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Aslanzadeh M, Stanicek L, Tarbier M, Mármol-Sánchez E, Biryukova I, Friedländer M. Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells. NAR Genom Bioinform 2024; 6:lqae045. [PMID: 38711862 PMCID: PMC11071118 DOI: 10.1093/nargab/lqae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/14/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role in stem cells is largely unexplored. We here perform a nuclear knockdown of Malat1 in mouse embryonic stem cells, causing the de-regulation of 320 genes and aberrant splicing of 90 transcripts, some of which potentially affecting the translated protein sequence. We find evidence that Malat1 directly interacts with gene bodies and aberrantly spliced transcripts, and that it locates upstream of down-regulated genes at their putative enhancer regions, in agreement with functional genomics data. Consistent with this, we find these genes affected at both exon and intron levels, suggesting that they are transcriptionally regulated by Malat1. Besides, the down-regulated genes are regulated by specific transcription factors and bear both activating and repressive chromatin marks, suggesting that some of them might be regulated by bivalent promoters. We propose a model in which Malat1 facilitates the transcription of genes involved in chromatid dynamics and mitosis in one pathway, and affects the splicing of transcripts that are themselves involved in RNA processing in a distinct pathway. Lastly, we compare our findings with Malat1 perturbation studies performed in other cell systems and in vivo.
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Affiliation(s)
- Morteza Aslanzadeh
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Laura Stanicek
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory and Center for Palaeogenetics. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
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202
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Shboul M, Bani Domi A, Abu Zahra A, Khasawneh AG, Darweesh R. Plasma miRNAs as potential biomarkers for schizophrenia in a Jordanian cohort. Noncoding RNA Res 2024; 9:350-358. [PMID: 38511065 PMCID: PMC10950580 DOI: 10.1016/j.ncrna.2024.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/15/2024] [Accepted: 01/30/2024] [Indexed: 03/22/2024] Open
Abstract
Background Schizophrenia (SZ), a complex and chronic neuropsychiatric disorder affecting approximately 1 % of the general population, presents diagnostic challenges due to the absence of reliable biomarkers, and relying mainly on clinical observations. MicroRNAs (miRNAs) signatures in a wide range of diseases, including psychiatric disorders, hold immense potential for serving as biomarkers. This study aimed to analyze the expression levels of specific microRNAs (miRNAs) namely miR-29b-3p, miR-106b-5p, and miR-199a-3p and explore their diagnostic potential for SZ in Jordanian patients. Methods Small RNAs (miRNAs) were extracted from plasma samples of 30 SZ patients and 35 healthy controls. RNA was reverse transcribed and quantified by real-time polymerase chain reaction (qRT-PCR). The expression levels of three miRNAs (miR-29b-3p, miR-106b-5p and miR-199a-3p) were analyzed. Receiver operating characteristic (ROC) curves analysis was performed to evaluate diagnostic value of these miRNAs. Target genes prediction, functional enrichment and pathway analyses were done using miRWalk and Metascape. STRING database was used to construct protein-protein network and identify hub genes. Results Notably, miR-106b-5p and miR-199a-3p were significantly upregulated (p < 0.0001), while miRNA-29b-3p was downregulated (p < 0.0001) in SZ patients compared to controls. The diagnostic potential was assessed through ROC curves, revealing substantial diagnostic value for miR-199a-3p (AUC: 0.979) followed by miR-106b-5p (AUC: 0.774), with limited diagnostic efficacy for miR-29b-3p. Additionally, bioinformatic analyses for the predicted target genes of the diagnostically significant miRNAs uncovered Gene Ontology (GO) terms related to neurological development, including morphogenesis, which is involved in neuron differentiation, brain development, head development, and neuron projection morphogenesis. These findings highlight a potential connection between the identified miRNAs and SZ pathophysiology in the studied Jordanian population. Furthermore, a protein-protein interaction network from the target genes identified in association with neurological development in the Gene Ontology (GO) terms deepens our comprehension of the molecular landscape of the regulated target genes. Conclusions This comprehensive exploration highlights the promising role of miRNAs in unraveling intricate molecular pathways associated with SZ in the Jordanian cohort and suggests that plasma miRNAs could serve as reliable biomarkers for SZ diagnosis and disease progression. Remarkably, this study represents the first investigation into the role of circulating miRNA expression among Jordanian patients with SZ, providing valuable insights into the diagnostic landscape of this disorder.
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Affiliation(s)
- Mohammad Shboul
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
| | - Amal Bani Domi
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
| | - Abdulmalek Abu Zahra
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
| | - Aws G. Khasawneh
- Department of Neurosciences, Faculty of Medicine, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
| | - Reem Darweesh
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid, 22110, Jordan
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203
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Rajendran P, Sekar R, Abdallah BM, Fathima JH S, Ali EM, Jayaraman S, Abdelsalam SA, Veeraraghavan V. Epigenetic modulation of long noncoding RNA H19 in oral squamous cell carcinoma-A narrative review. Noncoding RNA Res 2024; 9:602-611. [PMID: 38532798 PMCID: PMC10963247 DOI: 10.1016/j.ncrna.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 03/28/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) showed a seemingly increasing incidence in the last decade. In India, despite the use of tobacco decreased rapidly, in the past five years, the incidence pattern of OSCC over gender and age showed a drastic shift. About 51 % of the head and neck cancers are not associated with habits. Studies exploring various contributing factors in the incidence of this malignancy have documented. Recently, the epigenetic factors associated with the induction and progression of OSCC were explored. More than 90 % of the human genome is made up of non-coding transcriptome, which believed to be noises. However, these non-coding RNAs were identified to be the major epigenetic modulators, which raises concern over incidence of carcinoma in non-habit patients. H19 is a long non coding RNA which proved to be an effective biomarker in various carcinoma. Its role in oral squamous cell cancer was not investigated in depth. This review discusses in detail the various epigenetic role of H19 in inducing oral carcinogenesis.
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Affiliation(s)
- Peramaiyan Rajendran
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Ramya Sekar
- Department of Oral Pathology & Microbiology, Meenakshi Ammal Dental College & Hospital, Alapakkam Main Road, Maduravoyal, Chennai, 95, TN, India
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Basem M. Abdallah
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Shazia Fathima JH
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
- Department of Oral Pathology and Microbiology, Ragas Dental College and Hospitals, Chennai, 600119, Tamil Nadu, India
| | - Enas M. Ali
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Cairo, 12613, Egypt
| | - Selvaraj Jayaraman
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
| | - Salaheldin Abdelraouf Abdelsalam
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Department of Zoology, Faculty of Science, Assiut University, Assiut, 71515, Egypt
| | - Vishnupriya Veeraraghavan
- COMManD, Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Velappanchavadi, Chennai, 600 077, Tamil Nadu, India
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204
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Ding W, Xiao Q, Yue Y, Chen S, She X, Pan B, Zhou L, Yin Y, Li Y, Wang S, Xu M. Deciphering alternative splicing events and their therapeutic implications in colorectal Cancer. Cell Signal 2024; 118:111134. [PMID: 38484942 DOI: 10.1016/j.cellsig.2024.111134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors with complex molecular regulatory mechanisms. Alternative splicing (AS), a fundamental regulatory process of gene expression, plays an important role in the occurrence and development of CRC. This study analyzed AS Percent Spliced In (PSI) values from 49 pairs of CRC and normal samples in the TCGA SpliceSeq database. Using Lasso and SVM, AS features that can differentiate colorectal cancer from normal were screened. Univariate COX regression analysis identified prognosis-related AS events. A risk model was constructed and validated using machine learning, Kaplan-Meier analysis, and Decision Curve Analysis. The regulatory effect of protein arginine methyltransferase 5 (PRMT5) on poly(RC) binding protein 1 (PCBP1) was verified by immunoprecipitation experiments, and the effect of PCBP1 on the AS of Obscurin (OBSCN) was verified by PCR. Five AS events, including HNF4A.59461.AP and HNF4A.59462.AP, were identified, which can distinguish CRC from normal tissue. A machine learning model using 21 key AS events accurately predicted CRC prognosis. High-risk patients had significantly shorter survival times. PRMT5 was found to regulate PCBP1 function and then influence OBSCN AS, which may drive CRC progression. The study concluded that some AS events is significantly different in CRC and normal tissues, and some of these AS events are related to the prognosis of CRC. In addition, PRMT family-driven arginine modifications play an important role in CRC-specific AS events.
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Affiliation(s)
- Wenbo Ding
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Qianni Xiao
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yanzhe Yue
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Shuyu Chen
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Xiangjian She
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Bei Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Linpeng Zhou
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yujuan Yin
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Youyue Li
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shukui Wang
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China.; Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China..
| | - Mu Xu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China..
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Yin Z, Liang J, Zhang M, Chen B, Yu Z, Tian X, Deng X, Peng L. Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus. Sci Total Environ 2024; 927:172251. [PMID: 38604355 DOI: 10.1016/j.scitotenv.2024.172251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.
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Affiliation(s)
- Zhiqiu Yin
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Jiaxin Liang
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Mujie Zhang
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Baozhu Chen
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Zhanpeng Yu
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Xiaoyan Tian
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China
| | - Xiaoyan Deng
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China.
| | - Liang Peng
- Department of Clinical Laboratory, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510700, Guangdong, China; KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou 510180, Guangdong, China.
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206
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Siemers M, Lippegaus A, Papenfort K. ChimericFragments: computation, analysis and visualization of global RNA networks. NAR Genom Bioinform 2024; 6:lqae035. [PMID: 38633425 PMCID: PMC11023125 DOI: 10.1093/nargab/lqae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/08/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
RNA-RNA interactions are a key feature of post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA duplex formation on a genome-wide scale, computational methods for the analysis and interpretation of the underlying data are lagging behind. Here, we present ChimericFragments, an analysis framework for RNA-seq experiments that produce chimeric RNA molecules. ChimericFragments implements a novel statistical method based on the complementarity of the base-pairing RNAs around their ligation site and provides an interactive graph-based visualization for data exploration and interpretation. ChimericFragments detects true RNA-RNA interactions with high precision and is compatible with several widely used experimental procedures such as RIL-seq, LIGR-seq or CLASH. We further demonstrate that ChimericFragments enables the systematic detection of novel RNA regulators and RNA-target pairs with crucial roles in microbial physiology and virulence. ChimericFragments is written in Julia and available at: https://github.com/maltesie/ChimericFragments.
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Affiliation(s)
- Malte Siemers
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
- Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Anne Lippegaus
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
| | - Kai Papenfort
- Friedrich Schiller University, Institute of Microbiology, 07745 Jena, Germany
- Microverse Cluster, Friedrich Schiller University Jena, 07743 Jena, Germany
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207
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Liu R, Guo L, Zhao Y, Wu D, Yu J, Liu P. Study on multi-target effects of the novel HDAC6 inhibitor W5 on Aβ/Cu 2+-induced Alzheimer's disease model of rats. Brain Res 2024; 1832:148847. [PMID: 38442843 DOI: 10.1016/j.brainres.2024.148847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/08/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Histone deacetylase 6 (HDAC6) is a key therapeutic target in neurodegenerative diseases such as Alzheimer's disease (AD), which has been demonstrated to play an essential role in memory function and microtubule-associated tau physiology. In this study, W5 was used to treat AD model rats induced by Aβ/Cu2+ to study the improving effect of W5 on learning and memory impairment in AD rats and its related mechanism, to provide the basis for the subsequent development of W5 as an anti-AD drug. Results showed that W5 could decrease the expression of Aβ, Tau, and p-Tau proteins in the hippocampus of AD rats to inhibit the formation of senile plaques and neurofibrillary tangles, down-regulate the expression of Bax mRNA and Caspase-3 mRNA, and up-regulate the expression of Bcl-2 mRNA to reduce the apoptosis of neuron cells, reverse the expression of TNF-α, IL-1β and IL-6 mRNA to regulate neuroinflammatory response in AD rat brain. W5 also could regulate the oxidative stress state of AD rats, and balance the neurotransmitter disorder in AD rats' brain tissue. Overall, W5 could recover the morphology of hippocampal neurons and improve the learning and memory dysfunction in AD rats by regulating multiple targets in AD rats, providing a promising therapeutic avenue for the treatment of AD.
