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Snelleksz M, Dean B. Higher levels of AKT-interacting protein in the frontal pole from people with schizophrenia are limited to a sub-group who have a marked deficit in cortical muscarinic M1 receptors. Psychiatry Res 2024; 341:116156. [PMID: 39236366 DOI: 10.1016/j.psychres.2024.116156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 06/29/2024] [Accepted: 07/03/2024] [Indexed: 09/07/2024]
Abstract
We are studying the molecular pathology of a sub-group within schizophrenia (∼ 25 %: termed Muscarinic Receptor Deficit subgroup of Schizophrenia (MRDS)) who can be separated because they have very low levels of cortical muscarinic M1 receptors (CHRM1). Based on our transcriptomic data from Brodmann's area ((BA) 9, 10 and 33 (controls, schizophrenia and mood disorders) and the cortex of the CHRM1-/- mouse (a molecular model of aberrant CHRM1 signaling), we predicted levels of AKT interacting protein (AKTIP), but not tubulin alpha 1b (TUBA1B) or AKT serine/threonine kinase 1 (AKT1) and pyruvate dehydrogenase kinase 1 (PDK1) (two AKTIP-functionally associated proteins), would be changed in MRDS. Hence, we used Western blotting to measure AKTIP (BA 10: controls, schizophrenia and mood disorders; BA 9: controls and schizophrenia) plus TUBA1B, AKT1 and PDK1 (BA 10: controls and schizophrenia) proteins. The only significant change with diagnosis was higher levels of AKTIP protein in BA 10 (Cohen's d = 0.73; p = 0.02) in schizophrenia compared to controls due to higher levels of AKTIP only in people with MRDS (Cohen's d = 0.80; p = 0.03). As AKTIP is involved in AKT1 signaling, our data suggests that signaling pathway is particularly disturbed in BA 10 in MRDS.
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Affiliation(s)
- Megan Snelleksz
- The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia.
| | - Brian Dean
- The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
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2
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Abebe BK, Wang J, Guo J, Wang H, Li A, Zan L. A review of emerging technologies, nutritional practices, and management strategies to improve intramuscular fat composition in beef cattle. Anim Biotechnol 2024; 35:2388704. [PMID: 39133095 DOI: 10.1080/10495398.2024.2388704] [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: 11/21/2023] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
The flavour, tenderness and juiciness of the beef are all impacted by the composition of the intramuscular fat (IMF), which is a key determinant of beef quality. Thus, enhancing the IMF composition of beef cattle has become a major area of research. Consequently, the aim of this paper was to provide insight and synthesis into the emerging technologies, nutritional practices and management strategies to improve IMF composition in beef cattle. This review paper examined the current knowledge of management techniques and nutritional approaches relevant to cattle farming in the beef industry. It includes a thorough investigation of animal handling, weaning age, castration, breed selection, sex determination, environmental factors, grazing methods, slaughter weight and age. Additionally, it rigorously explored dietary energy levels and optimization of fatty acid profiles, as well as the use of feed additives and hormone implant techniques with their associated regulations. The paper also delved into emerging technologies that are shaping future beef production, such as genomic selection methods, genome editing techniques, epigenomic analyses, microbiome manipulation strategies, transcriptomic profiling approaches and metabolomics analyses. In conclusion, a holistic approach combining genomic, nutritional and management strategies is imperative for achieving targeted IMF content and ensuring high-quality beef production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- Department of Animal Science, Werabe University, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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3
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Reina C, Šabanović B, Lazzari C, Gregorc V, Heeschen C. Unlocking the future of cancer diagnosis - promises and challenges of ctDNA-based liquid biopsies in non-small cell lung cancer. Transl Res 2024; 272:41-53. [PMID: 38838851 DOI: 10.1016/j.trsl.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/29/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
The advent of liquid biopsies has brought significant changes to the diagnosis and monitoring of non-small cell lung cancer (NSCLC), presenting both promise and challenges. Molecularly targeted drugs, capable of enhancing survival rates, are now available to around a quarter of NSCLC patients. However, to ensure their effectiveness, precision diagnosis is essential. Circulating tumor DNA (ctDNA) analysis as the most advanced liquid biopsy modality to date offers a non-invasive method for tracking genomic changes in NSCLC. The potential of ctDNA is particularly rooted in its ability to furnish comprehensive (epi-)genetic insights into the tumor, thereby aiding personalized treatment strategies. One of the key advantages of ctDNA-based liquid biopsies in NSCLC is their ability to capture tumor heterogeneity. This capability ensures a more precise depiction of the tumor's (epi-)genomic landscape compared to conventional tissue biopsies. Consequently, it facilitates the identification of (epi-)genetic alterations, enabling informed treatment decisions, disease progression monitoring, and early detection of resistance-causing mutations for timely therapeutic interventions. Here we review the current state-of-the-art in ctDNA-based liquid biopsy technologies for NSCLC, exploring their potential to revolutionize clinical practice. Key advancements in ctDNA detection methods, including PCR-based assays, next-generation sequencing (NGS), and digital PCR (dPCR), are discussed, along with their respective strengths and limitations. Additionally, the clinical utility of ctDNA analysis in guiding treatment decisions, monitoring treatment response, detecting minimal residual disease, and identifying emerging resistance mechanisms is examined. Liquid biopsy analysis bears the potential of transforming NSCLC management by enabling non-invasive monitoring of Minimal Residual Disease and providing early indicators for response to targeted treatments including immunotherapy. Furthermore, considerations regarding sample collection, processing, and data interpretation are highlighted as crucial factors influencing the reliability and reproducibility of ctDNA-based assays. Addressing these challenges will be essential for the widespread adoption of ctDNA-based liquid biopsies in routine clinical practice, ultimately paving the way toward personalized medicine and improved outcomes for patients with NSCLC.
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Affiliation(s)
- Chiara Reina
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Berina Šabanović
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Chiara Lazzari
- Department of Medical Oncology, Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Vanesa Gregorc
- Department of Medical Oncology, Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy
| | - Christopher Heeschen
- Pancreatic Cancer Heterogeneity, Candiolo Cancer Institute FPO-IRCCS, Candiolo, Turin, Italy;.
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Marchante-Gayón JM, Nicolás Carcelén J, Potes Rodríguez H, Pineda-Cevallos D, Rodas Sánchez L, González-Gago A, Rodríguez-González P, García Alonso JI. Quantification of modified nucleotides and nucleosides by isotope dilution mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:998-1018. [PMID: 37597182 DOI: 10.1002/mas.21865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 08/21/2023]
Abstract
Epigenetic modifications are closely related to certain disorders of the organism, including the development of tumors. One of the main epigenetic modifications is the methylation of DNA cytosines, 5-methyl-2'-deoxycycytidine. Furthermore, 5-mdC can be oxidized to form three new modifications, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxy-2'-deoxycytidine. The coupling of liquid chromatography with tandem mass spectrometry has been widely used for the total determination of methylated DNA cytosines in samples of biological and clinical interest. These methods are based on the measurement of the free compounds (e.g., urine) or after complete hydrolysis of the DNA (e.g., tissues) followed by a preconcentration, derivatization, and/or clean-up step. This review highlights the main advances in the quantification of modified nucleotides and nucleosides by isotope dilution using isotopically labeled analogs combined with liquid or gas chromatography coupled to mass spectrometry reported in the last 20 years. The different possible sources of labeled compounds are indicated. Special emphasis has been placed on the different types of chromatography commonly used (reverse phase and hydrophilic interaction liquid chromatography) and the derivatization methods developed to enhance chromatographic resolution and ionization efficiency. We have also revised the application of bidimensional chromatography and indicated significant biological and clinical applications of these determinations.
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Affiliation(s)
- Juan M Marchante-Gayón
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Jesús Nicolás Carcelén
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Helí Potes Rodríguez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Daniela Pineda-Cevallos
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Laura Rodas Sánchez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Adriana González-Gago
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Jose I García Alonso
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
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Arshi A, Mahmoudi E, Raeisi F, Dehghan Tezerjani M, Bahramian E, Ahmed Y, Peng C. Exploring potential roles of long non-coding RNAs in cancer immunotherapy: a comprehensive review. Front Immunol 2024; 15:1446937. [PMID: 39257589 PMCID: PMC11384988 DOI: 10.3389/fimmu.2024.1446937] [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: 06/10/2024] [Accepted: 08/05/2024] [Indexed: 09/12/2024] Open
Abstract
Cancer treatment has long been fraught with challenges, including drug resistance, metastasis, and recurrence, making it one of the most difficult diseases to treat effectively. Traditional therapeutic approaches often fall short due to their inability to target cancer stem cells and the complex genetic and epigenetic landscape of tumors. In recent years, cancer immunotherapy has revolutionized the field, offering new hope and viable alternatives to conventional treatments. A particularly promising area of research focuses on non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs), and their role in cancer resistance and the modulation of signaling pathways. To address these challenges, we performed a comprehensive review of recent studies on lncRNAs and their impact on cancer immunotherapy. Our review highlights the crucial roles that lncRNAs play in affecting both innate and adaptive immunity, thereby influencing the outcomes of cancer treatments. Key observations from our review indicate that lncRNAs can modify the tumor immune microenvironment, enhance immune cell infiltration, and regulate cytokine production, all of which contribute to tumor growth and resistance to therapies. These insights suggest that lncRNAs could serve as potential targets for precision medicine, opening up new avenues for developing more effective cancer immunotherapies. By compiling recent research on lncRNAs across various cancers, this review aims to shed light on their mechanisms within the tumor immune microenvironment.
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Affiliation(s)
- Asghar Arshi
- Department of Biology, York University, Toronto, ON, Canada
| | - Esmaeil Mahmoudi
- Young Researchers and Elite Club, Islamic Azad University, Shahrekord, Iran
| | | | - Masoud Dehghan Tezerjani
- Department of bioinformatics, School of Advanced Medical Technologies, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Bahramian
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Yeasin Ahmed
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Chun Peng
- Department of Biology, York University, Toronto, ON, Canada
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Zhong A, Zou X, Wei Z, Gan L, Peng J, Li Y, Wang Z, Liu Y. Cotton Pectate Lyase GhPEL48_Dt Promotes Fiber Initiation Mediated by Histone Acetylation. PLANTS (BASEL, SWITZERLAND) 2024; 13:2356. [PMID: 39273840 DOI: 10.3390/plants13172356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/18/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024]
Abstract
GhPEL48_Dt, a Pectate lyase (PEL, EC4.2.2.2), is a crucial enzyme involved in cell-wall modification and pectin degradation. Studies have shown that the GhPEL48_Dt also plays a significant role in cotton-fiber development; however, the specific function and regulatory mechanism of GhPEL48_Dt in cotton-fiber development are still not fully understood. Here, we found that the histone deacetylase inhibitor-Trichostatin A significantly reduces the transcript levels of GhPEL48_Dt and its enzyme activity. Further, silencing of GhPEL48_Dt significantly inhibits the initiation and elongation of cotton fibers by promoting pectin degradation, and the heterologous expression of GhPEL48_Dt promotes the development of trichomes and root hairs in Arabidopsis, which suggests that GhPEL48_Dt plays a positive and conserved role in single cell i.e., fiber, root hair, and leaf trichome development. Collectively, this paper provides a comprehensive analysis of the fundamental characteristics and functions of GhPEL48_Dt in fiber development, including the regulatory role of histone acetylation on GhPEL48_Dt, which contributes to the understanding of pectin degradation pathways and establishes a theoretical foundation for elucidating its regulatory mechanism.
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Affiliation(s)
- Anlin Zhong
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Xianyan Zou
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Zhenzhen Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Lei Gan
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jun Peng
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yonghui Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yuanyuan Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
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Yang M, Feng Y, Liu J, Wang H, Wu S, Zhao W, Kim P, Zhou X. SexAnnoDB, a knowledgebase of sex-specific regulations from multi-omics data of human cancers. Biol Sex Differ 2024; 15:64. [PMID: 39175079 PMCID: PMC11342657 DOI: 10.1186/s13293-024-00638-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Sexual differences across molecular levels profoundly impact cancer biology and outcomes. Patient gender significantly influences drug responses, with divergent reactions between men and women to the same drugs. Despite databases on sex differences in human tissues, understanding regulations of sex disparities in cancer is limited. These resources lack detailed mechanistic studies on sex-biased molecules. METHODS In this study, we conducted a comprehensive examination of molecular distinctions and regulatory networks across 27 cancer types, delving into sex-biased effects. Our analyses encompassed sex-biased competitive endogenous RNA networks, regulatory networks involving sex-biased RNA binding protein-exon skipping events, sex-biased transcription factor-gene regulatory networks, as well as sex-biased expression quantitative trait loci, sex-biased expression quantitative trait methylation, sex-biased splicing quantitative trait loci, and the identification of sex-biased cancer therapeutic drug target genes. All findings from these analyses are accessible on SexAnnoDB ( https://ccsm.uth.edu/SexAnnoDB/ ). RESULTS From these analyses, we defined 126 cancer therapeutic target sex-associated genes. Among them, 9 genes showed sex-biased at both the mRNA and protein levels. Specifically, S100A9 was the target of five drugs, of which calcium has been approved by the FDA for the treatment of colon and rectal cancers. Transcription factor (TF)-gene regulatory network analysis suggested that four TFs in the SARC male group targeted S100A9 and upregulated the expression of S100A9 in these patients. Promoter region methylation status was only associated with S100A9 expression in KIRP female patients. Hypermethylation inhibited S100A9 expression and was responsible for the downregulation of S100A9 in these female patients. CONCLUSIONS Comprehensive network and association analyses indicated that the sex differences at the transcriptome level were partially the result of corresponding sex-biased epigenetic and genetic molecules. Overall, SexAnnoDB offers a discipline-specific search platform that could potentially assist basic experimental researchers or physicians in developing personalized treatment plans.
