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An Z, Jiang A, Chen J. Toward understanding the role of genomic repeat elements in neurodegenerative diseases. Neural Regen Res 2025; 20:646-659. [PMID: 38886931 DOI: 10.4103/nrr.nrr-d-23-01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/02/2024] [Indexed: 06/20/2024] Open
Abstract
Neurodegenerative diseases cause great medical and economic burdens for both patients and society; however, the complex molecular mechanisms thereof are not yet well understood. With the development of high-coverage sequencing technology, researchers have started to notice that genomic repeat regions, previously neglected in search of disease culprits, are active contributors to multiple neurodegenerative diseases. In this review, we describe the association between repeat element variants and multiple degenerative diseases through genome-wide association studies and targeted sequencing. We discuss the identification of disease-relevant repeat element variants, further powered by the advancement of long-read sequencing technologies and their related tools, and summarize recent findings in the molecular mechanisms of repeat element variants in brain degeneration, such as those causing transcriptional silencing or RNA-mediated gain of toxic function. Furthermore, we describe how in silico predictions using innovative computational models, such as deep learning language models, could enhance and accelerate our understanding of the functional impact of repeat element variants. Finally, we discuss future directions to advance current findings for a better understanding of neurodegenerative diseases and the clinical applications of genomic repeat elements.
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Affiliation(s)
- Zhengyu An
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Aidi Jiang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
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2
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Liang W, Zhu Z, Zheng C. Application of Proteomics Technology Based on LC-MS Combined with Western Blotting and Co-IP in Antiviral Innate Immunity. Methods Mol Biol 2025; 2854:93-106. [PMID: 39192122 DOI: 10.1007/978-1-0716-4108-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
As an interferon-stimulating factor protein, STING plays a role in the response and downstream liaison in antiviral natural immunity. Upon viral invasion, the immediate response of STING protein leads to a series of changes in downstream proteins, which ultimately leads to an antiviral immune response in the form of proinflammatory cytokines and type I interferons, thus triggering an innate immune response, an adaptive immune response in vivo, and long-term protection of the host. In the field of antiviral natural immunity, it is particularly important to rigorously and sequentially probe the dynamic changes in the antiviral natural immunity connector protein STING caused by the entire anti-inflammatory and anti-pathway mechanism and the differences in upstream and downstream proteins. Traditionally, proteomics technology has been validated by detecting proteins in a 2D platform, for which it is difficult to sensitively identify changes in the nature and abundance of target proteins. With the development of mass spectrometry (MS) technology, MS-based proteomics has made important contributions to characterizing the dynamic changes in the natural immune proteome induced by viral infections. MS analytical techniques have several advantages, such as high throughput, rapidity, sensitivity, accuracy, and automation. The most common techniques for detecting complex proteomes are liquid chromatography (LC) and mass spectrometry (MS). LC-MS (Liquid Chromatography-Mass Spectrometry), which combines the physical separation capability of LC and the mass analysis capability of MS, is a powerful technique mainly used for analyzing the proteome of cells, tissues, and body fluids. To explore the combination of traditional proteomics techniques such as Western blotting, Co-IP (co-Immunoprecipitation), and the latest LC-MS methods to probe the anti-inflammatory pathway and the differential changes in upstream and downstream proteins induced by the antiviral natural immune junction protein STING.