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Affiliation(s)
- Ruihua Liu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Linli Guo
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yanan Zhao
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Dan Wu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jiasi Yu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ping Liu
- Department of Physical and Chemical Inspection, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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208
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Ioachimescu OC. Contribution of Obstructive Sleep Apnea to Asthmatic Airway Inflammation and Impact of Its Treatment on the Course of Asthma. Sleep Med Clin 2024; 19:261-274. [PMID: 38692751 DOI: 10.1016/j.jsmc.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Asthma and obstructive sleep apnea (OSA) are very common respiratory disorders in the general population. Beyond their high prevalence, shared risk factors, and genetic linkages, bidirectional relationships between asthma and OSA exist, each disorder affecting the other's presence and severity. The author reviews here some of the salient links between constituents of the alternative overlap syndrome, that is, OSA comorbid with asthma, with an emphasis on the effects of OSA or its treatment on inflammation in asthma. In the directional relationship from OSA toward asthma, beyond direct influences, multiple factors and comorbidities seem to contribute.
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Affiliation(s)
- Octavian C Ioachimescu
- Clinical and Translational Science Institute of Southeast Wisconsin, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
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209
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Xiang T, Quan X, Jia H, Wang H, Liang B, Li S, Wang X, Li H, Feng X, Fan L, Xu L, Wang T, Xiong S, Yang D, Liu J, Zheng X. Omicron breakthrough infections after triple-dose inactivated COVID-19 vaccination: A comprehensive analysis of antibody and T-cell responses. Immunology 2024; 172:313-327. [PMID: 38462236 DOI: 10.1111/imm.13764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 01/28/2024] [Indexed: 03/12/2024] Open
Abstract
This study longitudinally evaluated the immune response in individuals over a year after receiving three doses of an inactivated SARS-CoV-2 vaccine, focusing on reactions to Omicron breakthrough infections. From 63 blood samples of 37 subjects, results showed that the third booster enhanced the antibody response against Alpha, Beta, and Delta VOCs but was less effective against Omicron. Although antibody titres decreased post-vaccination, SARS-CoV-2-specific T-cell responses, both CD4+ and CD8+, remained stable. Omicron breakthrough infections significantly improved neutralization against various VOCs, including Omicron. However, the boost in antibodies against WT, Alpha, Beta, and Delta variants was more pronounced. Regarding T cells, breakthrough infection predominantly boosted the CD8+ T-cell response, and the intensity of the spike protein-specific T-cell response was roughly comparable between WT and Omicron BA.5.
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Affiliation(s)
- Tiandan Xiang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xufeng Quan
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Hang Jia
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Boyun Liang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Sumeng Li
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyan Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Huadong Li
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Xuemei Feng
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Fan
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Xu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Tong Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Shue Xiong
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Dongliang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Liu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Zheng
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan, China
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210
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Zanoteli E, França MC, Marques W. Gene-based therapies for neuromuscular disorders. Arq Neuropsiquiatr 2024; 82:1-10. [PMID: 38325390 PMCID: PMC10849828 DOI: 10.1055/s-0043-1777755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Neuromuscular diseases (NMD) include a broad group of medical conditions with both acquired and genetic causes. In recent years, important advances have been made in the treatment of genetically caused NMD, and most of these advances are due to the implementation of therapies aimed at gene regulation. Among these therapies, gene replacement, small interfering RNA (siRNA), and antisense antinucleotides are the most promising approaches. More importantly, some of these therapies have already gained regulatory approval or are in the final stages of approval. The review focuses on motor neuron diseases, neuropathies, and Duchenne muscular dystrophy, summarizing the most recent developments in gene-based therapies for these conditions.
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Affiliation(s)
- Edmar Zanoteli
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Neurologia, São Paulo SP, Brazil.
| | - Marcondes Cavalcante França
- Universidade Estadual de Campinas, Faculdade de Ciências Médicas, Departamento de Neurologia, Campinas SP, Brazil.
| | - Wilson Marques
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Neurociências e Ciências do Comportamento, Ribeirão Preto SP, Brazil.
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211
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Peng A, Yin G, Zuo W, Zhang L, Du G, Chen J, Wang Y, Kang Z. Regulatory RNAs in Bacillus subtilis: A review on regulatory mechanism and applications in synthetic biology. Synth Syst Biotechnol 2024; 9:223-233. [PMID: 38385150 PMCID: PMC10877136 DOI: 10.1016/j.synbio.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Bacteria exhibit a rich repertoire of RNA molecules that intricately regulate gene expression at multiple hierarchical levels, including small RNAs (sRNAs), riboswitches, and antisense RNAs. Notably, the majority of these regulatory RNAs lack or have limited protein-coding capacity but play pivotal roles in orchestrating gene expression by modulating transcription, post-transcription or translation processes. Leveraging and redesigning these regulatory RNA elements have emerged as pivotal strategies in the domains of metabolic engineering and synthetic biology. While previous investigations predominantly focused on delineating the roles of regulatory RNA in Gram-negative bacterial models such as Escherichia coli and Salmonella enterica, this review aims to summarize the mechanisms and functionalities of endogenous regulatory RNAs inherent to typical Gram-positive bacteria, notably Bacillus subtilis. Furthermore, we explore the engineering and practical applications of these regulatory RNA elements in the arena of synthetic biology, employing B. subtilis as a foundational chassis.
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Affiliation(s)
- Anqi Peng
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guobin Yin
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wenjie Zuo
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Luyao Zhang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yang Wang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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212
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Liang L, Liang M, Zuo Z, Ai Y. Label-free single-cell analysis in microdroplets using a light-scattering-based optofluidic chip. Biosens Bioelectron 2024; 253:116148. [PMID: 38428071 DOI: 10.1016/j.bios.2024.116148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
Droplet-based single-cell analysis is a very powerful tool for studying phenotypic and genomic heterogeneity at single-cell resolution for a variety of biological problems. In conventional two-phase droplet microfluidics, due to the mismatch in optical properties between oil and aqueous phases, light scattering mainly happens at the oil/water interface that disables light-scattering-based cell analysis confined in microdroplets. Detection and analysis of cells in microdroplets thus mostly rely on the fluorescence labeling of cell samples, which may suffer from complex operation, cytotoxicity, and low fluorescence stability. In this work, we propose a novel light-scattering-based droplet screening (LSDS) that can effectively detect and characterize single cells confined in droplets by adjusting the optical properties of droplets in a multiangle optofluidic chip. Theoretical and simulated calculations suggest that refractive index (RI) matching in droplet two-phase materials can reduce or eliminate droplets' scattered signals (background signal), enabling the differentiation of scattered signals from single cells and particles within droplets. Furthermore, by using a set of multiangle (from -145° to 140°) optical fibers integrated into the optofluidic chip, the scattered light properties of droplets with the RI ranging from 1.334 to 1.429 are measured. We find that the smaller the RI and size of microparticles inside droplets are, the smaller the RI difference between two-phase materials Δn is required. Especially, when Δn is smaller than 0.02, single cells in droplets can be detected and analyzed solely based on light scattering. This capability allows to accurately detect droplets containing one single cell and one single gel bead, a typical droplet encapsulation for single-cell sequencing. Altogether, this work provides a powerful platform for high-throughput label-free single-cell analysis in microdroplets for diverse single-cell related biological assays.
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Affiliation(s)
- Li Liang
- School of Physics and Electronic Information, Anhui Normal University, Wuhu, 241000, China
| | - Minhui Liang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, 487372, Singapore
| | - Zewen Zuo
- School of Physics and Electronic Information, Anhui Normal University, Wuhu, 241000, China
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, Singapore, 487372, Singapore.
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213
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Hartewig A, Huhtala L, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Rautajoki KJ. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance 2024; 7:e202302088. [PMID: 38499326 PMCID: PMC10948937 DOI: 10.26508/lsa.202302088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.
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Affiliation(s)
- Meeri Pekkarinen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kristiina Nordfors
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Unit of Pediatric Hematology and Oncology, Tampere University Hospital, Tampere, Finland
| | - Joonas Uusi-Mäkelä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ville Kytölä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Laura Huhtala
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Minna Rauhala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Henna Urhonen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Sergei Häyrynen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Olli Yli-Harja
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Pauli Helen
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Olli Lohi
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Rautajoki
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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214
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Li S, Ye Z, Moreb EA, Menacho-Melgar R, Golovsky M, Lynch MD. 2-Stage microfermentations. Metab Eng Commun 2024; 18:e00233. [PMID: 38665924 PMCID: PMC11043886 DOI: 10.1016/j.mec.2024.e00233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Cell based factories can be engineered to produce a wide variety of products. Advances in DNA synthesis and genome editing have greatly simplified the design and construction of these factories. It has never been easier to generate hundreds or even thousands of cell factory strain variants for evaluation. These advances have amplified the need for standardized, higher throughput means of evaluating these designs. Toward this goal, we have previously reported the development of engineered E. coli strains and associated 2-stage production processes to simplify and standardize strain engineering, evaluation and scale up. This approach relies on decoupling growth (stage 1), from production, which occurs in stationary phase (stage 2). Phosphate depletion is used as the trigger to stop growth as well as induce heterologous expression. Here, we describe in detail the development of protocols for the evaluation of engineered E. coli strains in 2-stage microfermentations. These protocols are readily adaptable to the evaluation of strains producing a wide variety of protein as well as small molecule products. Additionally, by detailing the approach to protocol development, these methods are also adaptable to additional cellular hosts, as well as other 2-stage processes with various additional triggers.
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Affiliation(s)
- Shuai Li
- Department of Chemistry, Duke University, Durham, NC, USA
| | - Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Eirik A. Moreb
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | | | - Michael D. Lynch
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
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215
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Sanaei MJ, Pourbagheri-Sigaroodi A, Rezvani A, Zaboli E, Salari S, Masjedi MR, Bashash D. Lung cancer vaccination from concept to reality: A critical review of clinical trials and latest advances. Life Sci 2024; 346:122652. [PMID: 38641048 DOI: 10.1016/j.lfs.2024.122652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Lung cancer is a highly lethal malignancy that poses a significant burden on public health worldwide. There have been numerous therapeutic approaches, among which cancer vaccines have emerged as a promising approach to harnessing the patient's immune system to induce long-lasting anti-tumor immunity. The current study aims to provide an overview of cancer vaccination in the context of lung cancer to establish a clearer landscape for lung cancer treatment. To provide a comprehensive review, we not only gathered the published studies of lung cancer vaccination and discussed their effectiveness and safety profile but also analyzed all the relevant clinical trials registered on www.clinicaltrials.gov until March 2024. We demonstrated all utilized vaccine platforms along with having a glance at novel technologies such as mRNA vaccines. The present review discussed the challenges and shortcomings of lung cancer vaccination, as well as the way they could be managed to pave the way for reaching the most optimized vaccine formulation.