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Affiliation(s)
- Mengyuan Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yuzhou Feng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Shihezi University School of Medicine, Shihezi University, Shihezi , 832003, China
| | - Jiajia Liu
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, 77030, USA
| | - Hong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Sijia Wu
- School of Life Sciences and Technology, Xidian University, Xi'an, 710126, China
| | - Weiling Zhao
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, 77030, USA.
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, 77030, USA.
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Wall LL, Brown D. Personhood Begins at Birth: The Rational Foundation for Abortion Policy in a Secular State. JOURNAL OF BIOETHICAL INQUIRY 2024:10.1007/s11673-024-10352-0. [PMID: 39172346 DOI: 10.1007/s11673-024-10352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/03/2024] [Indexed: 08/23/2024]
Abstract
The struggle over legal abortion access in the United States is a religious controversy, not a scientific debate. Religious activists who believe that meaningful individual life (i.e., "personhood") begins at a specific "moment-of-conception" are attempting to pass laws that force this view upon all pregnant persons, irrespective of their medical circumstances, individual preferences, or personal religious beliefs. This paper argues that such actions promote a constitutionally prohibited "establishment of religion." Abortion policy in a secular state must be based upon scientifically accurate biology, not unprovable theological presuppositions. The scientific facts regarding human pregnancy do not support the position that personhood begins with fertilization-at which point a pregnancy does not yet even exist. Abortion policy should regard the embryo/fetus as part of the pregnant individual's body until delivery. We argue that individual "personhood" only begins when the latent potentialities of the fetal nervous system are actualized in the newborn after delivery. The paper argues that instantiating non-scientific beliefs concerning embryonic/fetal "personhood" into the law as the basis for abortion policy establishes a state-sponsored religion. The protection of religious liberty requires that abortion be decriminalized. Abortion should be treated like any other medical procedure and regulated similarly. To protect both religious freedom and sound medical practice, individual legal personhood should be recognized as beginning only at birth.
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Affiliation(s)
- L Lewis Wall
- Departments of Obstetrics & Gynecology and Anthropology, Washington University in St. Louis, St. Louis, MO, United States.
| | - Douglas Brown
- Department of Surgery, Washington University in St. Louis, St. Louis, MO, United States
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Gupta I, Badrzadeh F, Tsentalovich Y, Gaykalova DA. Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma. J Exp Clin Cancer Res 2024; 43:239. [PMID: 39169426 PMCID: PMC11337877 DOI: 10.1186/s13046-024-03141-5] [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: 05/20/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) accounts for around 90% of all oral cancers and is the eighth most common cancer worldwide. Despite progress in managing OSCC, the overall prognosis remains poor, with a survival rate of around 50-60%, largely due to tumor size and recurrence. The challenges of late-stage diagnosis and limitations in current methods emphasize the urgent need for less invasive techniques to enable early detection and treatment, crucial for improving outcomes in this aggressive form of oral cancer. Research is currently aimed at unraveling tumor-specific metabolite profiles to identify candidate biomarkers as well as discover underlying pathways involved in the onset and progression of cancer that could be used as new targets for diagnostic and therapeutic purposes. Metabolomics is an advanced technological approach to identify metabolites in different sample types (biological fluids and tissues). Since OSCC promotes metabolic reprogramming influenced by a combination of genetic predisposition and environmental factors, including tobacco and alcohol consumption, and viral infections, the identification of distinct metabolites through screening may aid in the diagnosis of this condition. Moreover, studies have shown the use of metabolites during the catalysis of epigenetic modification, indicating a link between epigenetics and metabolism. In this review, we will focus on the link between environmental, genetic, and epigenetic influences in metabolomic alterations in OSCC. In addition, we will discuss therapeutic targets of tumor metabolism, which may prevent oral tumor growth, metastasis, and drug resistance.
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Affiliation(s)
- Ishita Gupta
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Fariba Badrzadeh
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Yuri Tsentalovich
- International tomography center CB RAS, Institutskaya str. 3a, Novosibirsk, 630090, Russia
| | - Daria A Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Institute for Genome Sciences, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
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Aljabali AAA, Alkaraki AK, Gammoh O, Tambuwala MM, Mishra V, Mishra Y, Hassan SS, El-Tanani M. Deciphering Depression: Epigenetic Mechanisms and Treatment Strategies. BIOLOGY 2024; 13:638. [PMID: 39194576 DOI: 10.3390/biology13080638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
Depression, a significant mental health disorder, is under intense research scrutiny to uncover its molecular foundations. Epigenetics, which focuses on controlling gene expression without altering DNA sequences, offers promising avenues for innovative treatment. This review explores the pivotal role of epigenetics in depression, emphasizing two key aspects: (I) identifying epigenetic targets for new antidepressants and (II) using personalized medicine based on distinct epigenetic profiles, highlighting potential epigenetic focal points such as DNA methylation, histone structure alterations, and non-coding RNA molecules such as miRNAs. Variations in DNA methylation in individuals with depression provide opportunities to target genes that are associated with neuroplasticity and synaptic activity. Aberrant histone acetylation may indicate that antidepressant strategies involve enzyme modifications. Modulating miRNA levels can reshape depression-linked gene expression. The second section discusses personalized medicine based on epigenetic profiles. Analyzing these patterns could identify biomarkers associated with treatment response and susceptibility to depression, facilitating tailored treatments and proactive mental health care. Addressing ethical concerns regarding epigenetic information, such as privacy and stigmatization, is crucial in understanding the biological basis of depression. Therefore, researchers must consider these issues when examining the role of epigenetics in mental health disorders. The importance of epigenetics in depression is a critical aspect of modern medical research. These findings hold great potential for novel antidepressant medications and personalized treatments, which would significantly improve patient outcomes, and transform psychiatry. As research progresses, it is expected to uncover more complex aspects of epigenetic processes associated with depression, enhance our comprehension, and increase the effectiveness of therapies.
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Affiliation(s)
- Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid 21163, Jordan
| | - Almuthanna K Alkaraki
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid 21163, Jordan
| | - Omar Gammoh
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Yarmouk University, P.O. Box 566, Irbid 21163, Jordan
| | - Murtaza M Tambuwala
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Yachana Mishra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India
| | - Mohamed El-Tanani
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah P.O. Box 11172, United Arab Emirates
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11
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An W, Zhou J, Qiu Z, Wang P, Han X, Cheng Y, He Z, An Y, Li S. Identification of crosstalk genes and immune characteristics between Alzheimer's disease and atherosclerosis. Front Immunol 2024; 15:1443464. [PMID: 39188714 PMCID: PMC11345154 DOI: 10.3389/fimmu.2024.1443464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024] Open
Abstract
Background Advancements in modern medicine have extended human lifespan, but they have also led to an increase in age-related diseases such as Alzheimer's disease (AD) and atherosclerosis (AS). Growing research evidence indicates a close connection between these two conditions. Methods We downloaded four gene expression datasets related to AD and AS from the Gene Expression Omnibus (GEO) database (GSE33000, GSE100927, GSE44770, and GSE43292) and performed differential gene expression (DEGs) analysis using the R package "limma". Through Weighted gene correlation network analysis (WGCNA), we selected the gene modules most relevant to the diseases and intersected them with the DEGs to identify crosstalk genes (CGs) between AD and AS. Subsequently, we conducted functional enrichment analysis of the CGs using DAVID. To screen for potential diagnostic genes, we applied the least absolute shrinkage and selection operator (LASSO) regression and constructed a logistic regression model for disease prediction. We established a protein-protein interaction (PPI) network using STRING (https://cn.string-db.org/) and Cytoscape and analyzed immune cell infiltration using the CIBERSORT algorithm. Additionally, NetworkAnalyst (http://www.networkanalyst.ca) was utilized for gene regulation and interaction analysis, and consensus clustering was employed to determine disease subtypes. All statistical analyses and visualizations were performed using various R packages, with a significance level set at p<0.05. Results Through intersection analysis of disease-associated gene modules identified by DEGs and WGCNA, we identified a total of 31 CGs co-existing between AD and AS, with their biological functions primarily associated with immune pathways. LASSO analysis helped us identify three genes (C1QA, MT1M, and RAMP1) as optimal diagnostic CGs for AD and AS. Based on this, we constructed predictive models for both diseases, whose accuracy was validated by external databases. By establishing a PPI network and employing four topological algorithms, we identified four hub genes (C1QB, CSF1R, TYROBP, and FCER1G) within the CGs, closely related to immune cell infiltration. NetworkAnalyst further revealed the regulatory networks of these hub genes. Finally, defining C1 and C2 subtypes for AD and AS respectively based on the expression profiles of CGs, we found the C2 subtype exhibited immune overactivation. Conclusion This study utilized gene expression matrices and various algorithms to explore the potential links between AD and AS. The identification of CGs revealed interactions between these two diseases, with immune and inflammatory imbalances playing crucial roles in their onset and progression. We hope these findings will provide valuable insights for future research on AD and AS.
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Affiliation(s)
- Wenhao An
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jiajun Zhou
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Zhiqiang Qiu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Peishen Wang
- Department of Research and Development, Beijing Yihua Biotechnology Co., Ltd, Beijing, China
| | - Xinye Han
- Department of Research and Development, Beijing Yihua Biotechnology Co., Ltd, Beijing, China
| | - Yanwen Cheng
- Department of Research and Development, Beijing Yihua Biotechnology Co., Ltd, Beijing, China
| | - Zi He
- Department of Research and Development, Beijing Yihua Biotechnology Co., Ltd, Beijing, China
| | - Yihua An
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Shouwei Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
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12
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Muto Y, Dixon EE, Yoshimura Y, Ledru N, Kirita Y, Wu H, Humphreys BD. Epigenetic reprogramming driving successful and failed repair in acute kidney injury. SCIENCE ADVANCES 2024; 10:eado2849. [PMID: 39110788 PMCID: PMC11305376 DOI: 10.1126/sciadv.ado2849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Acute kidney injury (AKI) causes epithelial damage followed by subsequent repair. While successful repair restores kidney function, this process is often incomplete and can lead to chronic kidney disease (CKD) in a process called failed repair. To better understand the epigenetic reprogramming driving this AKI-to-CKD transition, we generated a single-nucleus multiomic atlas for the full mouse AKI time course, consisting of ~280,000 single-nucleus transcriptomes and epigenomes. We reveal cell-specific dynamic alterations in gene regulatory landscapes reflecting, especially, activation of proinflammatory pathways. We further generated single-nucleus multiomic data from four human AKI samples including validation by genome-wide identification of nuclear factor κB binding sites. A regularized regression analysis identifies key regulators involved in both successful and failed repair cell fate, identifying the transcription factor CREB5 as a regulator of both successful and failed tubular repair that also drives proximal tubular cell proliferation after injury. Our interspecies multiomic approach provides a foundation to comprehensively understand cell states in AKI.
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Affiliation(s)
- Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E. Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicolas Ledru
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yuhei Kirita
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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13
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Gigliotti G, Joshi R, Khalid A, Widmer D, Boccellino M, Viggiano D. Epigenetics, Microbiome and Personalized Medicine: Focus on Kidney Disease. Int J Mol Sci 2024; 25:8592. [PMID: 39201279 PMCID: PMC11354516 DOI: 10.3390/ijms25168592] [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: 07/03/2024] [Revised: 07/25/2024] [Accepted: 07/31/2024] [Indexed: 09/02/2024] Open
Abstract
Personalized medicine, which involves modifying treatment strategies/drug dosages based on massive laboratory/imaging data, faces large statistical and study design problems. The authors believe that the use of continuous multidimensional data, such as those regarding gut microbiota, or binary multidimensional systems properly transformed into a continuous variable, such as the epigenetic clock, offer an advantageous scenario for the design of trials of personalized medicine. We will discuss examples focusing on kidney diseases, specifically on IgA nephropathy. While gut dysbiosis can provide a treatment strategy to restore the standard gut microbiota using probiotics, transforming epigenetic omics data into epigenetic clocks offers a promising tool for personalized acute and chronic kidney disease care. Epigenetic clocks involve a complex transformation of DNA methylome data into estimated biological age. These clocks can identify people at high risk of developing kidney problems even before symptoms appear. Some of the effects of both the epigenetic clock and microbiota on kidney diseases seem to be mediated by endothelial dysfunction. These "big data" (epigenetic clocks and microbiota) can help tailor treatment plans by pinpointing patients likely to experience rapid declines or those who might not need overly aggressive therapies.