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Affiliation(s)
- Weizheng Liang
- Central Laboratory, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China
| | - Zhenpeng Zhu
- Department of General Surgery, The First Affiliated Hospital of Hebei North University, Zhangjiakou, Hebei, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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3
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Xu H, Wang Z, Sa S, Yang Y, Zhang X, Li D. Identification of novel compound heterozygous variants of the ALMS1 gene in a child with Alström syndrome by whole genome sequencing. Gene 2024; 929:148827. [PMID: 39122231 DOI: 10.1016/j.gene.2024.148827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/24/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Alström syndrome (ALMS), a rare recessively inherited ciliopathy caused by mutations in ALMS1, is characterized by retinal dystrophy, childhood obesity, sensorineural hearing loss, and type 2 diabetes mellitus. The majority of pathogenic variants in ALMS1 are nonsense and frameshift mutations, which would lead to premature protein truncation, whereas copy number variants are seldom reported. METHODS Herein, we present a 10-year-old Chinese girl with ALMS. The potential causative genetic variant was confirmed through whole genome sequencing, quantitative real-time PCR analysis, and Sanger sequencing. Additionally, breakpoint analysis was performed to determine the exact breakpoint site of the large deletion and elucidate its probable formation mechanism. RESULTS The patient had a cor triatriatum sinister (CTS) structure. Genetic analysis identified novel compound heterozygous variants in the patient, consisting of a frameshift variant c.4414_4415delGT (p.V1472Nfs*26) in ALMS1 and a novel large deletion at chr2:73,612,355-73,626,339, which encompasses exon 1 of the ALMS1 gene. Moreover, breakpoint analysis revealed that the large deletion probably formed through the microhomology-mediated end joining (MMEJ) mechanism due to the 6-bp microhomologies (TCCTTC) observed at both ends of the breakpoints. CONCLUSIONS In this study, novel compound heterozygous variants in the ALMS1 gene were identified in an ALMS patient with a CTS structure. The molecular confirmation of these variants expands the mutational spectrum of ALMS1, while the manifestation of ALMS in the patient provides additional clinical insights into this syndrome.
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Affiliation(s)
- Haikun Xu
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130033, P.R. China
| | - Ziju Wang
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun 130033, P.R. China
| | - Sha Sa
- Department of Radiology, China-Japan Union Hospital of Jilin University, Changchun 130033, P.R. China
| | - Ying Yang
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun 130033, P.R. China
| | - Xiaofei Zhang
- Department of Pediatrics, China-Japan Union Hospital of Jilin University, Changchun 130033, P.R. China.
| | - Dejun Li
- Center for Reproductive Medicine and Prenatal Diagnosis, The First Hospital of Jilin University, Changchun 130021, P.R. China.
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4
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Moeckel C, Mareboina M, Konnaris MA, Chan CS, Mouratidis I, Montgomery A, Chantzi N, Pavlopoulos GA, Georgakopoulos-Soares I. A survey of k-mer methods and applications in bioinformatics. Comput Struct Biotechnol J 2024; 23:2289-2303. [PMID: 38840832 PMCID: PMC11152613 DOI: 10.1016/j.csbj.2024.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024] Open
Abstract
The rapid progression of genomics and proteomics has been driven by the advent of advanced sequencing technologies, large, diverse, and readily available omics datasets, and the evolution of computational data processing capabilities. The vast amount of data generated by these advancements necessitates efficient algorithms to extract meaningful information. K-mers serve as a valuable tool when working with large sequencing datasets, offering several advantages in computational speed and memory efficiency and carrying the potential for intrinsic biological functionality. This review provides an overview of the methods, applications, and significance of k-mers in genomic and proteomic data analyses, as well as the utility of absent sequences, including nullomers and nullpeptides, in disease detection, vaccine development, therapeutics, and forensic science. Therefore, the review highlights the pivotal role of k-mers in addressing current genomic and proteomic problems and underscores their potential for future breakthroughs in research.