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Affiliation(s)
- Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Rezvani
- Department of Internal Medicine, Hematology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ehsan Zaboli
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sina Salari
- Department of Medical Oncology-Hematology, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Masjedi
- Cancer Control Research Center, Cancer Control Foundation, Iran University of Medical Sciences, Tehran, Iran; Department of Pulmonary Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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216
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Wu X, Wang S, Guo Y, Zeng S. Overexpression of KAT8 induces a failure in early embryonic development in mice. Theriogenology 2024; 221:31-37. [PMID: 38537319 DOI: 10.1016/j.theriogenology.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/23/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024]
Abstract
Embryo quality is strongly associated with subsequent embryonic developmental efficiency. However, the detailed function of lysine acetyltransferase 8 (KAT8) during early embryonic development in mice remains elusive. In this study, we reported that KAT8 played a pivotal role in the first cleavage of mouse embryos. Immunostaining results revealed that KAT8 predominantly accumulated in the nucleus throughout the entire embryonic developmental process. Kat8 overexpression (Kat8-OE) was correlated with early developmental potential of embryos to the blastocyst stage. We also found that Kat8-OE embryos showed spindle-assembly defects and chromosomal misalignment, and that Kat8-OE in embryos led to increased levels of reactive oxygen species (ROS), accumulation of phosphorylated γH2AX by affecting the expression of critical genes related to mitochondrial respiratory chain and antioxidation pathways. Subsequently, cellular apoptosis was activated as confirmed by TUNEL (Terminal Deoxynucleotidyl Transferase mediated dUTP Nick-End Labeling) assay. Furthermore, we revealed that KAT8 was related to regulating the acetylation status of H4K16 in mouse embryos, and Kat8-OE induced the hyperacetylation of H4K16, which might be a key factor for the defective spindle/chromosome apparatus. Collectively, our data suggest that KAT8 constitutes an important regulator of spindle assembly and redox homeostasis during early embryonic development in mice.
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Affiliation(s)
- Xuan Wu
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiwei Wang
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yajun Guo
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shenming Zeng
- State Key Laboratory of Animal Biotech Breeding, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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217
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Filippi M, Demoliner M, Gularte JS, de Abreu Goes Pereira VM, da Silva MS, Girardi V, Hansen AW, Spilki FR. Relative frequency of genomic mutations in SARS-CoV-2 recovered from southern Brazilian cases of COVID-19 through the Gamma, Delta and Omicron waves. Infect Genet Evol 2024; 120:105590. [PMID: 38574833 DOI: 10.1016/j.meegid.2024.105590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/06/2024]
Abstract
The presence of different mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can be related to changes in coronavirus disease (COVID-19) infection. Besides, these viral alterations associated with factors such as massive number of positive cases, vaccination and reinfections can be important in the viral evolution process. As well as, mutations found at low frequencies may have a more neutral action and consequently be less inclined to negative selection, facilitating their spread through the population. Related to that, we aimed to present mutations that are possibly relevant in the process of viral evolution found in 115 SARS-CoV-2 sequences from samples of individuals residing in the metropolitan region of Porto Alegre in the state of Rio Grande do Sul, Brazil. The genome from clinical samples was sequenced using High-Throughput Sequencing (HTS) and analyzed using a workflow to map reads and find variations/SNPs. The samples were separated into 3 groups considering the sample lineage. Of the total number of analyzed sequences, 35 were from the Gamma lineage, 35 from Delta and 45 from Omicron. Amino acid changes present in frequencies lower than 80% of the reads in the sequences were evaluated. 11 common mutations among the samples were found in the Gamma lineage, 1 in the ORF1ab gene, 7 in the S gene, 2 in the ORF6 gene and 1 in the ORF7a gene. While in the Delta lineage, a total of 11 mutations distributed in the ORF1ab, S, ORF7a and N genes, 2, 7, 1 and 1 mutation were found in each gene, respectively. And finally, in the Omicron, 16 mutations were identified, 2 in the ORF1ab gene, 12 in the S gene and 2 in the M gene. In conclusion, we emphasize that genomic surveillance can be a useful tool to assess how mutations play a key role in virus adaptation, and its process of susceptibility to new hosts showing the possible signs of viral evolution.
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Affiliation(s)
- Micheli Filippi
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil.
| | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | | | - Mariana Soares da Silva
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Viviane Girardi
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Alana Witt Hansen
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
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218
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Marash I, Leibman-Markus M, Gupta R, Israeli A, Teboul N, Avni A, Ori N, Bar M. Abolishing ARF8A activity promotes disease resistance in tomato. Plant Sci 2024; 343:112064. [PMID: 38492890 DOI: 10.1016/j.plantsci.2024.112064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/18/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Auxin response factors (ARFs) are a family of transcription factors that regulate auxin-dependent developmental processes. Class A ARFs function as activators of auxin-responsive gene expression in the presence of auxin, while acting as transcriptional repressors in its absence. Despite extensive research on the functions of ARF transcription factors in plant growth and development, the extent, and mechanisms of their involvement in plant resistance, remain unknown. We have previously reported that mutations in the tomato AUXIN RESPONSE FACTOR8 (ARF8) genes SlARF8A and SlARF8B result in the decoupling of fruit development from pollination and fertilization, leading to partial or full parthenocarpy and increased yield under extreme temperatures. Here, we report that fine-tuning of SlARF8 activity results in increased resistance to fungal and bacterial pathogens. This resistance is mostly preserved under fluctuating temperatures. Thus, fine-tuning SlARF8 activity may be a potent strategy for increasing overall growth and yield.
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Affiliation(s)
- Iftah Marash
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel; School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Meirav Leibman-Markus
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Rupali Gupta
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel
| | - Alon Israeli
- Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Naama Teboul
- Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Adi Avni
- School of Plant Science and Food Security, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Naomi Ori
- Institute of Plant Science and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maya Bar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Bet Dagan 50250, Israel.
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Nicol DA, Saldivia P, Summerfield TC, Heads M, Lord JM, Khaing EP, Larcombe MJ. Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications. Mol Phylogenet Evol 2024; 195:108064. [PMID: 38508479 DOI: 10.1016/j.ympev.2024.108064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
The tribe Astereae (Asteraceae) includes 36 subtribes and 252 genera, and is distributed worldwide in temperate and tropical regions. One of the subtribes, Celmisiinae Saldivia, has been recently circumscribed to include six genera and ca. 160 species, and is restricted to eastern Australia, New Zealand, and New Guinea. The species show an impressive range of growth habit, from small herbs and ericoid subshrubs to medium-sized trees. They live in a wide range of habitats and are often dominant in subalpine and alpine vegetation. Despite the well-supported circumscription of Celmisiinae, uncertainties have remained about their internal relationships and classification at genus and species levels. This study exploited recent advances in high-throughput sequencing to build a robust multi-gene phylogeny for the subtribe Celmisiinae. The target enrichment Angiosperms353 bait set and the hybpiper-nf and paragone-nf pipelines were used to retrieve, infer, and assemble orthologous loci from 75 taxa representing all the main putative clades within the subtribe. Because of the diploidised ploidy level in Celmisiinae, as well as missing data in the assemblies, uncertainty remains surrounding the inference of orthology detection. However, based on a variety of gene-family sets, coalescent and concatenation-based phylogenetic reconstructions recovered similar topologies. Paralogy and missing data in the gene-families caused some problems, but the estimated phylogenies were well-supported and well-resolved. The phylogenomic evidence supported Celmisiinae and three main clades: the Pleurophyllum clade (Pleurophyllum, Macrolearia and Damnamenia), mostly in the New Zealand Subantarctic Islands, Celmisia of mainland New Zealand and Australia, and Shawia (including 'Olearia pro parte' and Pachystegia) of New Zealand, Australia and New Guinea. The results presented here add to the accumulating support for the Angiosperms353 bait set as an efficient method for documenting plant diversity.
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Affiliation(s)
- Duncan A Nicol
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand.
| | - Patricio Saldivia
- Biota Ltda. Av. Miguel Claro 1224, Providencia, Santiago, Chile; Museo Regional de Aysén, Km 3 Camino a Coyhaique Alto, Coyhaique, Chile
| | - Tina C Summerfield
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Michael Heads
- Buffalo Museum of Science, Buffalo, NY 14211-1293, USA
| | - Janice M Lord
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Ei P Khaing
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56, Dunedin, New Zealand
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G/meskel W, Desta K, Diriba R, Belachew M, Evans M, Cantarelli V, Urrego M, Sisay A, Gebreegziabxier A, Abera A. SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction-based assays in Addis Ababa, Ethiopia. IJID Reg 2024; 11:100363. [PMID: 38634071 PMCID: PMC11021353 DOI: 10.1016/j.ijregi.2024.100363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024]
Abstract
Objectives This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)-based variant detection in Addis Ababa, Ethiopia. Methods A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 μl RNA and 20 μl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive. Results A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30. Conclusions The study data demonstrated that reverse transcription-PCR-based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.
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Affiliation(s)
- Wodneh G/meskel
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Kassu Desta
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Regasa Diriba
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | - Mahlet Belachew
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Martin Evans
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Vlademir Cantarelli
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Maritza Urrego
- Global Public Health Programs, American Society for Microbiology, Washington, USA
| | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Science, Addis Ababa University, P.O.Box 1176, Addis Ababa, Ethiopia
| | | | - Adugna Abera
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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221
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Koyama Y, Nawa N, Ochi M, Surkan PJ, Fujiwara T. Joint Roles of Oxytocin- and Dopamine-Related Genes and Childhood Parenting Experience in Maternal Supportive Social Network. Child Psychiatry Hum Dev 2024; 55:614-621. [PMID: 36098825 DOI: 10.1007/s10578-022-01434-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/31/2022] [Indexed: 11/03/2022]
Abstract
How genes and parenting determine maternal social support availability, an important preventive factor of postpartum depression, has been little studied. Our study aimed to examine the interaction effects of maternal sociality-related gene and parenting on maternal social support. We analyzed data of 115 triads of Japanese grandmothers, mothers, and their infants. An interaction between parenting and cumulative genetic risk, calculated on the sociality-related genes (OXTR rs53576, rs2254298, rs1042778; COMT rs4680), was found. Mothers with high genetic risk received less social support if received poorer parenting (B = - 0.02, 95%CI = - 0.04 to - 0.01), while no association among low-risk mothers. Poorer social support was associated with severer depression in high-risk mothers (B = - 0.88, 95%CI = - 1.45 to -0.30). Our results suggest that mothers carrying risk alleles of sociality-related genes are particularly sensitive to childhood parenting, underscoring the importance of childhood parenting and genetic risk to understand maternal help-seeking behavior.
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Affiliation(s)
- Yuna Koyama
- Department of Global Health Promotion, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Nobutoshi Nawa
- Department of Medical Education Research and Development, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
| | - Manami Ochi
- Department of Global Health Promotion, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan
- Department of Social Medicine, National Center for Child Health and Development, Tokyo, 157-8535, Japan
- Department of Health and Welfare Services, National Institute of Public Health, Saitama, 351-0197, Japan
| | - Pamela J Surkan
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Takeo Fujiwara
- Department of Global Health Promotion, Tokyo Medical and Dental University (TMDU), Tokyo, 113-8510, Japan.
- Department of Social Medicine, National Center for Child Health and Development, Tokyo, 157-8535, Japan.