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Affiliation(s)
| | - Rashmi Joshi
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
| | - Anam Khalid
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
| | | | - Mariarosaria Boccellino
- Department Experimental Medicine, University of Campania, 81100 Naples, Italy
- Department Life Sciences, Health and Health Professions, Link University, 00165 Rome, Italy
| | - Davide Viggiano
- Department Translational Medical Sciences, University of Campania, 81100 Naples, Italy; (R.J.); (A.K.); (D.V.)
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14
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Orlandi E, Ceccuzzi L, Belpinati F, Rodolfo M, Malerba G, Trabetti E, Gomez-Lira M, Romanelli MG. Sex-dependent interaction of PTGS2 with miR-146a as risk factor for melanoma and the impact of sex hormones in gene expression in skin cells. Melanoma Res 2024; 34:296-306. [PMID: 38934060 DOI: 10.1097/cmr.0000000000000978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Gender disparity in melanoma is a complex issue where sex hormones could be engaged. Differences in genetic variations are important in understanding the mechanisms of sex disparity in melanoma. Post-transcriptional regulation of prostaglandin-endoperoxide synthase (PTGS2) mRNA occurs through a complex interplay of specific trans-acting RNA-binding proteins and microRNAs. MiR-146a is a key player in melanoma, modulating immune responses and tumor microenvironment (TME). Polymorphisms in PTGS2 gene rs20415GC have been associated with an increased risk of melanoma. Epistasis between polymorphisms rs20415GC was investigated by genotyping 453 melanoma patients and 382 control individuals. The effects of testosterone and 17β-estradiol were analyzed in keratinocytes and two melanoma cell lines. The rs2910164GG showed a higher risk in the presence of the genotype rs20417CC in the male population. Testosterone and 17β-estradiol act differently on PTGS2 and miR-146a expression, depending on the cell type. Testosterone augments PTGS2 gene expression in keratinocytes and miR-146a in melanoma cells. While 17β-estradiol only increases miR-146a expression in HaCaT cells. The present study indicates a sex-specific relation between miR-146a and PTGS2 polymorphisms with melanoma cancer risk. Testosterone and 17β-estradiol act differently on the expression of PTGS2 and miR-146a depending on the skin cell type.
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Affiliation(s)
- Elisa Orlandi
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, Verona
| | - Laura Ceccuzzi
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, Verona
| | - Francesca Belpinati
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, Verona
| | - Monica Rodolfo
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giovanni Malerba
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, Verona
| | - Elisabetta Trabetti
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, Verona
| | - Macarena Gomez-Lira
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, Verona
| | - Maria Grazia Romanelli
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, Verona
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15
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Hu W, Peng Z, Lv J, Zhang Q, Wang X, Xia Q. Developmental and nuclear proteomic signatures characterize the temporal regulation of fibroin synthesis during the last molting-feeding transition of silkworm. Int J Biol Macromol 2024; 274:133028. [PMID: 38857725 DOI: 10.1016/j.ijbiomac.2024.133028] [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: 06/27/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/12/2024]
Abstract
Silkworm fibroins are natural proteinaceous macromolecules and provide core mechanical properties to silk fibers. The synthesis process of fibroins is posterior silk gland (PSG)-exclusive and appears active at the feeding stage and inactive at the molting stage. However, the molecular mechanisms controlling it remain elusive. Here, the silk gland's physiological and nuclear proteomic features were used to characterize changes in its structure and development from molting to feeding stages. The temporal expression profile and immunofluorescence analyses revealed a synchronous transcriptional on-off mode of fibroin genes. Next, the comparative nuclear proteome of the PSG during the last molting-feeding transition identified 798 differentially abundant proteins (DAPs), including 42 transcription factors and 15 epigenetic factors. Protein-protein interaction network analysis showed a "CTCF-FOX-HOX-SOX" association with activated expressions at the molting stage, suggesting a relatively complex and multifactorial regulation of the PSG at the molting stage. In addition, FAIRE-seq verification indicated "closed" and "open" conformations of fibroin gene promoters at the molting and feeding stages, respectively. Such proteome combined with chromatin accessibility analysis revealed the detailed signature of protein factors involved in the temporal regulation of fibroin synthesis and provided insights into silk gland development as well as silk production in silkworms.
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Affiliation(s)
- Wenbo Hu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
| | - Zhangchuan Peng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China; Chongqing Institute of Advanced Pathology, Jinfeng Laboratory, Chongqing 401329, China
| | - Jinfeng Lv
- Institute for Silk and Related Biomaterials Research, Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Quan Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Xiaogang Wang
- School of Basic Medical Science, Chongqing College of Traditional Chinese Medicine, Chongqing 400065, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing 400715, China.
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16
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Sajjanar B, Aalam MT, Khan O, Dhara SK, Ghosh J, Gandham RK, Gupta PK, Chaudhuri P, Dutt T, Singh G, Mishra BP. Genome-wide DNA methylation profiles regulate distinct heat stress response in zebu (Bos indicus) and crossbred (Bos indicus × Bos taurus) cattle. Cell Stress Chaperones 2024; 29:603-614. [PMID: 38936463 PMCID: PMC11264184 DOI: 10.1016/j.cstres.2024.06.005] [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: 11/23/2023] [Revised: 05/22/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024] Open
Abstract
Epigenetic variations result from long-term adaptation to environmental factors. The Bos indicus (zebu) adapted to tropical conditions, whereas Bos taurus adapted to temperate conditions; hence native zebu cattle and its crossbred (B indicus × B taurus) show differences in responses to heat stress. The present study evaluated genome-wide DNA methylation profiles of these two breeds of cattle that may explain distinct heat stress responses. Physiological responses to heat stress and estimated values of Iberia heat tolerance coefficient and Benezra's coefficient of adaptability revealed better relative thermotolerance of Hariana compared to the Vrindavani cattle. Genome-wide DNA methylation patterns were different for Hariana and Vrindavani cattle. The comparison between breeds indicated the presence of 4599 significant differentially methylated CpGs with 756 hypermethylated and 3845 hypomethylated in Hariana compared to the Vrindavani cattle. Further, we found 79 genes that showed both differential methylation and differential expression that are involved in cellular stress response functions. Differential methylations in the microRNA coding sequences also revealed their functions in heat stress responses. Taken together, epigenetic differences represent the potential regulation of long-term adaptation of Hariana (B indicus) cattle to the tropical environment and relative thermotolerance.
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Affiliation(s)
- Basavaraj Sajjanar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India; ICAR-Indian Veterinary Research Institute, Bengaluru Campus, Bengaluru, Karnataka, India.
| | - Mohd Tanzeel Aalam
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Owais Khan
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Sujoy K Dhara
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Jyotirmoy Ghosh
- ICAR-National Institute of Animal Nutrition and Physiology, Bengaluru, Karnataka, India
| | - Ravi Kumar Gandham
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Praveen K Gupta
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Pallab Chaudhuri
- ICAR-Indian Veterinary Research Institute, Bengaluru Campus, Bengaluru, Karnataka, India
| | - Triveni Dutt
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Gyanendra Singh
- ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India.
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17
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Wan Z, Chibnik LB, Valeri L, Hughes TM, Blacker D, Ma Y. DNA Methylation Mediates the Association Between Cardiometabolic Risk Factors and Cognition: Findings From the Health and Retirement Study. J Gerontol A Biol Sci Med Sci 2024; 79:glae167. [PMID: 38943310 DOI: 10.1093/gerona/glae167] [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: 12/21/2023] [Indexed: 07/01/2024] Open
Abstract
The association between cardiometabolic risk factors and cognitive function has been well documented, but the underlying mechanisms are not fully understood. This longitudinal study aimed to investigate the potential mediating role of DNA methylation in this association. We conducted the analyses in 3 708 participants (mean [standard deviation {SD}] age: 67.3 [9.5], women: 57.9%) from the Health and Retirement Study who were assessed in the 2014-2020 waves, had Infinium Methylation EPIC BeadChip methylation assays from the 2016 Venous Blood Study, and had cognitive assessment between 2016 and 2020. Causal mediation analyses were used to test the mediation role of DNA methylation in the associations between cardiometabolic risk factors and cognition, adjusting for demographic, socioeconomic, and lifestyle factors. Hypertension (-0.061 in composite cognitive z-score; 95% confidence interval [CI: -0.119, -0.004]) and diabetes (-0.134; 95% CI: [-0.198, -0.071]) were significantly associated with worse cognitive function while abnormal body weight and hypercholesterolemia were not. An increased number of cardiometabolic risk factors was associated with worse cognitive function (p = .002). DNA methylation significantly mediated the association of hypertension (mediated effect on composite cognitive z-score: -0.023; 95% CI: -0.033, -0.014), diabetes (-0.022; 95% CI: -0.032, -0.014), and obesity (-0.021; 95% CI: -0.033, -0.011) with cognitive function, whereas the mediation effect was not observed for having hypercholesterolemia. The estimated proportions mediated were 37.4% for hypertension and 16.7% for diabetes. DNA methylation may be an important mediator linking cardiometabolic risk factors to worse cognition and might even provide a potential target for dementia prevention.
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Affiliation(s)
- Zengyi Wan
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Lori B Chibnik
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Linda Valeri
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Timothy M Hughes
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Alzheimer's Disease Research Center, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Deborah Blacker
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yuan Ma
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA
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18
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Toustou C, Boulogne I, Gonzalez AA, Bardor M. Comparative RNA-Seq of Ten Phaeodactylum tricornutum Accessions: Unravelling Criteria for Robust Strain Selection from a Bioproduction Point of View. Mar Drugs 2024; 22:353. [PMID: 39195469 DOI: 10.3390/md22080353] [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: 04/30/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
The production of biologics in mammalian cells is hindered by some limitations including high production costs, prompting the exploration of other alternative expression systems that are cheaper and sustainable like microalgae. Successful productions of biologics such as monoclonal antibodies have already been demonstrated in the diatom Phaeodactylum tricornutum; however, limited production yields still remain compared to mammalian cells. Therefore, efforts are needed to make this microalga more competitive as a cell biofactory. Among the seventeen reported accessions of P. tricornutum, ten have been mainly studied so far. Among them, some have already been used to produce high-value-added molecules such as biologics. The use of "omics" is increasingly being described as useful for the improvement of both upstream and downstream steps in bioprocesses using mammalian cells. Therefore, in this context, we performed an RNA-Seq analysis of the ten most used P. tricornutum accessions (Pt1 to Pt10) and deciphered the differential gene expression in pathways that could affect bioproduction of biologics in P. tricornutum. Our results highlighted the benefits of certain accessions such as Pt9 or Pt4 for the production of biologics. Indeed, these accessions seem to be more advantageous. Moreover, these results contribute to a better understanding of the molecular and cellular biology of P. tricornutum.
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Affiliation(s)
- Charlotte Toustou
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
| | - Isabelle Boulogne
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
| | - Anne-Alicia Gonzalez
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Muriel Bardor
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
- ALGA BIOLOGICS, CURIB, 25 rue Tesnières, 76821 Mont-Saint-Aignan, France
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Ghosh Dastidar R, Jaroslawska J, Malinen M, Tuomainen TP, Virtanen JK, Bendik I, Carlberg C. In vivo vitamin D targets reveal the upregulation of focal adhesion-related genes in primary immune cells of healthy individuals. Sci Rep 2024; 14:17552. [PMID: 39080417 PMCID: PMC11289414 DOI: 10.1038/s41598-024-68741-9] [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: 04/10/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024] Open
Abstract
Vitamin D modulates innate and adaptive immunity, the molecular mechanisms of which we aim to understand under human in vivo conditions. Therefore, we designed the study VitDHiD (NCT03537027) as a human investigation, in which 25 healthy individuals were supplemented with a single vitamin D3 bolus (80,000 IU). Transcriptome-wide differential gene expression analysis of peripheral blood mononuclear cells (PBMCs), which were isolated directly before and 24 h after supplementation, identified 452 genes significantly (FDR < 0.05) responding to vitamin D. In vitro studies using PBMCs from the same individuals confirmed 138 of these genes as targets of 1α,25-dihydroxyvitamin D3. A subset of the 91 most regulated in vivo vitamin D target genes indicated focal adhesion as the major pathway being upregulated by vitamin D3 supplementation of healthy individuals. Differences in the individual-specific responsiveness of in vivo vitamin D target genes in relation to the increase of the person's vitamin D status allowed a segregation of the VitDHiD participants into 9 high, 12 mid and 4 low responders. The expression profile of nearly 600 genes elucidate the difference between high and low vitamin D responders, the most prominent of which is the HLA-C (major histocompatibility complex, class I, C) gene.