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Affiliation(s)
- Camille Moeckel
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Manvita Mareboina
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Maxwell A. Konnaris
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Candace S.Y. Chan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ioannis Mouratidis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
| | - Austin Montgomery
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikol Chantzi
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | | | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Huck Institute of the Life Sciences, Penn State University, University Park, Pennsylvania, USA
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5
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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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Lai SK, Luo AC, Chiu IH, Chuang HW, Chou TH, Hung TK, Hsu JS, Chen CY, Yang WS, Yang YC, Chen PL. A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis. Comput Struct Biotechnol J 2024; 23:1562-1571. [PMID: 38650588 PMCID: PMC11035020 DOI: 10.1016/j.csbj.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/20/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4 and -DRB5) from 44 high-quality HPRC personal genome assemblies. For sequencing, we crafted HLA-specific probes and conducted capture-based targeted sequencing of the genomic DNA of the HPRC cohort, ensuring focused and comprehensive coverage of the HLA region of interest. We used publicly available short-read whole-genome sequencing (WGS) data from identical samples to offer a comparative perspective. To decipher the vast amount of sequencing data, we employed seven distinct software tools: OptiType, HLA-VBseq, HISAT genotype, SpecHLA, T1K, QzType, and DRAGEN. Each tool offers unique capabilities and algorithms for HLA genotyping, allowing comprehensive analysis and validation of the results. We then compared these results with benchmarks derived from personal genome assemblies. Our findings present a comprehensive four-field-resolution HLA allele annotation for 44 HPRC samples. Significantly, our innovative targeted next-generation sequencing (NGS) approach for HLA genes showed superior accuracy compared with conventional short-read WGS. An integrated analysis involving QzType, T1K, and DRAGEN was developed, achieving 100% accuracy for all 11 HLA genes. In conclusion, our study highlighted the combination of targeted short-read sequencing and astute computational analysis as a robust approach for HLA genotyping. Furthermore, the HPRC cohort has emerged as a valuable assembly-based reference in this realm.
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Affiliation(s)
- Sheng-Kai Lai
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Allen Chilun Luo
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - I-Hsuan Chiu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Wen Chuang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ting-Hsuan Chou
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsung-Kai Hung
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jacob Shujui Hsu
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Yu Chen
- Department of Biomechatronics Engineering, National Taiwan University, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Ya-Chien Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Endocrinology and Metabolism, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
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7
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Fare CM, Rothstein JD. Nuclear pore dysfunction and disease: a complex opportunity. Nucleus 2024; 15:2314297. [PMID: 38383349 PMCID: PMC10883112 DOI: 10.1080/19491034.2024.2314297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
The separation of genetic material from bulk cytoplasm has enabled the evolution of increasingly complex organisms, allowing for the development of sophisticated forms of life. However, this complexity has created new categories of dysfunction, including those related to the movement of material between cellular compartments. In eukaryotic cells, nucleocytoplasmic trafficking is a fundamental biological process, and cumulative disruptions to nuclear integrity and nucleocytoplasmic transport are detrimental to cell survival. This is particularly true in post-mitotic neurons, where nuclear pore injury and errors to nucleocytoplasmic trafficking are strongly associated with neurodegenerative disease. In this review, we summarize the current understanding of nuclear pore biology in physiological and pathological contexts and discuss potential therapeutic approaches for addressing nuclear pore injury and dysfunctional nucleocytoplasmic transport.
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Affiliation(s)
- Charlotte M Fare
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey D Rothstein
- Department of Neurology and Brain Science Institute, Johns Hopkins University, Baltimore, MD, USA
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8
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Alyami AS, Madkhali Y, Majrashi NA, Alwadani B, Elbashir M, Ali S, Ageeli W, El-Bahkiry HS, Althobity AA, Refaee T. The role of molecular imaging in detecting fibrosis in Crohn's disease. Ann Med 2024; 56:2313676. [PMID: 38346385 PMCID: PMC10863520 DOI: 10.1080/07853890.2024.2313676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
Fibrosis is a pathological process that occurs due to chronic inflammation, leading to the proliferation of fibroblasts and the excessive deposition of extracellular matrix (ECM). The process of long-term fibrosis initiates with tissue hypofunction and progressively culminates in the ultimate manifestation of organ failure. Intestinal fibrosis is a significant complication of Crohn's disease (CD) that can result in persistent luminal narrowing and strictures, which are difficult to reverse. In recent years, there have been significant advances in our understanding of the cellular and molecular mechanisms underlying intestinal fibrosis in inflammatory bowel disease (IBD). Significant progress has been achieved in the fields of pathogenesis, diagnosis, and management of intestinal fibrosis in the last few years. A significant amount of research has also been conducted in the field of biomarkers for the prediction or detection of intestinal fibrosis, including novel cross-sectional imaging modalities such as positron emission tomography (PET) and single photon emission computed tomography (SPECT). Molecular imaging represents a promising biomedical approach that enables the non-invasive visualization of cellular and subcellular processes. Molecular imaging has the potential to be employed for early detection, disease staging, and prognostication in addition to assessing disease activity and treatment response in IBD. Molecular imaging methods also have a potential role to enabling minimally invasive assessment of intestinal fibrosis. This review discusses the role of molecular imaging in combination of AI in detecting CD fibrosis.