- Department of Global Health Promotion, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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222
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Awad S, Valleriani A, Chiarugi D. A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length. NAR Genom Bioinform 2024; 6:lqae036. [PMID: 38638702 PMCID: PMC11025885 DOI: 10.1093/nargab/lqae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
Ribosomes are the molecular machinery that catalyse all the fundamental steps involved in the translation of mRNAs into proteins. Given the complexity of this process, the efficiency of protein synthesis depends on a large number of factors among which ribosome drop-off (i.e. the premature detachment of the ribosome from the mRNA template) plays an important role. However, an in vitro quantification of the extent to which ribosome drop-off occurs is not trivial due to difficulties in obtaining the needed experimental evidence. In this work we focus on the study of ribosome drop-off in Saccharomyces cerevisiae by using 'Ribofilio', a novel software tool that relies on a high sensitive strategy to estimate the ribosome drop-off rate from ribosome profiling data. Our results show that ribosome drop-off events occur at a significant rate also when S. cerevisiae is cultured in standard conditions. In this context, we also identified a correlation between the ribosome drop-off rate and the genes length: the longer the gene, the lower the drop-off rate.
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Affiliation(s)
- Sherine Awad
- Genomics and Bioinformatics Core Facility, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Davide Chiarugi
- Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraße 1a, 04103 Leipzig - Germany
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223
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Aparicio-Blanco J, Vishwakarma N, Lehr CM, Prestidge CA, Thomas N, Roberts RJ, Thorn CR, Melero A. Antibiotic resistance and tolerance: What can drug delivery do against this global threat? Drug Deliv Transl Res 2024; 14:1725-1734. [PMID: 38341386 PMCID: PMC11052818 DOI: 10.1007/s13346-023-01513-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2023] [Indexed: 02/12/2024]
Abstract
Antimicrobial resistance and tolerance (AMR&T) are urgent global health concerns, with alarmingly increasing numbers of antimicrobial drugs failing and a corresponding rise in related deaths. Several reasons for this situation can be cited, such as the misuse of traditional antibiotics, the massive use of sanitizing measures, and the overuse of antibiotics in agriculture, fisheries, and cattle. AMR&T management requires a multifaceted approach involving various strategies at different levels, such as increasing the patient's awareness of the situation and measures to reduce new resistances, reduction of current misuse or abuse, and improvement of selectivity of treatments. Also, the identification of new antibiotics, including small molecules and more complex approaches, is a key factor. Among these, novel DNA- or RNA-based approaches, the use of phages, or CRISPR technologies are some potent strategies under development. In this perspective article, emerging and experienced leaders in drug delivery discuss the most important biological barriers for drugs to reach infectious bacteria (bacterial bioavailability). They explore how overcoming these barriers is crucial for producing the desired effects and discuss the ways in which drug delivery systems can facilitate this process.
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Affiliation(s)
- Juan Aparicio-Blanco
- Department of Pharmaceutics and Food Technology, Faculty of Pharmacy, Complutense University of Madrid, 28040, Madrid, Spain
| | - Nikhar Vishwakarma
- Department of Pharmacy, Gyan Ganga Institute of Technology and Sciences, Jabalpur, 482003, Madhya Pradesh, India
| | - Claus-Michael Lehr
- Department Drug Delivery across Biological Barriers (DDEL), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8 1, 66123, Saarbrücken, Germany
| | - Clive A Prestidge
- Centre for Pharmaceutical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Nicky Thomas
- Centre for Pharmaceutical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | | | - Chelsea R Thorn
- Biotherapeutics Pharmaceutical Research and Development, Pfizer, Inc., 1 Burtt Road, Andover, MA, 01810, USA.
| | - Ana Melero
- Department of Pharmacy and Pharmaceutical Technology and Parasitology, Faculty of Pharmacy, University of Valencia, 46100, Burjassot, Spain.
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224
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Yu V, Yong F, Marta A, Khadayate S, Osakwe A, Bhattacharya S, Varghese SS, Chabosseau P, Tabibi SM, Chen K, Georgiadou E, Parveen N, Suleiman M, Stamoulis Z, Marselli L, De Luca C, Tesi M, Ostinelli G, Delgadillo-Silva L, Wu X, Hatanaka Y, Montoya A, Elliott J, Patel B, Demchenko N, Whilding C, Hajkova P, Shliaha P, Kramer H, Ali Y, Marchetti P, Sladek R, Dhawan S, Withers DJ, Rutter GA, Millership SJ. Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity. Diabetologia 2024; 67:1079-1094. [PMID: 38512414 PMCID: PMC11058053 DOI: 10.1007/s00125-024-06123-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 03/23/2024]
Abstract
AIMS/HYPOTHESIS Beta cells within the pancreatic islet represent a heterogenous population wherein individual sub-groups of cells make distinct contributions to the overall control of insulin secretion. These include a subpopulation of highly connected 'hub' cells, important for the propagation of intercellular Ca2+ waves. Functional subpopulations have also been demonstrated in human beta cells, with an altered subtype distribution apparent in type 2 diabetes. At present, the molecular mechanisms through which beta cell hierarchy is established are poorly understood. Changes at the level of the epigenome provide one such possibility, which we explore here by focusing on the imprinted gene Nnat (encoding neuronatin [NNAT]), which is required for normal insulin synthesis and secretion. METHODS Single-cell RNA-seq datasets were examined using Seurat 4.0 and ClusterProfiler running under R. Transgenic mice expressing enhanced GFP under the control of the Nnat enhancer/promoter regions were generated for FACS of beta cells and downstream analysis of CpG methylation by bisulphite sequencing and RNA-seq, respectively. Animals deleted for the de novo methyltransferase DNA methyltransferase 3 alpha (DNMT3A) from the pancreatic progenitor stage were used to explore control of promoter methylation. Proteomics was performed using affinity purification mass spectrometry and Ca2+ dynamics explored by rapid confocal imaging of Cal-520 AM and Cal-590 AM. Insulin secretion was measured using homogeneous time-resolved fluorescence imaging. RESULTS Nnat mRNA was differentially expressed in a discrete beta cell population in a developmental stage- and DNA methylation (DNMT3A)-dependent manner. Thus, pseudo-time analysis of embryonic datasets demonstrated the early establishment of Nnat-positive and -negative subpopulations during embryogenesis. NNAT expression is also restricted to a subset of beta cells across the human islet that is maintained throughout adult life. NNAT+ beta cells also displayed a discrete transcriptome at adult stages, representing a subpopulation specialised for insulin production, and were diminished in db/db mice. 'Hub' cells were less abundant in the NNAT+ population, consistent with epigenetic control of this functional specialisation. CONCLUSIONS/INTERPRETATION These findings demonstrate that differential DNA methylation at Nnat represents a novel means through which beta cell heterogeneity is established during development. We therefore hypothesise that changes in methylation at this locus may contribute to a loss of beta cell hierarchy and connectivity, potentially contributing to defective insulin secretion in some forms of diabetes. DATA AVAILABILITY The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD048465.
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Affiliation(s)
- Vanessa Yu
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Fiona Yong
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore
| | - Angellica Marta
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | | | - Adrien Osakwe
- Quantitative Life Sciences Program, McGill University, Montréal, QC, Canada
| | - Supriyo Bhattacharya
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sneha S Varghese
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Pauline Chabosseau
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Sayed M Tabibi
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Keran Chen
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eleni Georgiadou
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Nazia Parveen
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Mara Suleiman
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Zoe Stamoulis
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Carmela De Luca
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Marta Tesi
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Giada Ostinelli
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada
| | - Luis Delgadillo-Silva
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada
| | - Xiwei Wu
- Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Yuki Hatanaka
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | | | | | | | - Nikita Demchenko
- MRC Laboratory of Medical Sciences, London, UK
- Imaging Resource Facility, Research Operations, St George's, University of London, London, UK
| | | | - Petra Hajkova
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Yusuf Ali
- Nutrition, Metabolism and Health Programme & Centre for Microbiome Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Republic of Singapore
- Singapore Eye Research Institute (SERI), Singapore General Hospital, Singapore, Republic of Singapore
- Clinical Research Unit, Khoo Teck Puat Hospital, National Healthcare Group, Singapore, Republic of Singapore
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, and AOUP Cisanello University Hospital, University of Pisa, Pisa, Italy
| | - Robert Sladek
- Quantitative Life Sciences Program, McGill University, Montréal, QC, Canada
- Departments of Medicine and Human Genetics, McGill University, Montréal, QC, Canada
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Dominic J Withers
- MRC Laboratory of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Guy A Rutter
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore.
- CHUM Research Center and Faculty of Medicine, University of Montréal, Montréal, QC, Canada.
| | - Steven J Millership
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
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Thoeni V, Dimova EY, Kietzmann T, Usselman RJ, Egg M. Therapeutic nuclear magnetic resonance and intermittent hypoxia trigger time dependent on/off effects in circadian clocks and confirm a central role of superoxide in cellular magnetic field effects. Redox Biol 2024; 72:103152. [PMID: 38593630 PMCID: PMC11016797 DOI: 10.1016/j.redox.2024.103152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/11/2024] Open
Abstract
Cellular magnetic field effects are assumed to base on coherent singlet-triplet interconversion of radical pairs that are sensitive to applied radiofrequency (RF) and weak magnetic fields (WEMFs), known as radical pair mechanism (RPM). As a leading model, the RPM explains how quantum effects can influence biochemical and cellular signalling. Consequently, radical pairs generate reactive oxygen species (ROS) that link the RPM to redox processes, such as the response to hypoxia and the circadian clock. Therapeutic nuclear magnetic resonance (tNMR) occupies a unique position in the RPM paradigm because of the used frequencies, which are far below the range of 0.1-100 MHz postulated for the RPM to occur. Nonetheless, tNMR was shown to induce RPM like effects, such as increased extracellular H2O2 levels and altered cellular bioenergetics. In this study we compared the impact of tNMR and intermittent hypoxia on the circadian clock, as well as the role of superoxide in tNMR induced ROS partitioning. We show that both, tNMR and intermittent hypoxia, exert on/off effects on cellular clocks that are dependent on the time of application (day versus night). In addition, our data provide further evidence that superoxide plays a central role in magnetic signal transduction. tNMR used in combination with scavengers, such as Vitamin C, led to strong ROS product redistributions. This discovery might represent the first indication of radical triads in biological systems.
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Affiliation(s)
- Viktoria Thoeni
- Institute of Zoology, University Innsbruck, Technikerstraße 25, 6020, Innsbruck, Tyrol, A-6020, Austria
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Robert J Usselman
- Faculty of Chemistry and Chemical Engineering, Florida Institute of Technology, 150 W University Blvd, Melbourne, FL, 32901, USA
| | - Margit Egg
- Institute of Zoology, University Innsbruck, Technikerstraße 25, 6020, Innsbruck, Tyrol, A-6020, Austria.
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226
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Xing W, Li S. LncRNA ENSGALG00000021686 regulates fat metabolism in chicken hepatocytes via miR-146b/AGPAT2 pathway. Anim Genet 2024; 55:420-429. [PMID: 38369771 DOI: 10.1111/age.13405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
The liver contributes to lipid metabolism as the hub of fat synthesis. Long non-coding RNAs (lncRNAs) are considered the regulators of cellular processes. Since LncRNA ENSGALG00000021686 (lncRNA 21 686) has been described as a regulator of lipid metabolism, the present study aimed to clarify the role of lncRNA 21 686 in chicken hepatocytes' lipid metabolism. Thirty-two chickens were divided into four groups and were treated with diets containing different amounts of fat, and the hepatic expression of lncRNA 21 686 and miR-146b along with the levels of proteins involved in the regulation of fat metabolism, lipid indices and oxidative stress were measured. Moreover, primary chicken hepatocytes were transfected with lncRNA 21 686 small interfering RNA or microRNA (miRNA, miR)-146b mimics to measure the consequences of suppressing lncRNA or inducing miRNA expression on the levels of proteins involved in fat metabolism and stress markers. The results showed that the high-fat diet modulated the expression of lncRNA 21 686 and miR-146b (p-value < 0.001). Moreover, there was a significant increase in 1-acyl-sn-glycerol-3-phosphate acyltransferase 2 (AGPAT2) gene expression and protein levels and modulated fat-related markers. Furthermore, the results showed that lncRNA 21 686 suppression reduced the expression of AGPAT2 and its downstream proteins (p-value < 0.05). Overexpression of miR-146b regulated fat metabolism indicator expression. Transfection experiments revealed that lncRNA 21 686 suppression increased miR-146b expression. The findings suggested a novel mechanism containing lncRNA 21 686/miR-146b/AGPAT2 in the regulation of fat metabolism in chicken hepatocytes.