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Affiliation(s)
- Ranjini Ghosh Dastidar
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Ul. J. Tuwima 10, 10-748, Olsztyn, Poland
| | - Julia Jaroslawska
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Ul. J. Tuwima 10, 10-748, Olsztyn, Poland
| | - Marjo Malinen
- Department of Forestry and Environmental Engineering, South-Eastern Finland University of Applied Sciences, Kouvola, Finland
| | - Tomi-Pekka Tuomainen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Jyrki K Virtanen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Igor Bendik
- dsm-Firmenich AG, Health, Nutrition and Care (HNC), Kaiseraugst, Switzerland
| | - Carsten Carlberg
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Ul. J. Tuwima 10, 10-748, Olsztyn, Poland.
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland.
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20
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Wang H, Wang EZR, Feng B, Chakrabarti S. CircRNA_012164/MicroRNA-9-5p axis mediates cardiac fibrosis in diabetic cardiomyopathy. PLoS One 2024; 19:e0302772. [PMID: 39042659 PMCID: PMC11265710 DOI: 10.1371/journal.pone.0302772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/11/2024] [Indexed: 07/25/2024] Open
Abstract
Noncoding RNAs play a part in many chronic diseases and interact with each other to regulate gene expression. MicroRNA-9-5p (miR9) has been thought to be a potential inhibitor of diabetic cardiomyopathy. Here we examined the role of miR9 in regulating cardiac fibrosis in the context of diabetic cardiomyopathy. We further expanded our studies through investigation of a regulatory circularRNA, circRNA_012164, on the action of miR9. We showed at both the in vivo and in vitro level that glucose induced downregulation of miR9 and upregulation of circRNA_012164 resulted in the subsequent upregulation of downstream fibrotic genes. Further, knockdown of circRNA_012164 shows protective effects in cardiac endothelial cells and reverses increased transcription of genes associated with fibrosis and fibroblast proliferation through a regulatory axis with miR9. This study presents a novel regulatory axis involving noncoding RNA that is evidently important in the development of cardiac fibrosis in diabetic cardiomyopathy.
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Affiliation(s)
- Honglin Wang
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Eric Zi Rui Wang
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Biao Feng
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Subrata Chakrabarti
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
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Pradhan UK, Meher PK, Naha S, Sharma NK, Agarwal A, Gupta A, Parsad R. DBPMod: a supervised learning model for computational recognition of DNA-binding proteins in model organisms. Brief Funct Genomics 2024; 23:363-372. [PMID: 37651627 DOI: 10.1093/bfgp/elad039] [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: 05/08/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023] Open
Abstract
DNA-binding proteins (DBPs) play critical roles in many biological processes, including gene expression, DNA replication, recombination and repair. Understanding the molecular mechanisms underlying these processes depends on the precise identification of DBPs. In recent times, several computational methods have been developed to identify DBPs. However, because of the generic nature of the models, these models are unable to identify species-specific DBPs with higher accuracy. Therefore, a species-specific computational model is needed to predict species-specific DBPs. In this paper, we introduce the computational DBPMod method, which makes use of a machine learning approach to identify species-specific DBPs. For prediction, both shallow learning algorithms and deep learning models were used, with shallow learning models achieving higher accuracy. Additionally, the evolutionary features outperformed sequence-derived features in terms of accuracy. Five model organisms, including Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli, Homo sapiens and Mus musculus, were used to assess the performance of DBPMod. Five-fold cross-validation and independent test set analyses were used to evaluate the prediction accuracy in terms of area under receiver operating characteristic curve (auROC) and area under precision-recall curve (auPRC), which was found to be ~89-92% and ~89-95%, respectively. The comparative results demonstrate that the DBPMod outperforms 12 current state-of-the-art computational approaches in identifying the DBPs for all five model organisms. We further developed the web server of DBPMod to make it easier for researchers to detect DBPs and is publicly available at https://iasri-sg.icar.gov.in/dbpmod/. DBPMod is expected to be an invaluable tool for discovering DBPs, supplementing the current experimental and computational methods.
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Affiliation(s)
- Upendra K Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Prabina K Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Nitesh K Sharma
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, 1540 Alcazar Street, Los Angeles, CA 90033, USA
| | - Aarushi Agarwal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
| | - Rajender Parsad
- ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi 110012, India
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22
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Li H, Li D, Humphreys BD. Chromatin conformation and histone modification profiling across human kidney anatomic regions. Sci Data 2024; 11:797. [PMID: 39025878 PMCID: PMC11258246 DOI: 10.1038/s41597-024-03648-8] [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: 03/18/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
The three major anatomic regions of the human kidney include the cortex, medulla and papilla, with different functions and vulnerabilities to kidney diseases. Epigenetic mechanisms underlying these anatomic structures are incompletely understood. Here, we performed chromatin conformation capture with Hi-C and histone modification H3K4me3/H3K27me3 Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing on the kidney cortex, medulla and papilla dissected from one individual donor. Nuclear suspensions were generated from each region and split subjected to paired Hi-C and CUT&RUN sequencing. We evaluated the quality of next-generation sequencing data, Hi-C chromatin contact matrices and CUT&RUN peak calling. H3K4me3 and H3K27me3 histone modifications represent active and repressive gene transcription, respectively, and differences in chromatin conformation between kidney regions can be analyzed with this dataset. All raw and processed data files are publicly available, allowing researchers to survey the epigenetic landscape across regional human kidney anatomy.
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Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Dian Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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23
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Chang WJ, Baker MS, Laritsky E, Gunasekara CJ, Maduranga U, Galliou JC, McFadden JW, Waltemyer JR, Berggren-Thomas B, Tate BN, Zhang H, Rosen BD, Van Tassell CP, Liu GE, Coarfa C, Ren YA, Waterland RA. Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans. Genome Biol 2024; 25:185. [PMID: 39004763 PMCID: PMC11247883 DOI: 10.1186/s13059-024-03307-6] [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: 09/22/2023] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND We recently identified ~ 10,000 correlated regions of systemic interindividual epigenetic variation (CoRSIVs) in the human genome. These methylation variants are amenable to population studies, as DNA methylation measurements in blood provide information on epigenetic regulation throughout the body. Moreover, establishment of DNA methylation at human CoRSIVs is labile to periconceptional influences such as nutrition. Here, we analyze publicly available whole-genome bisulfite sequencing data on multiple tissues of each of two Holstein cows to determine whether CoRSIVs exist in cattle. RESULTS Focusing on genomic blocks with ≥ 5 CpGs and a systemic interindividual variation index of at least 20, our approach identifies 217 cattle CoRSIVs, a subset of which we independently validate by bisulfite pyrosequencing. Similar to human CoRSIVs, those in cattle are strongly associated with genetic variation. Also as in humans, we show that establishment of DNA methylation at cattle CoRSIVs is particularly sensitive to early embryonic environment, in the context of embryo culture during assisted reproduction. CONCLUSIONS Our data indicate that CoRSIVs exist in cattle, as in humans, suggesting these systemic epigenetic variants may be common to mammals in general. To the extent that individual epigenetic variation at cattle CoRSIVs affects phenotypic outcomes, assessment of CoRSIV methylation at birth may become an important tool for optimizing agriculturally important traits. Moreover, adjusting embryo culture conditions during assisted reproduction may provide opportunities to tailor agricultural outcomes by engineering CoRSIV methylation profiles.
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Affiliation(s)
- Wen-Jou Chang
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Maria S Baker
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Eleonora Laritsky
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Chathura J Gunasekara
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Uditha Maduranga
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Justine C Galliou
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Joseph W McFadden
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | | | | | - Brianna N Tate
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Hanxue Zhang
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, United States
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States
| | - Yi Athena Ren
- Department of Animal Science, Cornell University, Ithaca, NY, United States.
| | - Robert A Waterland
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States.
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, United States.
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24
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Brativnyk A, Ankill J, Helland Å, Fleischer T. Multi-omics analysis reveals epigenetically regulated processes and patient classification in lung adenocarcinoma. Int J Cancer 2024; 155:282-297. [PMID: 38489486 DOI: 10.1002/ijc.34915] [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: 09/01/2023] [Revised: 12/27/2023] [Accepted: 01/24/2024] [Indexed: 03/17/2024]
Abstract
Aberrant DNA methylation is a hallmark of many cancer types. Despite our knowledge of epigenetic and transcriptomic alterations in lung adenocarcinoma (LUAD), we lack robust multi-modal molecular classifications for patient stratification. This is partly because the impact of epigenetic alterations on lung cancer development and progression is still not fully understood. To that end, we identified disease-associated processes under epigenetic regulation in LUAD. We performed a genome-wide expression-methylation Quantitative Trait Loci (emQTL) analysis by integrating DNA methylation and gene expression data from 453 patients in the TCGA cohort. Using a community detection algorithm, we identified distinct communities of CpG-gene associations with diverse biological processes. Interestingly, we identified a community linked to hormone response and lipid metabolism; the identified CpGs in this community were enriched in enhancer regions and binding regions of transcription factors such as FOXA1/2, GRHL2, HNF1B, AR, and ESR1. Furthermore, the CpGs were connected to their associated genes through chromatin interaction loops. These findings suggest that the expression of genes involved in hormone response and lipid metabolism in LUAD is epigenetically regulated through DNA methylation and enhancer-promoter interactions. By applying consensus clustering on the integrated expression-methylation pattern of the emQTL-genes and CpGs linked to hormone response and lipid metabolism, we further identified subclasses of patients with distinct prognoses. This novel patient stratification was validated in an independent patient cohort of 135 patients and showed increased prognostic significance compared to previously defined molecular subtypes.
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Affiliation(s)
- Anastasia Brativnyk
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Jørgen Ankill
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Åslaug Helland
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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25
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Shastry S, Samal D, Pethe P. Histone H2A deubiquitinase BAP1 is essential for endothelial cell differentiation from human pluripotent stem cells. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00935-x. [PMID: 38976206 DOI: 10.1007/s11626-024-00935-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/25/2024] [Indexed: 07/09/2024]
Abstract
Polycomb group proteins (PcGs) add repressive post translational histone modifications such as H2AK119ub1, and histone H2A deubiquitinases remove it. Mice lacking histone H2A deubiquitinases such as Usp16 and Bap1 die in embryonic stage, while mice lacking Usp3, Mysm1, Usp12, and Usp21 have been shown to be deficient in hematopoietic lineage differentiation, cell cycle regulation, and DNA repair. Thus, it is likely that histone deubiquitinases may also be required for human endothelial cell differentiation; however, there are no reports about the role of histone H2A deubiquitinase BAP1 in human endothelial cell development. We differentiated human pluripotent stem cells into the endothelial lineage which expressed stable inducible shRNA against BAP1. Our results show that BAP1 is required for human endothelial cell differentiation.
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Affiliation(s)
- Shruti Shastry
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis International (Deemed University), Pune, India
- Worcester Polytechnic Institute (WPI), Boston, USA
| | - Dharitree Samal
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis International (Deemed University), Pune, India
| | - Prasad Pethe
- Symbiosis Centre for Stem Cell Research (SCSCR), Symbiosis International (Deemed University), Pune, India.
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26
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Shakeri M, Aminian A, Mokhtari K, Bahaeddini M, Tabrizian P, Farahani N, Nabavi N, Hashemi M. Unraveling the molecular landscape of osteoarthritis: A comprehensive review focused on the role of non-coding RNAs. Pathol Res Pract 2024; 260:155446. [PMID: 39004001 DOI: 10.1016/j.prp.2024.155446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024]
Abstract
Osteoarthritis (OA) poses a significant global health challenge, with its prevalence anticipated to increase in the coming years. This review delves into the emerging molecular biomarkers in OA pathology, focusing on the roles of various molecules such as metabolites, noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Advances in omics technologies have transformed biomarker identification, enabling comprehensive analyses of the complex pathways involved in OA pathogenesis. Notably, ncRNAs, especially miRNAs and lncRNAs, exhibit dysregulated expression patterns in OA, presenting promising opportunities for diagnosis and therapy. Additionally, the intricate interplay between epigenetic modifications and OA progression highlights the regulatory role of epigenetics in gene expression dynamics. Genome-wide association studies have pinpointed key genes undergoing epigenetic changes, providing insights into the inflammatory processes and chondrocyte hypertrophy typical of OA. Understanding the molecular landscape of OA, including biomarkers and epigenetic mechanisms, holds significant potential for developing innovative diagnostic tools and therapeutic strategies for OA management.