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Affiliation(s)
- Ali S. Alyami
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Yahia Madkhali
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Naif A. Majrashi
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Bandar Alwadani
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Meaad Elbashir
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Sarra Ali
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Wael Ageeli
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hesham S. El-Bahkiry
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Abdullah A. Althobity
- Department of Radiological Sciences and Medical Imaging, College of Applied Medical Sciences, Majmaah University, Majmaah, Saudi Arabia
| | - Turkey Refaee
- Department of Diagnostic Radiography Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
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9
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Katirtzoglou A, Hansen SB, Sveier H, Martin MD, Brealey JC, Limborg MT. Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon ( Salmo salar). Epigenetics 2024; 19:2392049. [PMID: 39151124 PMCID: PMC11332636 DOI: 10.1080/15592294.2024.2392049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/18/2024] Open
Abstract
The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA methylation and gene expression varies depending on the genomic location and is therefore more complex than initially thought. We examined DNA methylation levels in the gut epithelium of Atlantic salmon (Salmo salar) using whole-genome bisulfite sequencing, which we correlated with gene expression data from RNA sequencing of the same gut tissue sample (RNA-seq). Assuming epigenetic signals might be pronounced between distinctive phenotypes, we compared large and small fish, finding 22 significant associations between 22 differentially methylated regions and 21 genes. We did not detect significant methylation differences between large and small fish. However, we observed a consistent signal of methylation levels around the transcription start sites (TSS), being negatively correlated with the expression levels of those genes. We found both negative and positive associations of methylation levels with gene expression further upstream or downstream of the TSS, revealing a more unpredictable pattern. The 21 genes showing significant methylation-expression correlations were involved in biological processes related to salmon health, such as growth and immune responses. Deciphering how DNA methylation affects the expression of such genes holds great potential for future applications. For instance, our results suggest the importance of genomic context in targeting epigenetic modifications to improve the welfare of aquaculture species like Atlantic salmon.
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Affiliation(s)
- Aikaterini Katirtzoglou
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren B. Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Morten T. Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Cardoso Soares S, Schmidt Eler E, Eduardo Faresin E Silva C, Francisco Souza E Sousa J, Nazareth Ferreira da Silva M, Pereira Araújo N, Svartman M, Feldberg E. Mapping of SINEs in the genome of Proechimys (Mammalia: Rodentia). Gene 2024; 928:148781. [PMID: 39029769 DOI: 10.1016/j.gene.2024.148781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
This study aimed to analyze the distribution of short interspersed elements (SINEs) in the chromosomes of five species of rodents of the genus Proechimys and in a variant karyotype of P. guyannensis. Molecular cytogenetic techniques were used to characterize the sequences of the B1, B4, MAR and THER SINEs, which were used as probes for hybridization in metaphase chromosomes. A wide distribution of SINEs was observed in the chromosomes of the Proechimys species examined, thus indicating differentiation of these retroelements. The signal of the B4 SINE was more evident than that of the B1 SINE, especially in P. echinothrix, P. longicaudatus, and P. cuvieri. Although the signal of the MAR SINE was more explosive than that of the THER SINE, in the species P. echinothrix, P. guyannensis (2n = 46) and P. longicaudatus, its distribution in the karyotypes was similar. The signals of these retroelements occurred at specific heterochromatic sites and were centromeric/pericentromeric and at the terminal regions in most chromosomes. This appears to be a typical distribution pattern of the SINEs and may indicate involvement with rearrangements during karyotypic diversification in Proechimys. The variation of the SINEs in the genome of Proechimys species demonstrates that these elements are distributed in a specific way in this genus and the preference for some sites, considered hotspots for chromosomal breakage, allows us to propose that these elements are related to the karyotypic evolution of Proechimys.