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Affiliation(s)
- Wenhao Xing
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shijie Li
- Dongying Jintengsheng Medical Device Sales Co., Ltd., Dongying, Shandong Province, China
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227
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Saadat M. Evaluation of Hardy-Weinberg equilibrium in genetic association studies. Int J Immunogenet 2024; 51:183-186. [PMID: 38509453 DOI: 10.1111/iji.12668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
STrengthening the REporting of Genetic Association (STREGA) studies strongly recommend that researchers assess the Hardy-Weinberg equilibrium (HWE) in their control groups. The exact frequency of studies in which their control subjects show a significant deviation from the HWE is not well established. Therefore, the present study was conducted. The electronic database PubMed was searched using the terms: 'meta-analysis' and 'polymorphism'. Data of original articles were extracted from meta-analysis. The STREGA statement was published in 2009. Therefore, studies were divided into two groups, before and after the statement. After data collection, quartiles for sample size and minor allele frequency (MAF) were determined separately. A total of 772 independent studies were extracted from these meta-analyses and included in the current study. Multivariate analysis revealed the following associations: (1) Reports published after the STREGA statement (compared to before the statement) were associated with an increased prevalence of deviation from HWE. (2) Reports with sample size Q2-Q4 versus Q1 were associated with an increased prevalence of deviation from HWE. (3) Studies with MAF Q4 versus Q1 were negatively associated with the prevalence of reports of deviation from HWE. We conclude that the STREGA statement failed to change the attitudes and practices of researchers and editors towards the importance of HWE.
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Affiliation(s)
- Mostafa Saadat
- Department of Biology, School of Science, Shiraz University, Shiraz, Iran
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Zhang S, Liu Y, Zhang XL, Sun Y, Lu ZH. ANKRD22 aggravates sepsis-induced ARDS and promotes pulmonary M1 macrophage polarization. J Transl Autoimmun 2024; 8:100228. [PMID: 38225946 PMCID: PMC10788270 DOI: 10.1016/j.jtauto.2023.100228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/17/2024] Open
Abstract
Acute respiratory distress syndrome (ARDS) is independently associated with a poor prognosis in patients with sepsis. Macrophage M1 polarization plays an instrumental role in this process. Therefore, the exploration of key molecules affecting acute lung injury and macrophage M1 polarization may provide therapeutic targets for the treatment of septic ARDS. Here, we identified that elevated levels of Ankyrin repeat domain-containing protein 22 (ANKRD22) were associated with poor prognosis and more pronounced M1 macrophage polarization in septic patients by analyzing high-throughput data. ANKRD22 expression was also significantly upregulated in the alveolar lavage fluid, peripheral blood, and lung tissue of septic ARDS model mice. Knockdown of ANKRD22 significantly attenuated acute lung injury in mice with sepsis-induced ARDS and reduced the M1 polarization of lung macrophages. Furthermore, deletion of ANKRD22 in macrophages inhibited M1 macrophage polarization and reduced levels of phosphorylated IRF3 and intracellular interferon regulatory factor 3 (IRF3) expression, while re-expression of ANKRD22 reversed these changes. Further experiments revealed that ANKRD22 promotes IRF3 activation by binding to mitochondrial antiviral-signaling protein (MAVS). In conclusion, these findings suggest that ANKRD22 promotes the M1 polarization of lung macrophages and exacerbates sepsis-induced ARDS.
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Affiliation(s)
- Shi Zhang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, ZhongdaHospital, Southeast University, Nanjing, Jiangsu, China
- Department of Pulmonary and Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yao Liu
- Emergency Department of Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Gulou District, Nanjing, China
| | - Xiao-Long Zhang
- Department of Ultrasound, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yun Sun
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui Province, 230601, China
| | - Zhong-Hua Lu
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, 678 Furong Road, Hefei, Anhui Province, 230601, China
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229
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Liu X, Yao X, Chen L. Expanding roles of circRNAs in cardiovascular diseases. Noncoding RNA Res 2024; 9:429-436. [PMID: 38511061 PMCID: PMC10950605 DOI: 10.1016/j.ncrna.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 03/22/2024] Open
Abstract
CircRNAs are a class of single-stranded RNAs characterized by covalently looped structures. Emerging advances have promoted our understanding of circRNA biogenesis, nuclear export, biological functions, and functional mechanisms. Roles of circRNAs in diverse diseases have been increasingly recognized in the past decade, with novel approaches in bioinformatics analysis and new strategies in modulating circRNA levels, which have made circRNAs the hot spot for therapeutic applications. Moreover, due to the intrinsic features of circRNAs such as high stability, conservation, and tissue-/stage-specific expression, circRNAs are believed to be promising prognostic and diagnostic markers for diseases. Aiming cardiovascular disease (CVD), one of the leading causes of mortality worldwide, we briefly summarize the current understanding of circRNAs, provide the recent progress in circRNA functions and functional mechanisms in CVD, and discuss the future perspectives both in circRNA research and therapeutics based on existing knowledge.
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Affiliation(s)
- Xu Liu
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Xuelin Yao
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Liang Chen
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
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230
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Basu K, Dey A, Kiran M. CaTCH: Calculating transcript complexity of human genes. MethodsX 2024; 12:102697. [PMID: 38638454 PMCID: PMC11024653 DOI: 10.1016/j.mex.2024.102697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
The findings based on whole transcriptome sequencing suggest that alternative splicing occurs in approximately 95% of human multi-exon genes, thus, playing a crucial role in promoting proteome diversity. According to the latest GENCODE annotations, most genes have less than four transcripts, positively correlating with the number of exons. Thus, it is more accurate to measure the splice variant efficiency of a gene with respect to the number of exons, which is a measure of Transcript Complexity (TC). In addition to that, the theoretical number of transcripts is substantially higher than the actual number of transcripts produced by Alternative Splicing Events, and the features restricting this phenomenon need to be explored. In this method, we have extracted the data of various features contributing to TC from different databases. Linear regression is used to identify the determinant features and to train and test the model of TC. The results indicate that exon length is the determining feature of TC, followed by coding potential, presence of chromatin signature, and 5' splice site dinucleotide, all of which negatively affect a gene's TC, except exon length. To further classify the genes based on TC, random forest is used to identify the determinant features.•The splicing efficiency of a gene can be inferred by the transcript complexity, which is the number of transcripts per exon.•CaTCH is a linear regression-based model to calculate the transcript complexity of human genes, which can be calculated from the exon length, coding potentiality, presence of chromatin signature/s, and 5' splice site dinucleotide.
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Affiliation(s)
- Koushiki Basu
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500 046, India
| | - Anubha Dey
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500 046, India
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500 046, India
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231
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Filipovic D, Kana O, Marri D, Bhattacharya S. Unique challenges and best practices for single cell transcriptomic analysis in toxicology. Curr Opin Toxicol 2024; 38:100475. [PMID: 38645720 PMCID: PMC11027889 DOI: 10.1016/j.cotox.2024.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The application and analysis of single-cell transcriptomics in toxicology presents unique challenges. These include identifying cell sub-populations sensitive to perturbation; interpreting dynamic shifts in cell type proportions in response to chemical exposures; and performing differential expression analysis in dose-response studies spanning multiple treatment conditions. This review examines these challenges while presenting best practices for critical single cell analysis tasks. This covers areas such as cell type identification; analysis of differential cell type abundance; differential gene expression; and cellular trajectories. Towards enhancing the use of single-cell transcriptomics in toxicology, this review aims to address key challenges in this field and offer practical analytical solutions. Overall, applying appropriate bioinformatic techniques to single-cell transcriptomic data can yield valuable insights into cellular responses to toxic exposures.
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Affiliation(s)
- David Filipovic
- Institute for Quantitative Health Science & Engineering, East Lansing, MI, 48824, USA
| | - Omar Kana
- Institute for Quantitative Health Science & Engineering, East Lansing, MI, 48824, USA
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, 48824, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - Daniel Marri
- Institute for Quantitative Health Science & Engineering, East Lansing, MI, 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Sudin Bhattacharya
- Institute for Quantitative Health Science & Engineering, East Lansing, MI, 48824, USA
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, 48824, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, 48824, USA
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232
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Liu F, Tang J, Li T, Zhang Q. The microRNA miR482 regulates NBS-LRR genes in response to ALT1 infection in apple. Plant Sci 2024; 343:112078. [PMID: 38556113 DOI: 10.1016/j.plantsci.2024.112078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/01/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
Plants are frequently attacked by a variety of pathogens and thus have evolved a series of defense mechanisms, one important mechanism is resistance gene (R gene)-mediated disease resistance, but its expression is tightly regulated. NBS-LRR genes are the largest gene family of R genes. microRNAs (miRNAs) target to a number of NBS-LRR genes and trigger the production of phased small interfering RNAs (phasiRNAs) from these transcripts. phasiRNAs cis or trans regulate NBS-LRR genes, which can result in the repression of R gene expression. In this study, we screened for upregulated miR482 in the susceptible apple cultivar 'Golden Delicious' (GD) after inoculation with the fungal pathogen Alternaria alternata f. sp. mali (ALT1). Additionally, through combined degradome sequencing, we identified a gene targeted by miR482, named MdTNL1, a gene encoding a TIR-NBS-LRR (Toll/interleukin1 receptor-nucleotide binding site-leucine-rich repeat) protein. This gene exhibited a significant down-regulation post ALT1 inoculation, suggesting an impact on gene expression mediated by miRNA regulation. miR482 could cleave MdTNL1 and generate phasiRNAs at the cleavage site. We found that overexpression of miR482 inhibited the expression of MdTNL1 and thus reduced the disease resistance of GD, while silencing of miR482 increased the expression of MdTNL1 and thus improved the disease resistance of GD. This work elucidates key mechanisms underlying the immune response to Alternaria infection in apple. Identification of the resistance genes involved will enable molecular breeding for prevention and control of Alternaria leaf spot disease in this important fruit crop.
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Affiliation(s)
- Feiyu Liu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Jinqi Tang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China
| | - Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193 China.