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Affiliation(s)
- Mohammadreza Shakeri
- MD, Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, Department of Orthopedic, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Aminian
- MD, Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, Department of Orthopedic, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Khatere Mokhtari
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohammadreza Bahaeddini
- MD, Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, Department of Orthopedic, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Pouria Tabrizian
- MD, Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, Department of Orthopedic, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Najma Farahani
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Noushin Nabavi
- Independent Researcher, Victoria, British Columbia V8V 1P7, Canada
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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27
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Sayer M, Ng DQ, Chan R, Kober K, Chan A. Current evidence supporting associations of DNA methylation measurements with survivorship burdens in cancer survivors: A scoping review. Cancer Med 2024; 13:e7470. [PMID: 38963018 PMCID: PMC11222976 DOI: 10.1002/cam4.7470] [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: 01/17/2024] [Revised: 05/27/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
INTRODUCTION Identifying reliable biomarkers that reflect cancer survivorship symptoms remains a challenge for researchers. DNA methylation (DNAm) measurements reflecting epigenetic changes caused by anti-cancer therapy may provide needed insights. Given lack of consensus describing utilization of DNAm data to predict survivorship issues, a review evaluating the current landscape is warranted. OBJECTIVE Provide an overview of current studies examining associations of DNAm with survivorship burdens in cancer survivors. METHODS A literature review was conducted including studies if they focused on cohorts of cancer survivors, utilized peripheral blood cell DNAm data, and evaluated the associations of DNAm and survivorship issues. RESULTS A total of 22 studies were identified, with majority focused on breast (n = 7) or childhood cancer (n = 9) survivors, and half studies included less than 100 patients (n = 11). Survivorship issues evaluated included those related to neurocognition (n = 5), psychiatric health (n = 3), general wellness (n = 9), chronic conditions (n = 5), and treatment specific toxicities (n = 4). Studies evaluated epigenetic age metrics (n = 10) and DNAm levels at individual CpG sites or regions (n = 12) for their associations with survivorship issues in cancer survivors along with relevant confounding factors. Significant associations of measured DNAm in the peripheral blood samples of cancer survivors and survivorship issues were identified. DISCUSSION/CONCLUSION Studies utilizing epigenetic age metrics and differential methylation analysis demonstrated significant associations of DNAm measurements with survivorship burdens. Associations were observed encompassing diverse survivorship outcomes and timeframes relative to anti-cancer therapy initiation. These findings underscore the potential of these measurements as useful biomarkers in survivorship care and research.
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Affiliation(s)
- Michael Sayer
- School of Pharmacy and Pharmaceutical SciencesUniversity of California IrvineIrvineCaliforniaUSA
| | - Ding Quan Ng
- School of Pharmacy and Pharmaceutical SciencesUniversity of California IrvineIrvineCaliforniaUSA
| | - Raymond Chan
- School of Nursing and Health SciencesFlinders UniversityAdelaideSouth AustraliaAustralia
| | - Kord Kober
- School of NursingUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Alexandre Chan
- School of Pharmacy and Pharmaceutical SciencesUniversity of California IrvineIrvineCaliforniaUSA
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28
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Pal S, Dhar R. Living in a noisy world-origins of gene expression noise and its impact on cellular decision-making. FEBS Lett 2024; 598:1673-1691. [PMID: 38724715 DOI: 10.1002/1873-3468.14898] [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: 12/21/2023] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 07/23/2024]
Abstract
The expression level of a gene can vary between genetically identical cells under the same environmental condition-a phenomenon referred to as gene expression noise. Several studies have now elucidated a central role of transcription factors in the generation of expression noise. Transcription factors, as the key components of gene regulatory networks, drive many important cellular decisions in response to cellular and environmental signals. Therefore, a very relevant question is how expression noise impacts gene regulation and influences cellular decision-making. In this Review, we summarize the current understanding of the molecular origins of expression noise, highlighting the role of transcription factors in this process, and discuss the ways in which noise can influence cellular decision-making. As advances in single-cell technologies open new avenues for studying expression noise as well as gene regulatory circuits, a better understanding of the influence of noise on cellular decisions will have important implications for many biological processes.
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Affiliation(s)
- Sampriti Pal
- Department of Bioscience and Biotechnology, IIT Kharagpur, India
| | - Riddhiman Dhar
- Department of Bioscience and Biotechnology, IIT Kharagpur, India
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29
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Darvish S, Mahoney SA, Venkatasubramanian R, Rossman MJ, Clayton ZS, Murray KO. Socioeconomic status as a potential mediator of arterial aging in marginalized ethnic and racial groups: current understandings and future directions. J Appl Physiol (1985) 2024; 137:194-222. [PMID: 38813611 PMCID: PMC11389897 DOI: 10.1152/japplphysiol.00188.2024] [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: 03/13/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 05/31/2024] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death in the United States. However, disparities in CVD-related morbidity and mortality exist as marginalized racial and ethnic groups are generally at higher risk for CVDs (Black Americans, Indigenous People, South and Southeast Asians, Native Hawaiians, and Pacific Islanders) and/or development of traditional CVD risk factors (groups above plus Hispanics/Latinos) relative to non-Hispanic Whites (NHW). In this comprehensive review, we outline emerging evidence suggesting these groups experience accelerated arterial dysfunction, including vascular endothelial dysfunction and large elastic artery stiffening, a nontraditional CVD risk factor that may predict risk of CVDs in these groups with advancing age. Adverse exposures to social determinants of health (SDOH), specifically lower socioeconomic status (SES), are exacerbated in most of these groups (except South Asians-higher SES) and may be a potential mediator of accelerated arterial aging. SES negatively influences the ability of marginalized racial and ethnic groups to meet aerobic exercise guidelines, the first-line strategy to improve arterial function, due to increased barriers, such as time and financial constraints, lack of motivation, facility access, and health education, to performing conventional aerobic exercise. Thus, identifying alternative interventions to conventional aerobic exercise that 1) overcome these common barriers and 2) target the biological mechanisms of aging to improve arterial function may be an effective, alternative method to aerobic exercise to ameliorate accelerated arterial aging and reduce CVD risk. Importantly, dedicated efforts are needed to assess these strategies in randomized-controlled clinical trials in these marginalized racial and ethnic groups.
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Affiliation(s)
- Sanna Darvish
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States
| | - Sophia A Mahoney
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States
| | | | - Matthew J Rossman
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States
| | - Zachary S Clayton
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States
| | - Kevin O Murray
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, United States
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30
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Fuloria S, Yadav G, Menon SV, Ali H, Pant K, Kaur M, Deorari M, Sekar M, Narain K, Kumar S, Fuloria NK. Targeting the Wnt/β-catenin cascade in osteosarcoma: The potential of ncRNAs as biomarkers and therapeutics. Pathol Res Pract 2024; 259:155346. [PMID: 38781762 DOI: 10.1016/j.prp.2024.155346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/26/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Osteosarcoma (OS) is a bone cancer which stems from several sources and presents with diverse clinical features, making evaluation and treatment difficult. Chemotherapy tolerance and restricted treatment regimens hinder progress in survival rates, requiring new and creative therapeutic strategies. The Wnt/β-catenin system has been recognised as an essential driver of OS development, providing potential avenues for therapy. Non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), and microRNAs (miRNAs), are essential in modulating the Wnt/β-catenin cascade in OS. MiRNAs control the system by targeting vital elements, while lncRNAs and circRNAs interact with system genes, impacting OS growth and advancement. This paper thoroughly analyses the intricate interplay between ncRNAs and the Wnt/β-catenin cascade in OS. We examine how uncontrolled levels of miRNAs, lncRNAs, and circRNAs lead to an abnormal Wnt/β-catenin network, which elevates the development, spread, and susceptibility to the treatment of OS. We emphasise the potential of ncRNAs as diagnostic indicators and avenues for treatment in OS care. The review offers valuable insights for academics and clinicians studying OS aetiology and creating new treatment techniques for the ncRNA-Wnt/β-catenin cascade. Utilising the oversight roles of ncRNAs in the Wnt/β-catenin system shows potential for enhancing the outcomes of patients and progressing precision medicine in OS therapy.
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Affiliation(s)
| | - Geeta Yadav
- Chandigarh Pharmacy College, Chandigarh Group of Colleges, Jhanjheri, Mohali, Punjab 140307, India
| | - Soumya V Menon
- Department of Chemistry and Biochemistry, School of Sciences, JAIN (Deemed to be University), Bangalore, Karnataka, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Kumud Pant
- Graphic Era (Deemed to be University), Clement Town, Dehradun 248002, India; Graphic Era Hill University, Clement Town, Dehradun 248002, India
| | - Mandeep Kaur
- Department of Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | - Kamal Narain
- Faculty of Medicine, AIMST University, Kedah 08100, Malaysia
| | - Sokindra Kumar
- Faculty of Pharmacy, Swami Vivekanand Subharti University, Subhartipuram, Meerut-25005, U.P. India
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31
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Liu SX, Muelken P, Maxim ZL, Ramakrishnan A, Estill MS, LeSage MG, Smethells JR, Shen L, Tran PV, Harris AC, Gewirtz JC. Differential gene expression and chromatin accessibility in the medial prefrontal cortex associated with individual differences in rat behavioral models of opioid use disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582799. [PMID: 38979145 PMCID: PMC11230220 DOI: 10.1101/2024.02.29.582799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Opioid use disorder (OUD) is a neuropsychological disease that has a devastating impact on public health. Substantial individual differences in vulnerability exist, the neurobiological substrates of which remain unclear. To address this question, we investigated genome-wide gene transcription (RNA-seq) and chromatin accessibility (ATAC-seq) in the medial prefrontal cortex (mPFC) of male and female rats exhibiting differential vulnerability in behavioral paradigms modeling different phases of OUD: Withdrawal-Induced Anhedonia (WIA), Demand, and Reinstatement. Ingenuity Pathway Analysis (IPA) of RNA-seq revealed greater changes in canonical pathways in Resilient (vs. Saline) rats in comparison to Vulnerable (vs. Saline) rats across 3 paradigms, suggesting brain adaptations that might contribute to resilience to OUD across its trajectory. Analyses of gene networks and upstream regulators implicated processes involved in oligodendrocyte maturation and myelination in WIA, neuroinflammation in Demand, and metabolism in Reinstatement. Motif analysis of ATAC-seq showed changes in chromatin accessibility to a small set of transcription factor (TF) binding sites as a function either of opioid exposure (i.e., morphine versus saline) generally or of individual vulnerability specifically. Some of these were shared across the 3 paradigms and others were unique to each. In conclusion, we have identified changes in biological pathways, TFs, and their binding motifs that vary with paradigm and OUD vulnerability. These findings point to the involvement of distinct transcriptional and epigenetic mechanisms in response to opioid exposure, vulnerability to OUD, and different stages of the disorder.
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32
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Farzad N, Enninful A, Bao S, Zhang D, Deng Y, Fan R. Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nat Protoc 2024:10.1038/s41596-024-01013-y. [PMID: 38943021 DOI: 10.1038/s41596-024-01013-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/11/2024] [Indexed: 06/30/2024]
Abstract
Spatial epigenetic mapping of tissues enables the study of gene regulation programs and cellular functions with the dependency on their local tissue environment. Here we outline a complete procedure for two spatial epigenomic profiling methods: spatially resolved genome-wide profiling of histone modifications using in situ cleavage under targets and tagmentation (CUT&Tag) chemistry (spatial-CUT&Tag) and transposase-accessible chromatin sequencing (spatial-ATAC-sequencing) for chromatin accessibility. Both assays utilize in-tissue Tn5 transposition to recognize genomic DNA loci followed by microfluidic deterministic barcoding to incorporate spatial address codes. Furthermore, these two methods do not necessitate prior knowledge of the transcription or epigenetic markers for a given tissue or cell type but permit genome-wide unbiased profiling pixel-by-pixel at the 10 μm pixel size level and single-base resolution. To support the widespread adaptation of these methods, details are provided in five general steps: (1) sample preparation; (2) Tn5 transposition in spatial-ATAC-sequencing or antibody-controlled pA-Tn5 tagmentation in CUT&Tag; (3) library preparation; (4) next-generation sequencing; and (5) data analysis using our customed pipelines available at: https://github.com/dyxmvp/Spatial_ATAC-seq and https://github.com/dyxmvp/spatial-CUT-Tag . The whole procedure can be completed on four samples in 2-3 days. Familiarity with basic molecular biology and bioinformatics skills with access to a high-performance computing environment are required. A rudimentary understanding of pathology and specimen sectioning, as well as deterministic barcoding in tissue-specific skills (e.g., design of a multiparameter barcode panel and creation of microfluidic devices), are also advantageous. In this protocol, we mainly focus on spatial profiling of tissue region-specific epigenetic landscapes in mouse embryos and mouse brains using spatial-ATAC-sequencing and spatial-CUT&Tag, but these methods can be used for other species with no need for species-specific probe design.
