidin-20 for 4 weeks, whereas 5 mL/kg distilled water was administered to control rats. In addition, 1 h after the last dose of the above-mentioned oral treatment, 5 mL/kg (i.p.) EtOH was injected to induce liver injury. After 5 h of EtOH treatment, samples of blood were withdrawn for biochemical estimations. RESULTS Administration of europinidin at both doses restored all of the estimated serum, i.e., liver function tests (ALT, AST, ALP), biochemical test (Creatinine, albumin, BUN, direct bilirubin, and LDH), lipid assessment (TC and TG), endogenous antioxidants (GSH-Px, SOD, and CAT), malondialdehyde (MDA), nitric oxide (NO), cytokines (TGF-β, TNF-α, IL-1β, IL-6, IFN-γ, and IL-12), caspase-3, and nuclear factor kappa B (NF-κB) associated with the EtOH group. CONCLUSION The results of the investigation showed that europinidin had favorable effects in rats given EtOH and may have hepatoprotective potential property.
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Affiliation(s)
- Wael A. Mahdi
- Department
of Pharmaceutics, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Shareefa A. AlGhamdi
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Saudi Arabia
- Experimental
Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Amira M. Alghamdi
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Syed Sarim Imam
- Department
of Pharmaceutics, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Sultan Alshehri
- Department
of Pharmaceutics, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad A. Almaniea
- Department
of Pharmaceutics, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Baraa Mohammed Hajjar
- Department
of Pharmaceutics, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Fahad A. Al-Abbasi
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Nadeem Sayyed
- School
of Pharmacy, Glocal University, Saharanpur 247121, India
| | - Imran Kazmi
- Department
of Biochemistry, Faculty of Sciences, King
Abdulaziz University, Jeddah 21589, Saudi Arabia
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