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233
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Su T, Zhang XF, Wu GZ. Functional conservation of GENOMES UNCOUPLED1 in plastid-to-nucleus retrograde signaling in tomato. Plant Sci 2024; 343:112053. [PMID: 38417718 DOI: 10.1016/j.plantsci.2024.112053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/20/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Retrograde signaling between plastids and the nucleus is vital for chloroplast biogenesis and environmental responses. GENOMES UNCOUPLED1 (GUN1) was proposed to be a central integrator of multiple retrograde signaling pathways in the model plant Arabidopsis thaliana (Arabidopsis). However, the function of GUN1 orthologs in other plant species has not been well studied. Here, we found that many GUN1 orthologs from the Solanaceae family have a short N-terminus before the first pentatricopeptide repeat (PPR) motif which is predicted as intrinsically disordered regions (IDRs). Functional analyses of tomato (Solanum lycopersicum L.) GUN1 (SlGUN1), which does not contain N-terminal IDRs, show that it can complement the GUN phenotype of the Arabidopsis gun1 mutant (Atgun1). However, in contrast to the AtGUN1 protein, which does contain the N-terminal IDRs, the SlGUN1 protein is highly accumulated even after chloroplast biogenesis is completed, suggesting that the N-terminal IDRs may determine the stability of the GUN1 protein. Furthermore, we generated tomato Slgun1 genome-edited mutants via the CRISPR-Cas9 system. The Slgun1 mutants exhibited a typical GUN phenotype under lincomycin (Lin) or norflurazon (NF) treatment. Moreover, Slgun1 mutants are hypersensitive to low concentrations of Lin or NF. Taken together, our results suggest that, although lacking the N-terminal IDRs, SlGUN1 plays conserved roles in plastid retrograde signaling in tomato plants.
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Affiliation(s)
- Tong Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China
| | - Xiao-Fan Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai 200240, China.
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234
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Wang JQ, Li ZJ, Gao H, Sheng J, Liang CM, Hu YB, Xia X, Huang K, Wang SF, Zhu P, Hao JH, Tao FB. Gender associations between phthalate exposure and biomarkers of oxidative stress: A prospective cohort study. Toxicol Ind Health 2024; 40:312-322. [PMID: 38590048 DOI: 10.1177/07482337241245453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Previous epidemiologic research has shown that phthalate exposure in pregnant women is related to adverse birth outcomes in a sex-specific manner. However, the biological mechanism of phthalate exposure that causes these birth outcomes remains poorly defined. In this research, we investigated the association between phthalate exposure and placental oxidative stress in a large population-based cohort study, aiming to initially explore the relationship between phthalate exposure and gene expression in placental oxidative stress in a sex-specific manner. Quantitative PCR was performed to measure the expression of placental inflammatory mRNAs (HO-1, HIF1α, and GRP78) in 2469 placentae. The multiple linear regression models were used to investigate the associations between mRNA and urinary phthalate monoesters. Phthalate metabolites monomethyl phthalate (MMP) and mono-n-butyl phthalate (MBP) were positively correlated with higher HIF1α expression in placentae of male fetuses (p < .05). Mono-benzyl phthalate (MBzP) increased the expression of HO-1, HIF1α, and GRP78 in placentae of male fetuses, and mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) up-regulated the expression of HIF1α and GRP78. Additionally, mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP) was negatively correlated with HO-1, HIF1α, and GRP78 in placentae of female fetuses. Maternal phthalate exposure was associated with oxidative stress variations in placental tissues. The associations were closer in the placentas of male fetuses than in that of female ones. The placenta oxidative stress is worth further investigation as a potential mediator of maternal exposure-induced disease risk in children.
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Affiliation(s)
- Jian-Qing Wang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
- The Fourth Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Zhi-Juan Li
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
| | - Hui Gao
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
- Department of Pediatrics, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jie Sheng
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
| | - Chun-Mei Liang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
| | - Ya-Bin Hu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
| | - Xun Xia
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
- Department of Pediatrics, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Kun Huang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
| | - Su-Fang Wang
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
| | - Peng Zhu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
| | - Jia-Hu Hao
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
| | - Fang-Biao Tao
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, China
- MOE Key Laboratory of Population Health across Life Cycle, Hefei, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Hefei, China
- Anhui Provincial Key Laboratory of Population Health and Aristogenics, Anhui Medical University, Hefei, China
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235
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Zhang W, Zhang L, Feng Y, Lin D, Yang Z, Zhang Z, Ma Y. Genome-wide profiling of DNA methylome and transcriptome reveals epigenetic regulation of Urechis unicinctus response to sulfide stress. Sci Total Environ 2024; 927:172238. [PMID: 38582121 DOI: 10.1016/j.scitotenv.2024.172238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Sulfide is a well-known environmental pollutant that can have detrimental effects on most organisms. However, few metazoans living in sulfide-rich environments have developed mechanisms to tolerate and adapt to sulfide stress. Epigenetic mechanisms, including DNA methylation, have been shown to play a vital role in environmental stress adaptation. Nevertheless, the precise function of DNA methylation in biological sulfide adaptation remains unclear. Urechis unicinctus, a benthic organism inhabiting sulfide-rich intertidal environments, is an ideal model organism for studying adaptation to sulfide environments. In this study, we conducted a comprehensive analysis of the DNA methylome and transcriptome of U. unicinctus after exposure to 50 μM sulfide. The results revealed dynamic changes in the DNA methylation (5-methylcytosine) landscape in response to sulfide stress, with U. unicinctus exhibiting elevated DNA methylation levels following stress exposure. Integrating differentially expressed genes (DEGs) and differentially methylated regions (DMRs), we identified a crucial role of gene body methylation in predicting gene expression. Furthermore, using a DNA methyltransferase inhibitor, we validated the involvement of DNA methylation in the sulfide stress response and the gene regulatory network influenced by DNA methylation. The results indicated that by modulating DNA methylation levels during sulfide stress, the expression of glutathione S-transferase, glutamyl aminopeptidase, and cytochrome c oxidase could be up-regulated, thereby facilitating the metabolism and detoxification of exogenous sulfides. Moreover, DNA methylation was found to regulate and enhance the oxidative phosphorylation pathway, including NADH dehydrogenase, isocitrate dehydrogenase, and ATP synthase. Additionally, DNA methylation influenced the regulation of Cytochrome P450 and macrophage migration inhibitory factor, both of which are closely associated with oxidative stress and stress resistance. Our findings not only emphasize the role of DNA methylation in sulfide adaptation but also provide novel insights into the potential mechanisms through which marine organisms adapt to environmental changes.
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Affiliation(s)
- Wenqing Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Long Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Yuxin Feng
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Dawei Lin
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhi Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China
| | - Zhifeng Zhang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Ocean Institute, Ocean University of China, Sanya 572000, China; Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Yubin Ma
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
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236
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Zeinelabdeen Y, Abaza T, Yasser MB, Elemam NM, Youness RA. MIAT LncRNA: A multifunctional key player in non-oncological pathological conditions. Noncoding RNA Res 2024; 9:447-462. [PMID: 38511054 PMCID: PMC10950597 DOI: 10.1016/j.ncrna.2024.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 03/22/2024] Open
Abstract
The discovery of non-coding RNAs (ncRNAs) has unveiled a wide range of transcripts that do not encode proteins but play key roles in several cellular and molecular processes. Long noncoding RNAs (lncRNAs) are specific class of ncRNAs that are longer than 200 nucleotides and have gained significant attention due to their diverse mechanisms of action and potential involvement in various pathological conditions. In the current review, the authors focus on the role of lncRNAs, specifically highlighting the Myocardial Infarction Associated Transcript (MIAT), in non-oncological context. MIAT is a nuclear lncRNA that has been directly linked to myocardial infarction and is reported to control post-transcriptional processes as a competitive endogenous RNA (ceRNA) molecule. It interacts with microRNAs (miRNAs), thereby limiting the translation and expression of their respective target messenger RNA (mRNA) and regulating protein expression. Yet, MIAT has been implicated in other numerous pathological conditions such as other cardiovascular diseases, autoimmune disease, neurodegenerative diseases, metabolic diseases, and many others. In this review, the authors emphasize that MIAT exhibits distinct expression patterns and functions across different pathological conditions and is emerging as potential diagnostic, prognostic, and therapeutic agent. Additionally, the authors highlight the regulatory role of MIAT and shed light on the involvement of lncRNAs and specifically MIAT in various non-oncological pathological conditions.
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Affiliation(s)
- Yousra Zeinelabdeen
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
- Faculty of Medical Sciences/UMCG, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, the Netherlands
| | - Tasneem Abaza
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
- Biotechnology and Biomolecular Biochemistry Program, Faculty of Science, Cairo University, Cairo, Egypt
| | - Montaser Bellah Yasser
- Bioinformatics Group, Center for Informatics Sciences (CIS), School of Information Technology and Computer Science (ITCS), Nile University, Giza, Egypt
| | - Noha M. Elemam
- Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Rana A. Youness
- Molecular Genetics Research Team, Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo, 11835, Egypt
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237
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Wu JD, Xu L, Chen W, Zhou Y, Zheng G, Gu W. LncRNA PCAT6 mediates UBFD1 expression via sponging miR-545-3p in breast cancer cells. Noncoding RNA Res 2024; 9:421-428. [PMID: 38511057 PMCID: PMC10950603 DOI: 10.1016/j.ncrna.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 03/22/2024] Open
Abstract
Background LncRNA PCAT6 has been shown to involve in carcinogenesis of different tumors. In this study, we investigated underline mechanism by which PCAT6 promoted breast cancer cell progression. Methods RIP was used to identify lncRNAs associated with IMP1. Bioinformatics assays were used to predict potential miRNAs that interact with PCAT6 and mRNAs that are targeted by miR-545-3p. RNA-seq and RT-qPCR were used to analyze differential expression of lncRNAs and miRNA-targeted genes. Luciferase reporter and RNA pull-down assays were performed to identify the molecular interactions between PCAT6 and individual miRNAs. The role of PCAT6-mediated cell proliferation and invasion were tested by CCK-8 and transwell assays following loss-of-function and gain-of-function effects. Results We identified that PCAT6 is one of the lncRNAs that associated with IMP1. PCAT6 not only binds to IMP1, but also acts as a ceRNA to interact with multiple miRNAs, including miR-545-3p. Binding of IMP1 destabilized PCAT6, while competitive interaction with miR-545-3p allowed PCAT6 to positively regulate UBFD1 expression. Silencing UBFD1 mRNA could effectively rescue PCAT6-induced cell proliferation and invasive abilities. Conclusions Our study provided evidence that PCAT6 activates UBFD1 expression via sponging miR-545-3p to increase carcinogenesis of breast cancer cells. Based on the nature of UBFD1 as a polyubiquitin binding protein, our study suggested that ubiquitin pathway might contribute to breast cancer progression.
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Affiliation(s)
- Jun-Dong Wu
- Breast Center, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Liqun Xu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Weibin Chen
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Yanchun Zhou
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Guiyu Zheng
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
| | - Wei Gu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province, 515041, China
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Liu X, Xie X, Sui C, Liu X, Song M, Luo Q, Zhan P, Feng J, Liu J. Unraveling the cross-talk between N6-methyladenosine modification and non-coding RNAs in breast cancer: Mechanisms and clinical implications. Int J Cancer 2024; 154:1877-1889. [PMID: 38429857 DOI: 10.1002/ijc.34900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
In recent years, breast cancer (BC) has surpassed lung cancer as the most common malignant tumor worldwide and remains the leading cause of cancer death in women. The etiology of BC usually involves dysregulation of epigenetic mechanisms and aberrant expression of certain non-coding RNAs (ncRNAs). N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, widely exists in ncRNAs to affect its biosynthesis and function, and is an important regulator of tumor-related signaling pathways. Interestingly, ncRNAs can also regulate or target m6A modification, playing a key role in cancer progression. However, the m6A-ncRNAs regulatory network in BC has not been fully elucidated, especially the regulation of m6A modification by ncRNAs. Therefore, in this review, we comprehensively summarize the interaction mechanisms and biological significance of m6A modifications and ncRNAs in BC. Meanwhile, we also focused on the clinical application value of m6A modification in BC diagnosis and prognosis, intending to explore new biomarkers and potential therapeutic targets.