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Affiliation(s)
- Negin Farzad
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Shuozhen Bao
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Pennsylvania, PA, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
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Graves C, Islam K. Development of a rapid mass spectrometric method for the analysis of ten-eleven translocation enzymes. Methods Enzymol 2024; 703:87-120. [PMID: 39261005 DOI: 10.1016/bs.mie.2024.06.001] [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] [Indexed: 09/13/2024]
Abstract
In DNA, methylation at the fifth position of cytosine (5mC) by DNA methyltransferases is essential for eukaryotic gene regulation. Methylation patterns are dynamically controlled by epigenetic machinery. Erasure of 5mC by Fe2+ and 2-ketoglutarate (2KG) dependent dioxygenases in the ten-eleven translocation family (TET1-3), plays a key role in nuclear processes. Through the event of active demethylation, TET proteins iteratively oxidize 5mC to 5-hydroxymethyl cytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5caC), each of which has been implicated in numerous diseases when aberrantly generated. A wide range of biochemical assays have been developed to characterize TET activity, many of which require multi-step processing to detect and quantify the 5mC oxidized products. Herein, we describe the development and optimization of a sensitive MALDI mass spectrometry-based technique that directly measures TET activity and eliminates tedious processing steps. Employing optimized assay conditions, we report the steady-state activity of wild type TET2 enzymes to furnish 5hmC, 5fC and 5caC. We next determine IC50 values of several small-molecule inhibitors of TETs. The utility of this assay is further demonstrated by analyzing the activity of V1395A which is an activating mutant of TET2 that primarily generates 5caC. Lastly, we describe the development of a secondary assay that utilizes bisulfite chemistry to further examine the activity of wildtype TET2 and V1395A in a base-resolution manner. The combined results demonstrate that the activity of TET proteins can be gauged, and their products accurately quantified using our methods.
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Affiliation(s)
- Clara Graves
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States.
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Wadood AA, Zhang X. The Omics Revolution in Understanding Chicken Reproduction: A Comprehensive Review. Curr Issues Mol Biol 2024; 46:6248-6266. [PMID: 38921044 PMCID: PMC11202932 DOI: 10.3390/cimb46060373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Omics approaches have significantly contributed to our understanding of several aspects of chicken reproduction. This review paper gives an overview of the use of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics to elucidate the mechanisms of chicken reproduction. Genomics has transformed the study of chicken reproduction by allowing the examination of the full genetic makeup of chickens, resulting in the discovery of genes associated with reproductive features and disorders. Transcriptomics has provided insights into the gene expression patterns and regulatory mechanisms involved in reproductive processes, allowing for a better knowledge of developmental stages and hormone regulation. Furthermore, proteomics has made it easier to identify and quantify the proteins involved in reproductive physiology to better understand the molecular mechanisms driving fertility, embryonic development, and egg quality. Metabolomics has emerged as a useful technique for understanding the metabolic pathways and biomarkers linked to reproductive performance, providing vital insights for enhancing breeding tactics and reproductive health. The integration of omics data has resulted in the identification of critical molecular pathways and biomarkers linked with chicken reproductive features, providing the opportunity for targeted genetic selection and improved reproductive management approaches. Furthermore, omics technologies have helped to create biomarkers for fertility and embryonic viability, providing the poultry sector with tools for effective breeding and reproductive health management. Finally, omics technologies have greatly improved our understanding of chicken reproduction by revealing the molecular complexities that underpin reproductive processes.
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Affiliation(s)
- Armughan Ahmed Wadood
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China;
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China;
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
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Manav N, Jit BP, Kataria B, Sharma A. Cellular and epigenetic perspective of protein stability and its implications in the biological system. Epigenomics 2024; 16:879-900. [PMID: 38884355 PMCID: PMC11370918 DOI: 10.1080/17501911.2024.2351788] [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: 11/29/2023] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Protein stability is a fundamental prerequisite in both experimental and therapeutic applications. Current advancements in high throughput experimental techniques and functional ontology approaches have elucidated that impairment in the structure and stability of proteins is intricately associated with the cause and cure of several diseases. Therefore, it is paramount to deeply understand the physical and molecular confounding factors governing the stability of proteins. In this review article, we comprehensively investigated the evolution of protein stability, examining its emergence over time, its relationship with organizational aspects and the experimental methods used to understand it. Furthermore, we have also emphasized the role of Epigenetics and its interplay with post-translational modifications (PTMs) in regulating the stability of proteins.
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Affiliation(s)
- Nisha Manav
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
| | - Bimal Prasad Jit
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
| | - Babita Kataria
- Department of Medical Oncology, National Cancer Institute, All India Institute of Medical Sciences, Jhajjar, 124105, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
- Department of Biochemistry, National Cancer Institute, All India Institute of Medical Sciences, Jhajjar, 124105, India
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Lei Y, Zhan E, Chen C, Hu Y, Lv Z, He Q, Wang X, Li X, Zhang F. ALKBH5-mediated m 6A demethylation of Runx2 mRNA promotes extracellular matrix degradation and intervertebral disc degeneration. Cell Biosci 2024; 14:79. [PMID: 38877576 PMCID: PMC11179301 DOI: 10.1186/s13578-024-01264-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) methylation is a prevalent RNA modification implicated in various diseases. However, its role in intervertebral disc degeneration (IDD), a common cause of low back pain, remains unclear. RESULTS In this investigation, we explored the involvement of m6A demethylation in the pathogenesis of IDD. Our findings revealed that ALKBH5 (alkylated DNA repair protein AlkB homolog 5), an m6A demethylase, exhibited upregulation in degenerative discs upon mild inflammatory stimulation. ALKBH5 facilitated m6A demethylation within the three prime untranslated region (3'-UTR) of Runx2 mRNA, consequently enhancing its mRNA stability in a YTHDF1 (YTH N6-methyladenosine RNA binding protein F1)-dependent manner. The subsequent elevation in Runx2 expression instigated the upregulation of ADAMTSs and MMPs, pivotal proteases implicated in extracellular matrix (ECM) degradation and IDD progression. In murine models, subcutaneous administration of recombinant Runx2 protein proximal to the lumbar disc in mice elicited complete degradation of intervertebral discs (IVDs). Injection of recombinant MMP1a and ADAMTS10 proteins individually induced mild to moderate degeneration of the IVDs, while co-administration of MMP1a and ADAMTS10 resulted in moderate to severe degeneration. Notably, concurrent injection of the Runx2 inhibitor CADD522 with recombinant Runx2 protein did not result in IVD degeneration in mice. Furthermore, genetic knockout of ALKBH5 and overexpression of YTHDF1 in mice, along with lipopolysaccharide (LPS) treatment to induce inflammation, did not alter the expression of Runx2, MMPs, and ADAMTSs, and no degeneration of the IVDs was observed. CONCLUSION Our study elucidates the role of ALKBH5-mediated m6A demethylation of Runx2 mRNA in activating MMPs and ADAMTSs, thereby facilitating ECM degradation and promoting the occurrence of IDD. Our findings suggest that targeting the ALKBH5/Runx2/MMPs/ADAMTSs axis may represent a promising therapeutic strategy for preventing IDD.
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Affiliation(s)
- Yu Lei
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China
| | - Enyu Zhan
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China
| | - Chao Chen
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China
| | - Yaoquan Hu
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China
| | - Zhengpin Lv
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China
| | - Qicong He
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China
| | - Xuenan Wang
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China
| | - Xingguo Li
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China
| | - Fan Zhang
- Department of Orthopedics, The First Affiliated Hospital of Kunming Medical University, 295 Xichang Rd, Wuhua District, Kunming, Yunnan, 650032, China.
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Lu H, Zhao H, Zhong T, Chen D, Wu Y, Xie Z. Molecular Regulatory Mechanisms Affecting Fruit Aroma. Foods 2024; 13:1870. [PMID: 38928811 PMCID: PMC11203305 DOI: 10.3390/foods13121870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Aroma, an important quality characteristic of plant fruits, is produced by volatile organic compounds (VOCs), mainly terpenes, aldehydes, alcohols, esters, ketones, and other secondary metabolites, in plant cells. There are significant differences in the VOC profile of various fruits. The main pathways involved in the synthesis of VOCs are the terpenoid, phenylalanine, and fatty acid biosynthesis pathways, which involve several key enzyme-encoding genes, transcription factors (TFs), and epigenetic factors. This paper reviews the main synthetic pathways of the main volatile components in fruit, summarizes studies on the regulation of aroma formation by key genes and TFs, summarizes the factors affecting the fruit aroma formation, describes relevant studies on the improvement of fruit flavor quality, and finally proposes potential challenges and prospects for future research directions. This study provides a theoretical basis for the further precise control of fruit aroma quality and variety improvement.
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Affiliation(s)
- Haifei Lu
- College of Urban Construction, Zhejiang Shuren University, Hangzhou 310015, China; (H.L.); (H.Z.); (T.Z.); (D.C.)
| | - Hongfei Zhao
- College of Urban Construction, Zhejiang Shuren University, Hangzhou 310015, China; (H.L.); (H.Z.); (T.Z.); (D.C.)
| | - Tailin Zhong
- College of Urban Construction, Zhejiang Shuren University, Hangzhou 310015, China; (H.L.); (H.Z.); (T.Z.); (D.C.)
| | - Danwei Chen
- College of Urban Construction, Zhejiang Shuren University, Hangzhou 310015, China; (H.L.); (H.Z.); (T.Z.); (D.C.)
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China
| | - Zhengwan Xie
- School of Tea and Coffee, Puer University, Puer 665000, China
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Liu X, Duan C, Yin X, Zhang L, Chen M, Zhao W, Li X, Liu Y, Zhang Y. Inhibition of Prolactin Affects Epididymal Morphology by Decreasing the Secretion of Estradiol in Cashmere Bucks. Animals (Basel) 2024; 14:1778. [PMID: 38929397 PMCID: PMC11201029 DOI: 10.3390/ani14121778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Yanshan Cashmere bucks are seasonal breeding animals and an important national genetic resource. This study aimed to investigate the involvement of prolactin (PRL) in the epididymal function of bucks. Twenty eleven-month-old Cashmere bucks were randomly divided into a control (CON) group and a bromocriptine (BCR, a prolactin inhibitor, 0.06 mg/kg body weight (BW)) treatment group. The experiment was conducted from September to October 2020 in Qinhuangdao City, China, and lasted for 30 days. Blood was collected on the last day before the BCR treatment (day 0) and on the 15th and 30th days after the BCR treatment (days 15 and 30). On the 30th day, all bucks were transported to the local slaughterhouse, where epididymal samples were collected immediately after slaughter. The left epididymis was preserved in 4% paraformaldehyde for histological observation, and the right epididymis was immediately preserved in liquid nitrogen for RNA sequencing (RNA-seq). The results show that the PRL inhibitor reduced the serum PRL and estradiol (E2) concentrations (p < 0.05) and tended to decrease luteinizing hormone (LH) concentrations (p = 0.052) by the 30th day, but no differences (p > 0.05) occurred by either day 0 or 15. There were no differences (p > 0.05) observed in the follicle-stimulating hormone (FSH), testosterone (T), and dihydrotestosterone (DHT) concentrations between the two groups. The PRL receptor (PRLR) protein was mainly located in the cytoplasm and intercellular substance of the epididymal epithelial cells. The PRL inhibitor decreased (p < 0.05) the expression of the PRLR protein in the epididymis. In the BCR group, the height of the epididymal epithelium in the caput and cauda increased, as did the diameter of the epididymal duct in the caput (p < 0.05). However, the diameter of the cauda epididymal duct decreased (p < 0.05). Thereafter, a total of 358 differentially expressed genes (DEGs) were identified in the epididymal tissues, among which 191 were upregulated and 167 were downregulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that ESR2, MAPK10, JUN, ACTL7A, and CALML4 were mainly enriched in the estrogen signaling pathway, steroid binding, calcium ion binding, the GnRH signaling pathway, the cAMP signaling pathway, and the chemical carcinogenesis-reactive oxygen species pathway, which are related to epididymal function. In conclusion, the inhibition of PRL may affect the structure of the epididymis by reducing the expression of the PRLR protein and the secretion of E2. ESR2, MAPK10, JUN, ACTL7A, and CALML4 could be the key genes of PRL in its regulation of epididymal reproductive function.