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Affiliation(s)
- Xuan Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Xuelong Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Chentao Sui
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Xuexue Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Miao Song
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Qing Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Ping Zhan
- Department of Obstetrics, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jia Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, Sichuan, China
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Zhu R, Zhang L, Zhang H, Hu Z. BRD4 promotes LPS-induced endothelial cells senescence via activating and cooperating STING-IRF3 pathway. Cell Signal 2024; 118:111127. [PMID: 38447881 DOI: 10.1016/j.cellsig.2024.111127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
Endothelial cells (ECs) senescence is closely associated with the initiation and development of multiple age-related cardiovascular diseases. It is necessary to explore the underlying molecular mechanisms of ECs senescence, which is not only the basis to decipher cellular senescence, but also a novel therapeutic target for the endothelial senescence-related diseases. BRD4, a key epigenetic regulator, is universally related to gene expression regulation and has been reported to accelerate cell senescence. Besides, emerging evidence has suggested that the stimulator of interferon genes protein (STING) can regulate inflammatory and senescence-related diseases. However, whether STING pathway activation is regulated by BRD4 in the context of ECs senescence remains largely unclear. Here, we observed that elevated BRD4 and activated STING-IRF3 signaling pathway during ECs senescence and further confirmed that BRD4 could abolish STING activation. We demonstrated that BRD4 could inhibit E3 ubiquitin ligase HRD1-mediated ubiquitination degradation of STING via inhibiting HRD1 transcription. In addition to the direct regulatory effect of BRD4 on STING activation, we have confirmed that BRD4 cooperates with IRF3 and P65 to promote SASP gene expression, thereby accelerating ECs senescence. Here, we proposed a novel mechanism underlying BRD4' key dual role in activating the STING pathway during ECs senescence.
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Affiliation(s)
- Ruigong Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing City 210023, China; State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang City 550014, China.
| | - Lei Zhang
- The Fifth People's Hospital of Huai'an, Huaiyin Hospital of Huai'an, Huai'an City 223300, China.
| | - Hao Zhang
- The Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong City 226006, China.
| | - Zhifeng Hu
- The Fifth People's Hospital of Huai'an, Huaiyin Hospital of Huai'an, Huai'an City 223300, China.
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240
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Köhne M, Diel E, Packeiser EM, Böttcher D, Tönissen A, Unruh C, Goericke-Pesch S, Ulrich R, Sieme H. Analysis of gene and protein expression in the endometrium for validation of an ex vivo model of the equine uterus using PCR, digital and visual histopathology. Theriogenology 2024; 221:38-46. [PMID: 38537320 DOI: 10.1016/j.theriogenology.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024]
Abstract
In the past, most research in equine reproduction has been performed in vivo but the use of in vitro and ex vivo models has recently increased. This study aimed to evaluate the functional stability of an ex vivo hemoperfused model for equine uteri with molecular characterization of marker genes and their proteins. In addition, the study validated the respective protein expression and the aptness of the software QuPath for identifying and scoring immunohistochemically stained equine endometrium. After collection, uteri (n = 12) were flushed with preservation solution, transported to the laboratory on ice, and perfused with autologous blood for 6 h. Cycle stage was determined by examination of the ovaries for presence of Graafian follicles or corpora lutea and analysis of plasma progesterone concentration (estrus: n = 4; diestrus: n = 4; anestrus: n = 4). Samples were obtained directly after slaughter, after transportation, and during perfusion (240, 300, 360 min). mRNA expression levels of progesterone (PGR), estrogen (ESR1) and oxytocin (OXTR) receptor as well as of MKI67 (marker of cell growth) and CASP3 (marker of apoptosis) were analyzed by RT-qPCR, and correlation to protein abundance was validated by immunohistochemical staining. Endometrial samples were analyzed by visual and computer-assisted evaluation of stained antigens via QuPath. For PGR, effects of the perfusion and cycle stage on expression were found (P < 0.05), while ESR1 was affected only by cycle stage (P < 0.05) and OXTR was unaffected by perfusion and cycle stage. MKI67 was lower after 360 min of perfusion as compared to samples collected before perfusion (P < 0.05). For CASP3, differences in gene expression were found after transport and samples taken after 240 min (P < 0.05). Immunohistochemical staining revealed effects of perfusion on stromal and glandular cells for steroid hormone receptors, but not for Ki-67 and active Caspase 3. OXTR was visualized in all layers of the endometrium and was unaffected by perfusion. Comparison of QuPath and visual analysis resulted in similar results. For most cell types and stained antigens, the correlation coefficient was r > 0.5. In conclusion, the isolated hemoperfused model of the equine uterus was successfully validated at the molecular level, demonstrating stability of key marker gene expression. The utility of computer-assisted immunohistochemical analysis of equine endometrial samples was also confirmed.
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Affiliation(s)
- Martin Köhne
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany.
| | - Emilia Diel
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Eva-Maria Packeiser
- Unit for Reproductive Medicine, Clinic for Small Animals, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Denny Böttcher
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, 04103, Leipzig, Germany
| | - Anna Tönissen
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Christin Unruh
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Sandra Goericke-Pesch
- Unit for Reproductive Medicine, Clinic for Small Animals, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
| | - Reiner Ulrich
- Institute of Veterinary Pathology, Faculty of Veterinary Medicine, Leipzig University, 04103, Leipzig, Germany
| | - Harald Sieme
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine, Foundation, 30559, Hannover, Germany
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241
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Heidarzadehpilehrood R, Pirhoushiaran M. Biomarker potential of competing endogenous RNA networks in Polycystic Ovary Syndrome (PCOS). Noncoding RNA Res 2024; 9:624-640. [PMID: 38571815 PMCID: PMC10988127 DOI: 10.1016/j.ncrna.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 04/05/2024] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common condition affecting women of reproductive age globally. PCOS continues to be the largest contributing factor to female infertility despite significant progress in our knowledge of the molecular underpinnings and treatment of the condition. The fact that PCOS is a very diverse condition makes it one of the key reasons why we haven't been able to overcome it. Non-coding RNAs (ncRNAs) are implicated in the development of PCOS, according to growing evidence. However, it is unclear how the complex regulatory relationships between the many ncRNA types contribute to the growth of this malignancy. Competing endogenous RNA (ceRNA), a recently identified mechanism in the RNA world, suggests regulatory interactions between various RNAs, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs), transcribed pseudogenes, and circular RNAs (circRNAs). Recent studies on PCOS have shown that dysregulation of multiple ceRNA networks (ceRNETs) between these ncRNAs plays crucial roles in developing the defining characteristics of PCOS development. And it is believed that such a finding may open a new door for a deeper comprehension of PCOS's unexplored facets. In addition, it may be able to provide fresh biomarkers and effective therapy targets for PCOS. This review will go over the body of information that exists about the primary roles of ceRNETs before highlighting the developing involvement of several newly found ceRNETs in a number of PCOS characteristics.
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Affiliation(s)
- Roozbeh Heidarzadehpilehrood
- Department of Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Maryam Pirhoushiaran
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, 1417613151, Iran
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242
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Liu G, Pan Q, Dai Y, Wang X, Li M, Zhu P, Zhou X. Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata. Mol Phylogenet Evol 2024; 195:108047. [PMID: 38460890 DOI: 10.1016/j.ympev.2024.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Molecular investigations have gathered a diverse set of mammals-predominantly African natives like elephants, hyraxes, and aardvarks-into a clade known as Afrotheria. Nevertheless, the precise phylogenetic relationships among these species remain contentious. Here, we sourced orthologous markers and ultraconserved elements to discern the interordinal connections among Afrotherian mammals. Our phylogenetic analyses bolster the common origin of Afroinsectiphilia and Paenungulata, and propose Afrosoricida as the closer relative to Macroscelidea rather than Tubulidentata, while also challenging the notion of Sirenia and Hyracoidea as sister taxa. The approximately unbiased test and the gene concordance factor uniformly recognized the alliance of Proboscidea with Hyracoidea as the dominant topology within Paenungulata. Investigation into sites with extremly high phylogenetic signal unveiled their potential to intensify conflicts in the Paenungulata topology. Subsequent exploration suggested that incomplete lineage sorting was predominantly responsible for the observed contentious relationships, whereas introgression exerted a subsidiary influence. The divergence times estimated in our study hint at the Cretaceous-Paleogene (K-Pg) extinction event as a catalyst for Afrotherian diversification. Overall, our findings deliver a tentative but insightful overview of Afrotheria phylogeny and divergence, elucidating these relationships through the lens of phylogenomics.
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Affiliation(s)
- Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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243
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Schäfer A, Gralinski LE, Leist SR, Hampton BK, Mooney MA, Jensen KL, Graham RL, Agnihothram S, Jeng S, Chamberlin S, Bell TA, Scobey DT, Linnertz CL, VanBlargan LA, Thackray LB, Hock P, Miller DR, Shaw GD, Diamond MS, de Villena FPM, McWeeney SK, Heise MT, Menachery VD, Ferris MT, Baric RS. Genetic loci regulate Sarbecovirus pathogenesis: A comparison across mice and humans. Virus Res 2024; 344:199357. [PMID: 38508400 PMCID: PMC10981091 DOI: 10.1016/j.virusres.2024.199357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
Coronavirus (CoV) cause considerable morbidity and mortality in humans and other mammals, as evidenced by the emergence of Severe Acute Respiratory CoV (SARS-CoV) in 2003, Middle East Respiratory CoV (MERS-CoV) in 2012, and SARS-CoV-2 in 2019. Although poorly characterized, natural genetic variation in human and other mammals modulate virus pathogenesis, as reflected by the spectrum of clinical outcomes ranging from asymptomatic infections to lethal disease. Using multiple human epidemic and zoonotic Sarbecoviruses, coupled with murine Collaborative Cross genetic reference populations, we identify several dozen quantitative trait loci that regulate SARS-like group-2B CoV pathogenesis and replication. Under a Chr4 QTL, we deleted a candidate interferon stimulated gene, Trim14 which resulted in enhanced SARS-CoV titers and clinical disease, suggesting an antiviral role during infection. Importantly, about 60 % of the murine QTL encode susceptibility genes identified as priority candidates from human genome-wide association studies (GWAS) studies after SARS-CoV-2 infection, suggesting that similar selective forces have targeted analogous genes and pathways to regulate Sarbecovirus disease across diverse mammalian hosts. These studies provide an experimental platform in rodents to investigate the molecular-genetic mechanisms by which potential cross mammalian susceptibility loci and genes regulate type-specific and cross-SARS-like group 2B CoV replication, immunity, and pathogenesis in rodent models. Our study also provides a paradigm for identifying susceptibility loci for other highly heterogeneous and virulent viruses that sporadically emerge from zoonotic reservoirs to plague human and animal populations.
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Affiliation(s)
- Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael A Mooney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Kara L Jensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Steven Chamberlin
- Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - Timothy A Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology2, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology3, Washington University School of Medicine, St. Louis, MO, USA
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon K McWeeney
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Bioinformatics and Computational Biology, Oregon Health & Science University, Portland, OR, USA; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA; Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston TX, USA; Department of Pathology and Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Rapidly Emerging Antiviral Drug Discovery Initiative, University of North Carolina, Chapel Hill NC, USA.