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Affiliation(s)
- Xiaona Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Chunhui Duan
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Xuejiao Yin
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, China; (X.Y.); (X.L.)
| | - Lechao Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Meijing Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Wen Zhao
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Xianglong Li
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, China; (X.Y.); (X.L.)
| | - Yueqin Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Yingjie Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
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Nist MD, Pickler RH, Shoben AB, Conley YP. DNA Methylation, Inflammation, and Neurobehavior in Preterm Infants. Biol Res Nurs 2024:10998004241257664. [PMID: 38840298 DOI: 10.1177/10998004241257664] [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: 06/07/2024]
Abstract
Objectives: Inflammation contributes to disparate neurodevelopmental outcomes between preterm and term-born infants. In this context, DNA methylation may contribute to inflammation by affecting gene expression. Brain-derived neurotrophic factor (BDNF) and nuclear factor-kappa-B-inhibitor alpha (NFKBIA) are important genes for targeted DNA methylation analysis. The aims of this study were to (1) identify associations between inflammatory factors and BDNF and NFKBIA methylation, and (2) identify associations between BDNF and NFKBIA methylation and early neurobehavior in preterm infants. Methods: In a longitudinal cohort study of preterm infants born 28-31 weeks gestational age, blood samples were collected weekly for the quantification of inflammatory factors. We extracted DNA from saliva samples and quantified methylation of six BDNF cytosine-phosphate-guanine (CpG) sites and five NFKBIA CpG sites. Neurobehavior was assessed using the Neurobehavioral Assessment of the Preterm Infant. Results: Sixty-five infants were included in the analysis. In females, inflammatory factors were positively associated with BDNF methylation of most CpG sites. Interleukin-1 receptor antagonist was negatively associated with NFKBIA methylation at two CpG sites. In males, interleukin-6 was negatively associated with BDNF and NFKBIA methylation at most CpG sites. In females, BDNF methylation at two sites was inversely associated with motor performance. In males, NFKBIA methylation at one site was inversely associated with motor performance. Conclusion: This study provides evidence for the relationship between inflammation and neurobehavior in preterm infants, working mechanistically through DNA methylation. The finding of a difference between males and females suggests that female infants are potentially more vulnerable to inflammation and warrants future study.
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Affiliation(s)
| | - Rita H Pickler
- College of Nursing, The Ohio State University, Columbus, OH, USA
| | - Abigail B Shoben
- College of Public Health, The Ohio State University, Columbus, OH, USA
| | - Yvette P Conley
- School of Nursing, University of Pittsburgh, Pittsburgh, PA, USA
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Ali F, Almuhaimeed A, Khalid M, Alshanbari H, Masmoudi A, Alsini R. DEEP-EP: Identification of epigenetic protein by ensemble residual convolutional neural network for drug discovery. Methods 2024; 226:49-53. [PMID: 38621436 DOI: 10.1016/j.ymeth.2024.04.004] [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: 02/27/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
Epigenetic proteins (EP) play a role in the progression of a wide range of diseases, including autoimmune disorders, neurological disorders, and cancer. Recognizing their different functions has prompted researchers to investigate them as potential therapeutic targets and pharmacological targets. This paper proposes a novel deep learning-based model that accurately predicts EP. This study introduces a novel deep learning-based model that accurately predicts EP. Our approach entails generating two distinct datasets for training and evaluating the model. We then use three distinct strategies to transform protein sequences to numerical representations: Dipeptide Deviation from Expected Mean (DDE), Dipeptide Composition (DPC), and Group Amino Acid (GAAC). Following that, we train and compare the performance of four advanced deep learning models algorithms: Ensemble Residual Convolutional Neural Network (ERCNN), Generative Adversarial Network (GAN), Convolutional Neural Network (CNN), and Gated Recurrent Unit (GRU). The DDE encoding combined with the ERCNN model demonstrates the best performance on both datasets. This study demonstrates deep learning's potential for precisely predicting EP, which can considerably accelerate research and streamline drug discovery efforts. This analytical method has the potential to find new therapeutic targets and advance our understanding of EP activities in disease.
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Affiliation(s)
- Farman Ali
- Department of Computer Science, Bahria University Islamabad Campus, Pakistan.
| | - Abdullah Almuhaimeed
- Digital Health Institute, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Majdi Khalid
- Department of Computer Science and Artificial Intelligence, College of Computing, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hanan Alshanbari
- Department of Computer Science and Artificial Intelligence, College of Computing, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Atef Masmoudi
- College of Computer Science, King Khalid University, Abha, Saudi Arabia
| | - Raed Alsini
- Department of Information Systems, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Nayan NM, Kadir SHSA, Husin A, Siran R. Neurodevelopmental effects of prenatal Bisphenol A exposure on the role of microRNA regulating NMDA receptor subunits in the male rat hippocampus. Physiol Behav 2024; 280:114546. [PMID: 38583549 DOI: 10.1016/j.physbeh.2024.114546] [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: 01/28/2024] [Revised: 03/22/2024] [Accepted: 04/05/2024] [Indexed: 04/09/2024]
Abstract
Maternal bisphenol A (BPA) exposure has been reported to cause learning and memory deficits in born offspring. However, little is known that this impairment is potentially caused by epigenetic modulation on the development of NMDA receptor subunits. This study investigates the effect of prenatal BPA exposure on the hippocampal miR-19a and miR-539, which are responsible for regulating NMDA receptor subunits as well as learning and memory functions. Pregnant Sprague Dawley rats were orally administered with 5 mg/kg/day of BPA from pregnancy day 1 (PD1) until gestation day 21 (GD21), while control mothers received no BPA. The mothers were observed daily until GD21 for either a cesarean section or spontaneous delivery. The male offspring were sacrificed when reaching GD21 (fetus), postnatal days 7, 14, 21 (PND7, 14, 21) and adolescent age 35 (AD35) where their hippocampi were dissected from the brain. The expression of targeted miR-19a, miR-539, GRIN2A, and GRIN2B were determined by qRT-PCR while the level of GluN2A and GluN2B were estimated by western blot. At AD35, the rats were assessed with neurobehavioral tests to evaluate their learning and memory function. The findings showed that prenatal BPA exposure at 5 mg/kg/day significantly reduces the expression of miR-19a, miR-539, GRIN2A, and GRIN2B genes in the male rat hippocampus at all ages. The level of GluN2A and GluN2B proteins is also significantly reduced when reaching adolescent age. Consequently, the rats showed spatial and fear memory impairments when reaching AD35. In conclusion, prenatal BPA exposure disrupts the role of miR-19a and miR-539 in regulating the NMDA receptor subunit in the hippocampus which may be one of the causes of memory and learning impairment in adolescent rats.
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Affiliation(s)
- Norazirah Mat Nayan
- Centre for Neuroscience Research (NeuRon), Faculty of Medicine, Universiti Teknologi MARA 47000, Sungai Buloh, Selangor, Malaysia; Laboratory Animal Care Unit (LACU), Faculty of Medicine, Universiti Teknologi MARA 47000, Sungai Buloh, Selangor, Malaysia; Institute for Molecular Medicine and Biotechnology (IMMB) Faculty of Medicine, Universiti Teknologi MARA 47000, Sungai Buloh, Selangor, Malaysia
| | - Siti Hamimah Sheikh Abd Kadir
- Institute for Molecular Medicine and Biotechnology (IMMB) Faculty of Medicine, Universiti Teknologi MARA 47000, Sungai Buloh, Selangor, Malaysia
| | - Andrean Husin
- Faculty of Dentistry, Universiti Teknologi MARA 47000, Sungai Buloh, Selangor, Malaysia; Neuroscience Research Group (NRG), Faculty of Medicine, Universiti Teknologi MARA, 47000, Sungai Buloh, Selangor, Malaysia
| | - Rosfaiizah Siran
- Centre for Neuroscience Research (NeuRon), Faculty of Medicine, Universiti Teknologi MARA 47000, Sungai Buloh, Selangor, Malaysia; Neuroscience Research Group (NRG), Faculty of Medicine, Universiti Teknologi MARA, 47000, Sungai Buloh, Selangor, Malaysia..
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Wang Y, Huang H, Chen J, Weng H. Crosstalk between histone/DNA modifications and RNA N 6-methyladenosine modification. Curr Opin Genet Dev 2024; 86:102205. [PMID: 38776766 DOI: 10.1016/j.gde.2024.102205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal RNA modification in eukaryotic messenger RNAs (mRNAs), regulating gene expression at the transcription and post-transcription levels. Complex interplay between m6A and other well-studied epigenetic modifications, including histone modifications and DNA modification, has been extensively reported in recent years. The crosstalk between RNA m6A modification and histone/DNA modifications plays a critical role in establishing the chromatin state for the precise and specific fine-tuning of gene expression and undoubtedly has profound impacts on both physiological and pathological processes. In this review, we discuss the crosstalk between RNA m6A modification and histone/DNA modifications, emphasizing their sophisticated communications and the mechanisms underlying to gain a comprehensive view of the biological relevance of m6A-based epigenetic network.
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Affiliation(s)
- Yushuai Wang
- Guangzhou National Laboratory, Guangzhou 510005, China
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Gehr Family Center for Leukemia Research & City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA 91010, USA.
| | - Hengyou Weng
- Guangzhou National Laboratory, Guangzhou 510005, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China; The First Affiliated Hospital, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou 510005, China.
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Chen H, Luo S, Deng X, Li S, Mao Y, Yan J, Cheng Y, Liu X, Pan J, Huang H. Pre-eclamptic foetal programming predisposes offspring to hepatic steatosis via DNA methylation. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167189. [PMID: 38648899 DOI: 10.1016/j.bbadis.2024.167189] [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: 11/23/2023] [Revised: 04/01/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
OBJECTIVES Gamete and embryo-foetal origins of adult diseases hypothesis proposes that adulthood chronic disorders are associated with adverse foetal and early life traits. Our study aimed to characterise developmental changes and underlying mechanisms of metabolic disorders in offspring of pre-eclampsia (PE) programmed pregnancy. METHODS Nω-Nitro-l-arginine methyl ester hydrochloride (L-NAME) induced pre-eclampsia-like C57BL/6J mouse model was used. Lipid profiling, histological morphology, indirect calorimetry, mRNA sequencing, and pyrosequencing were performed on PE offspring of both young and elderly ages. RESULTS PE offspring exhibited increased postnatal weight gain, hepatic lipid accumulation, enlarged adipocytes, and impaired energy balance that continued to adulthood. Integrated RNA sequencing of foetal and 52-week-old livers revealed that the differentially expressed genes were mainly enriched in lipid metabolism, including glycerol-3-phosphate acyl-transferase 3 (Gpat3), a key enzyme for de novo synthesis of triglycerides (TG), and carnitine palmitoyltransferase-1a (Cpt1a), a key transmembrane enzyme that mediates fatty acid degradation. Pyrosequencing of livers from PE offspring identified hypomethylated and hypermethylated regions in Gpat3 and Cpt1a promoters, which were associated with upregulated and downregulated expressions of Gpat3 and Cpt1a, respectively. These epigenetic alterations are persistent and consistent from the foetal stage to adulthood in PE offspring. CONCLUSION These findings suggest a methylation-mediated epigenetic mechanism for PE-induced intergenerational lipid accumulation, impaired energy balance and obesity in offspring, and indicate the potential benefits of early interventions in offspring exposed to maternal PE to reduce their susceptibility to metabolic disorder in their later life.
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Affiliation(s)
- Huixi Chen
- The International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200000, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China; Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200030, China; Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China; State Key Laboratory of Cardiology, Shanghai 200000, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Sisi Luo
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China
| | - Xiuyu Deng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200000, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China
| | - Sisi Li
- Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China; Reproductive Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China
| | - Yiting Mao
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China
| | - Jing Yan
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China
| | - Yi Cheng
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China
| | - Xia Liu
- The International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200000, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China
| | - Jiexue Pan
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China; Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200030, China.
| | - Hefeng Huang
- The International Peace Maternal and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200000, China; Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China; Shanghai Key Laboratory of Reproduction and Development, Shanghai 200011, China; Reproductive Medicine Center, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China; Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200030, China; Key Laboratory of Reproductive Genetics (Ministry of Education), Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China; State Key Laboratory of Cardiology, Shanghai 200000, China.
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D’Esposito F, Gagliano C, Bloom PA, Cordeiro MF, Avitabile A, Gagliano G, Costagliola C, Avitabile T, Musa M, Zeppieri M. Epigenetics in Glaucoma. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:905. [PMID: 38929522 PMCID: PMC11205742 DOI: 10.3390/medicina60060905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
Primary open angle glaucoma (POAG) is defined as a "genetically complex trait", where modifying factors act on a genetic predisposing background. For the majority of glaucomatous conditions, DNA variants are not sufficient to explain pathogenesis. Some genes are clearly underlying the more "Mendelian" forms, while a growing number of related polymorphisms in other genes have been identified in recent years. Environmental, dietary, or biological factors are known to influence the development of the condition, but interactions between these factors and the genetic background are poorly understood. Several studies conducted in recent years have led to evidence that epigenetics, that is, changes in the pattern of gene expression without any changes in the DNA sequence, appear to be the missing link. Different epigenetic mechanisms have been proven to lead to glaucomatous changes in the eye, principally DNA methylation, post-translational histone modification, and RNA-associated gene regulation by non-coding RNAs. The aim of this work is to define the principal epigenetic actors in glaucoma pathogenesis. The identification of such mechanisms could potentially lead to new perspectives on therapeutic strategies.