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244
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Ciocia A, Mestre-Farràs N, Vicent-Nacht I, Guitart T, Gebauer F. CSDE1: a versatile regulator of gene expression in cancer. NAR Cancer 2024; 6:zcae014. [PMID: 38600987 PMCID: PMC11005786 DOI: 10.1093/narcan/zcae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug development, particularly in the context of RNA-binding modulators of translation. This review focuses on one such modulator, the protein CSDE1, and its pivotal role in regulating cancer hallmarks. We discuss context-specific functions of CSDE1 in tumor development, its mechanisms of action, and highlight features that support its role as a molecular adaptor. Additionally, we discuss the regulation of CSDE1 itself and its potential value as biomarker and therapeutic target.
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Affiliation(s)
- Annagiulia Ciocia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Ignacio Vicent-Nacht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
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245
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Song Y, Yao S, Li X, Wang T, Jiang X, Bolan N, Warren CR, Northen TR, Chang SX. Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems. Eco Environ Health 2024; 3:227-237. [PMID: 38680731 PMCID: PMC11047296 DOI: 10.1016/j.eehl.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 05/01/2024]
Abstract
Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi Yao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaona Li
- School of Environment and Ecology, Jiangnan University, Wuxi 225127, China
| | - Tao Wang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610299, China
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nanthi Bolan
- School of Agriculture and Environment, The University of Western Australia, Nedland, WA-6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Nedland, WA-6009, Australia
- Healthy Environments and Lives (HEAL) National Research Network, Australia
| | - Charles R. Warren
- School of Life and Environmental Sciences, University of Sydney, Heydon-Laurence Building A08, NSW 2006, Australia
| | - Trent R. Northen
- Environmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Scott X. Chang
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
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246
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Yanes T, Blencoe M, Howard A, Tiller J, Wallingford C, Otlowski M, Keogh L, Lacaze P, McInerney-Leo A. Australian researcher's perspectives on the Australian industry-led moratorium on genetic tests in life insurance. Am J Med Genet A 2024; 194:e63565. [PMID: 38353314 DOI: 10.1002/ajmg.a.63565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 05/02/2024]
Abstract
Fear of insurance discrimination can inhibit genetic research participation. In 2019, an industry-led partial moratorium on using genetic results in Australian life insurance underwriting was introduced. This mixed-methods study used online surveys (n = 59 participants) and semi-structured interviews (n = 22 participants) to capture researchers' perceptions about the moratorium. 66% (n = 39/59) were aware of the moratorium before the survey. Of researchers returning genetic results, 56% (n = 22/39) reported that insurance implications were mentioned in consent forms, but a minority reported updating consent forms post-moratorium (n = 13/39, 33%). Most researchers reported that concerns regarding life insurers utilizing research results inhibited recruitment (35/59, 59%), and few perceived that the moratorium positively influenced participation (n = 9/39, 23%). These findings were supported by qualitative findings which revealed that genetic discrimination concerns were a major issue for some individuals, though these concerns could be eclipsed by the promise of a diagnosis through research participation. The majority thought a regulatory solution should be permanent (n = 34/51, 67%), have financial limits of at least ≥1,000,000 AUD (37/51, 73%), and involve government oversight/legislation (n = 44/51, 86%). In an era where an increasing number of research studies involve genomics as a primary or secondary objective, it is crucial that we have regulatory solutions to address participants' hesitation.
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Affiliation(s)
- Tatiane Yanes
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Marisa Blencoe
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | - Antonia Howard
- Graduate School of Health, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Jane Tiller
- School of Public Health and Preventive Medicine, Monash University Faculty of Medicine Nursing and Health Sciences, Melbourne, Victoria, Australia
| | - Courtney Wallingford
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
| | | | - Louise Keogh
- Centre for Health Equity, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Paul Lacaze
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Aideen McInerney-Leo
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Queensland, Australia
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247
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Bourassa KJ, Halverson TF, Garrett ME, Hair L, Dennis M, Ashley-Koch AE, Beckham JC, Kimbrel NA. Demographic characteristics and epigenetic biological aging among post-9/11 veterans: Associations of DunedinPACE with sex, race, and age. Psychiatry Res 2024; 336:115908. [PMID: 38626626 PMCID: PMC11070289 DOI: 10.1016/j.psychres.2024.115908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/01/2024] [Accepted: 04/06/2024] [Indexed: 04/18/2024]
Abstract
Measures of epigenetic aging derived from DNA methylation (DNAm) have enabled the assessment of biological aging in new populations and cohorts. In the present study, we used an epigenetic measure of aging, DunedinPACE, to examine rates of aging across demographic groups in a sample of 2,309 United States military veterans from the VISN 6 MIRECC's Post-Deployment Mental Health Study. As assessed by DunedinPACE, female veterans were aging faster than male veterans (β = 0.39, 95 % CI [0.29, 0.48], p < .001), non-Hispanic Black veterans were aging faster than non-Hispanic White veterans (β = 0.58, 95 % CI [0.50, 0.66], p < .001), and older veterans were biologically aging faster than younger veterans (β = 0.21, 95 % CI [0.18, 0.25], p < .001). In secondary analyses, these differences in rates of aging were not explained by a variety of biopsychosocial covariates. In addition, the percentage of European genetic admixture in non-Hispanic Black veterans was not associated with DunedinPACE. Our findings suggest that female and non-Hispanic Black veterans are at greater risk of accelerated aging among post-9/11 veterans. Interventions that slow aging might provide relatively greater benefit among veterans comprising these at-risk groups.
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Affiliation(s)
- Kyle J Bourassa
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Geriatric Research, Education, and Clinical Center, Durham VA Health Care System; Center for the Study of Aging and Human Development, Duke University Medical Center.
| | - Tate F Halverson
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System
| | | | - Lauren Hair
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine
| | - Michelle Dennis
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine
| | | | - Jean C Beckham
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine
| | - Nathan A Kimbrel
- VA Mid-Atlantic Mental Illness Research, Education and Clinical Center, Durham VA Health Care System; Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine; VA Health Services Research and Development Center of Innovation to Accelerate Discovery and Practice Transformation, Durham VA Health Care System
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248
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Chen J, Guo L, Wang C, Peng P, Wu J, Zhang H, Liu F, Li Q. Can irisin be developed as the molecular evolutionary clock based on the origin and functions? Gen Comp Endocrinol 2024; 352:114515. [PMID: 38582177 DOI: 10.1016/j.ygcen.2024.114515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/21/2023] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
Irisin, a myokine identified in 2012, has garnered research interest for its capacity to induce browning of adipocytes and improve metabolic parameters. As such, the potential therapeutic applications of this exercise-induced peptide continue to be explored. Though present across diverse animal species, sequence analysis has revealed subtle variation in the irisin protein. In this review, we consider the effects of irisin on disease states in light of its molecular evolution. We summarize current evidence for irisin's influence on pathologies and discuss how sequence changes may inform development of irisin-based therapies. Furthermore, we propose that the phylogenetic variations in irisin could potentially be leveraged as a molecular clock to elucidate evolutionary relationships.
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Affiliation(s)
- Junyu Chen
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Lijun Guo
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Chenglong Wang
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Peng Peng
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Jiaming Wu
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China
| | - Huaidong Zhang
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China; Engineering Research Center of Industrial Microbiology, Ministry of Education, PR China
| | - Feng Liu
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China; Engineering Research Center of Industrial Microbiology, Ministry of Education, PR China.
| | - Qin Li
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China; Engineering Research Center of Industrial Microbiology, Ministry of Education, PR China.
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249
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Zhang L, Wang Y, Gao J, Zhou X, Huang M, Wang X, He Z. Non‑coding RNA: A promising diagnostic biomarker and therapeutic target for esophageal squamous cell carcinoma (Review). Oncol Lett 2024; 27:255. [PMID: 38646493 PMCID: PMC11027111 DOI: 10.3892/ol.2024.14388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
Esophageal cancer (EC) is a common form of malignant tumor in the digestive system that is classified into two types: Esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinoma. ESCC is known for its early onset of symptoms, which can be difficult to identify, as well as its rapid progression and tendency to develop drug resistance to chemotherapy and radiotherapy. These factors contribute to the high incidence of disease and low cure rate. Therefore, a diagnostic biomarker and therapeutic target need to be identified for ESCC. Non-coding RNAs (ncRNAs) are a class of molecules that are transcribed from DNA but do not encode proteins. Initially, ncRNAs were considered to be non-functional segments generated during transcription. However, with advancements in high-throughput sequencing technologies in recent years, ncRNAs have been associated with poor prognosis, drug resistance and progression of ESCC. The present study provides a comprehensive overview of the biogenesis, characteristics and functions of ncRNAs, particularly focusing on microRNA, long ncRNAs and circular RNAs. Furthermore, the ncRNAs that could potentially be used as diagnostic biomarkers and therapeutic targets for ESCC are summarized to highlight their application value and prospects in ESCC.
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Affiliation(s)
- Longze Zhang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Yanyang Wang
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Cell Engineering Laboratory, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Jianmei Gao
- School of Pharmacy, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xue Zhou
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Minglei Huang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Xianyao Wang
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Zhixu He
- Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Cell Engineering Laboratory, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
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250
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Dos Santos CH, Gustani EC, Machado LPDB, Mateus RP. Dietary Variation Effect on Life History Traits and Energy Storage in Neotropical Species of Drosophila (Diptera; Drosophilidae). Neotrop Entomol 2024; 53:578-595. [PMID: 38687423 DOI: 10.1007/s13744-024-01147-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/08/2024] [Indexed: 05/02/2024]
Abstract
The ability of an organism to respond to nutritional stress can be a plastic character under the action of natural selection, affecting several characteristics, including life history and energy storage. The genus Drosophila (Diptera; Drosophilidae) presents high variability regarding natural resource exploration. However, most works on this theme have studied the model species D. melanogaster Meigen, 1830 and little is known about Neotropical drosophilids. Here we evaluate the effects of three diets, with different carbohydrate-to-protein ratios, on life history (viability and development time) and metabolic pools (triglycerides, glycogen, and total soluble protein contents) of three Neotropical species of Drosophila: D. maculifrons Duda, 1927; D. ornatifrons Duda, 1927, both of the subgenus Drosophila Sturtevant, 1939, and D. willistoni Sturtevant, 1916 of the subgenus Sophophora Sturtevant, 1939. Our results showed that only D. willistoni was viable on all diets, D. maculifrons was not viable on the sugary diet, while D. ornatifrons was barely viable on this diet. The sugary diet increased the development time of D. willistoni and D. ornatifrons, and D. willistoni glycogen content. Thus, the viability of D. maculifrons and D. ornatifrons seems to depend on a certain amount of protein and/or a low concentration of carbohydrate in the diet. A more evident effect of the diets on triglyceride and protein pools was detected in D. ornatifrons, which could be related to the adult attraction to dung and carrion baited pitfall as food resource tested in nature. Our results demonstrated that the evolutionary history and differential adaptations to natural macronutrient resources are important to define the amplitude of response that a species can present when faced with dietary variation.
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Affiliation(s)
- Camila Heloise Dos Santos
- Evolutionary Biology Graduate Program, Biological Sciences Department, UNICENTRO, Guarapuava, PR, Brazil
| | | | - Luciana Paes de Barros Machado
- Evolutionary Biology Graduate Program, Biological Sciences Department, UNICENTRO, Guarapuava, PR, Brazil
- Laboratory of Genetics and Evolution, Biological Sciences Department, UNICENTRO, Guarapuava, PR, Brazil
| | - Rogério Pincela Mateus
- Evolutionary Biology Graduate Program, Biological Sciences Department, UNICENTRO, Guarapuava, PR, Brazil.
- Laboratory of Genetics and Evolution, Biological Sciences Department, UNICENTRO, Guarapuava, PR, Brazil.
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