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Affiliation(s)
- Fabiana D’Esposito
- Imperial College Ophthalmic Research Group (ICORG) Unit, Imperial College, London NW1 5QH, UK; (F.D.)
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, 80131 Naples, Italy
- Department of Medicine and Surgery, University of Enna “Kore”, Piazza dell’Università, 94100 Enna, Italy
| | - Caterina Gagliano
- Department of Medicine and Surgery, University of Enna “Kore”, Piazza dell’Università, 94100 Enna, Italy
- Eye Clinic, Catania University San Marco Hospital, Viale Carlo Azeglio Ciampi, 95121 Catania, Italy
| | - Philip Anthony Bloom
- Imperial College Ophthalmic Research Group (ICORG) Unit, Imperial College, London NW1 5QH, UK; (F.D.)
- Western Eye Hospital, Imperial College Healthcare NHS Trust, London NW1 5QH, UK
| | - Maria Francesca Cordeiro
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, 80131 Naples, Italy
- Western Eye Hospital, Imperial College Healthcare NHS Trust, London NW1 5QH, UK
| | - Alessandro Avitabile
- Eye Clinic, Catania University San Marco Hospital, Viale Carlo Azeglio Ciampi, 95121 Catania, Italy
| | - Giuseppe Gagliano
- Eye Clinic, Catania University San Marco Hospital, Viale Carlo Azeglio Ciampi, 95121 Catania, Italy
| | - Ciro Costagliola
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, University of Naples Federico II, 80131 Naples, Italy
| | - Teresio Avitabile
- Eye Clinic, Catania University San Marco Hospital, Viale Carlo Azeglio Ciampi, 95121 Catania, Italy
| | - Mutali Musa
- Department of Optometry, University of Benin, Benin City 300238, Nigeria
| | - Marco Zeppieri
- Department of Ophthalmology, University Hospital of Udine, 33100 Udine, Italy
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Ahn SI, Choi SK, Kim MJ, Wie J, You JS. Mdivi-1: Effective but complex mitochondrial fission inhibitor. Biochem Biophys Res Commun 2024; 710:149886. [PMID: 38581953 DOI: 10.1016/j.bbrc.2024.149886] [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: 01/19/2024] [Revised: 03/19/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024]
Abstract
Mdivi-1, Mitochondrial DIVIsion inhibitor 1, has been widely employed in research under the assumption that it exclusively influences mitochondrial fusion, but effects other than mitochondrial dynamics have been underinvestigated. This paper provides transcriptome and DNA methylome-wide analysis for Mdivi-1 treated SH-SY5Y human neuroblastoma cells using RNA sequencing (RNA-seq) and methyl capture sequencing (MC-seq) methods. Gene ontology analysis of RNA sequences revealed that p53 transcriptional gene network and DNA replication initiation-related genes were significantly up and down-regulated, respectively, showing the correlation with the arrest cell cycle in the G1 phase. MC-seq, a powerful sequencing method for capturing DNA methylation status in CpG sites, revealed that although Mdivi-1 does not induce dramatic DNA methylation change, the subtle alterations were concentrated within the CpG island. Integrative analysis of both sequencing data disclosed that the p53 transcriptional network was activated while the Parkinson's disease pathway was halted. Next, we investigated several changes in mitochondria in response to Mdivi-1. Copy number and transcription of mitochondrial DNA were suppressed. ROS levels increased, and elevated ROS triggered mitochondrial retrograde signaling rather than inducing direct DNA damage. In this study, we could better understand the molecular network of Mdivi-1 by analyzing DNA methylation and mRNA transcription in the nucleus and further investigating various changes in mitochondria, providing inspiration for studying nuclear-mitochondrial communications.
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Affiliation(s)
- Seor I Ahn
- Department of Biochemistry, School of Medicine, Konkuk University, Chungju, Republic of Korea
| | - Sung Kyung Choi
- Department of Biochemistry, School of Medicine, Konkuk University, Chungju, Republic of Korea
| | - Myoung Jun Kim
- Department of Biochemistry, School of Medicine, Konkuk University, Chungju, Republic of Korea
| | - Jinhong Wie
- Department of Physiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jueng Soo You
- Department of Biochemistry, School of Medicine, Konkuk University, Chungju, Republic of Korea; KU Open Innovation Center, Research Institute of Medical Science, Konkuk University, Republic of Korea.
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Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024; 908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [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: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Department of Animal Science, Werabe University, P.O. Box 46, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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47
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Porebski G, Dziadowiec A, Rybka H, Kitel R, Kwitniewski M. Mast cell degranulation and bradykinin-induced angioedema - searching for the missing link. Front Immunol 2024; 15:1399459. [PMID: 38812508 PMCID: PMC11133555 DOI: 10.3389/fimmu.2024.1399459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Initiation of the bradykinin generation cascade is responsible for the occurrence of attacks in some types of angioedema without wheals. Hereditary angioedema due to C1 inhibitor deficiency (HAE-C1-INH) is one such clinical entity. In this paper, we explore the existing evidence that mast cells (MCs) degranulation may contribute to the activation of the kallikrein-kinin system cascade, followed by bradykinin formation and angioedema. We present the multidirectional effects of MC-derived heparin and other polyanions on the major components of the kinin-kallikrein system, particularly on the factor XII activation. Although, bradykinin- and histamine-mediated symptoms are distinct clinical phenomena, they share some common features, such as some similar triggers and a predilection to occur at sites where mast cells reside, namely the skin and mucous membranes. In addition, recent observations indicate a high incidence of hypersensitivity reactions associated with MC degranulation in the HAE-C1-INH patient population. However, not all of these can be explained by IgE-dependent mechanisms. Mast cell-related G protein-coupled receptor-X2 (MRGPRX2), which has recently attracted scientific interest, may be involved in the activation of MCs through a different pathway. Therefore, we reviewed MRGPRX2 ligands that HAE-C1-INH patients may be exposed to in their daily lives and that may affect MCs degranulation. We also discussed the known inter- and intra-individual variability in the course of HAE-C1-INH in relation to factors responsible for possible variability in the strength of the response to MRGPRX2 receptor stimulation. The above issues raise several questions for future research. It is not known to what extent a prophylactic or therapeutic intervention targeting the pathways of one mechanism (mast cell degranulation) may affect the other (bradykinin production), or whether the number of mast cells at a specific body site and their reactivity to triggers such as pressure, allergens or MRGPRX2 agonists may influence the occurrence of HAE-C1-INH attacks at that site.
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Affiliation(s)
- Grzegorz Porebski
- Department of Clinical and Environmental Allergology, Jagiellonian University Medical College, Krakow, Poland
| | - Alicja Dziadowiec
- Department of Clinical and Environmental Allergology, Jagiellonian University Medical College, Krakow, Poland
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Hubert Rybka
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Radoslaw Kitel
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Mateusz Kwitniewski
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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Lee J, Hong I, Lee C, Kim D, Kim S, Lee Y. SNPs in microRNA seed region and impact of miR-375 in concurrent regulation of multiple lipid accumulation-related genes. Sci Rep 2024; 14:10924. [PMID: 38740866 PMCID: PMC11091151 DOI: 10.1038/s41598-024-61673-4] [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: 02/18/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
Bovine intramuscular fat (IMF), commonly referred to as marbling, is regulated by lipid metabolism, which includes adipogenesis, lipogenesis, glycerolipid synthesis, and lipolysis. In recent years, breeding researchers have identified single nucleotide polymorphisms (SNPs) as useful marker-assisted selection tools for improving marbling scores in national breeding programs. These included causal SNPs that induce phenotypic variation. MicroRNAs (miRNAs) are small highly conserved non-coding RNA molecules that bind to multiple non-coding regions. They are involved in post-transcriptional regulation. Multiple miRNAs may regulate a given target. Previously, three SNPs in the GPAM 3' UTR and four miRNAs were identified through in silico assays. The aim of this study is to verify the binding ability of the four miRNAs to the SNPs within the 3'UTR of GPAM, and to identify the regulatory function of miR-375 in the expression of genes related to lipid metabolism in mammalian adipocytes. It was verified that the four miRNAs bind to the GPAM 3'UTR, and identified that the miR-375 sequence is highly conserved. Furthermore, it was founded that miR-375 upregulated the GPAM gene, C/EBPα, PPARγ and lipid metabolism-related genes and promoted lipid droplet accumulation in 3T3-L1 cells. In conclusion, these results suggest that miR-375 is a multifunctional regulator of multiple lipid metabolism-related genes and may aid in obesity research as a biomarker.
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Affiliation(s)
- Jiyeon Lee
- School of Biotechnology, Hankyong National University, Anseong, Gyeonggi-do, South Korea
| | - Inpyo Hong
- School of Biotechnology, Hankyong National University, Anseong, Gyeonggi-do, South Korea
| | - Chanwoo Lee
- Nuonbio Inc., 906, A, 302 Galmachi-ro, Jungwon-gu, Seongnam-si, South Korea
| | - Daehyun Kim
- Department of Animal Science, Chonnam National University, Gwangju, South Korea
| | - Sunghak Kim
- Department of Animal Science, Chonnam National University, Gwangju, South Korea.
| | - Yoonseok Lee
- School of Biotechnology, Hankyong National University, Anseong, Gyeonggi-do, South Korea.
- Center for Genetic Information, Hankyong National University, Anseong, Gyeonggi-do, South Korea.
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Liu Y, Li J, Zhu HJ. Regulation of carboxylesterases and its impact on pharmacokinetics and pharmacodynamics: an up-to-date review. Expert Opin Drug Metab Toxicol 2024; 20:377-397. [PMID: 38706437 PMCID: PMC11151177 DOI: 10.1080/17425255.2024.2348491] [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: 02/28/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
INTRODUCTION Carboxylesterase 1 (CES1) and carboxylesterase 2 (CES2) are among the most abundant hydrolases in humans, catalyzing the metabolism of numerous clinically important medications, such as methylphenidate and clopidogrel. The large interindividual variability in the expression and activity of CES1 and CES2 affects the pharmacokinetics (PK) and pharmacodynamics (PD) of substrate drugs. AREAS COVERED This review provides an up-to-date overview of CES expression and activity regulations and examines their impact on the PK and PD of CES substrate drugs. The literature search was conducted on PubMed from inception to January 2024. EXPERT OPINION Current research revealed modest associations of CES genetic polymorphisms with drug exposure and response. Beyond genomic polymorphisms, transcriptional and posttranslational regulations can also significantly affect CES expression and activity and consequently alter PK and PD. Recent advances in plasma biomarkers of drug-metabolizing enzymes encourage the research of plasma protein and metabolite biomarkers for CES1 and CES2, which could lead to the establishment of precision pharmacotherapy regimens for drugs metabolized by CESs. Moreover, our understanding of tissue-specific expression and substrate selectivity of CES1 and CES2 has shed light on improving the design of CES1- and CES2-activated prodrugs.
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Affiliation(s)
- Yaping Liu
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
| | - Jiapeng Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Hao-Jie Zhu
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
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50
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Hermans L, O’Sullivan TE. No time to die: Epigenetic regulation of natural killer cell survival. Immunol Rev 2024; 323:61-79. [PMID: 38426615 PMCID: PMC11102341 DOI: 10.1111/imr.13314] [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] [Indexed: 03/02/2024]
Abstract
NK cells are short-lived innate lymphocytes that can mediate antigen-independent responses to infection and cancer. However, studies from the past two decades have shown that NK cells can acquire transcriptional and epigenetic modifications during inflammation that result in increased survival and lifespan. These findings blur the lines between the innate and adaptive arms of the immune system, and suggest that the homeostatic mechanisms that govern the persistence of innate immune cells are malleable. Indeed, recent studies have shown that NK cells undergo continuous and strictly regulated adaptations controlling their survival during development, tissue residency, and following inflammation. In this review, we summarize our current understanding of the critical factors regulating NK cell survival throughout their lifespan, with a specific emphasis on the epigenetic modifications that regulate the survival of NK cells in various contexts. A precise understanding of the molecular mechanisms that govern NK cell survival will be important to enhance therapies for cancer and infectious diseases.
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Affiliation(s)
- Leen Hermans
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095
| | - Timothy E. O’Sullivan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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