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Affiliation(s)
- Simone Cardoso Soares
- Pós-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil; Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, AM, Brazil.
| | - Eduardo Schmidt Eler
- Pós-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil; Escola de Ciências da Saúde, Universidade Anhembi Morumbi, São José dos Campos, São Paulo, Brazil
| | - Carlos Eduardo Faresin E Silva
- Pós-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - José Francisco Souza E Sousa
- Pós-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | | | - Naiara Pereira Araújo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de Rondônia Campus Jaru, Jaru, RO, Brazil
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Eliana Feldberg
- Pós-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil; Laboratório de Genética Animal (LGA), Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
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11
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Kafi Z, Masoudi AA, Torshizi RV, Ehsani A. Copy number variations affecting growth curve parameters in a crossbred chicken population. Gene 2024; 927:148710. [PMID: 38901536 DOI: 10.1016/j.gene.2024.148710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 06/01/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Copy number variations (CNVs) are key structural variations in the genome and may contribute to phenotypic differences. In this study, we used a F2 chicken population created from reciprocal crossing between fast-growing Arian broiler line and Urmia native chickens. The chickens were genotyped by 60 K SNP BeadChip, and PennCNV algorithm was used to detect genome-wide CNVs. The growth curve parameters of W0, k, L, Wf, Wi, ti and average GR were used as phenotypic data. The association between CNV and growth curve parameters was carried out using the CNVRanger R/Bioconductor package. Five CNV regions (CNVRs) were chosen for the validation experiment using qPCR. Gene enrichment analysis was done using WebGestalt. The STRING database was used to search for significant pathways. The results identified 966 CNVs and 600 CNVRs including 468 gains, 67 losses, and 65 both events on autosomal chromosomes. Validation of the CNVRs obtained from the qPCR assay were 79 % consistent with the prediction by PennCNV. A total of 43 significant CNVs were obtained for the seven growth curve parameters. The 416 genes annotated for significant CNVs. Six genes out of 416 genes were most related to growth curve parameters. These genes were LCP2, Dock2, CD80, CYFIP1, NIPA1 and NIPA2. Some of these genes in their biological process were associated with the growth, reproduction and development of cells or organs that ultimately lead to the growth of the body. The results of the study could pave the way for better understanding the molecular process of CNVs and growth curve parameters in birds.
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Affiliation(s)
- Zeinab Kafi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Alireza Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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12
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Tiwari M, Gujar G, Shashank CG, Ponsuksili S. Selection signatures for high altitude adaptation in livestock: A review. Gene 2024; 927:148757. [PMID: 38986751 DOI: 10.1016/j.gene.2024.148757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
High altitude adapted livestock species (cattle, yak, goat, sheep, and horse) has critical role in the human socioeconomic sphere and acts as good source of animal source products including milk, meat, and leather, among other things. These species sustain production and reproduction even in harsh environments on account of adaptation resulting from continued evolution of beneficial traits. Selection pressure leads to various adaptive strategies in livestock whose footprints are evident at the different genomic sites as the "Selection Signature". Scrutiny of these signatures provides us crucial insight into the evolutionary process and domestication of livestock adapted to diverse climatic conditions. These signatures have the potential to change the sphere of animal breeding and further usher the selection programmes in right direction. Technological revolution and recent strides made in genomic studies has opened the routes for the identification of selection signatures. Numerous statistical approaches and bioinformatics tools have been developed to detect the selection signature. Consequently, studies across years have identified candidate genes under selection region found associated with numerous traits which have a say in adaptation to high-altitude environment. This makes it pertinent to have a better understanding about the selection signature, the ways to identify and how to utilize them for betterment of livestock populations as well as farmers. This review takes a closer look into the general concept, various methodologies, and bioinformatics tools commonly employed in selection signature studies and summarize the results of recent selection signature studies related to high-altitude adaptation in various livestock species. This review will serve as an informative and useful insight for researchers and students in the field of animal breeding and evolutionary biology.
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Affiliation(s)
- Manish Tiwari
- ICAR-National Dairy Research Institute, Karnal, India; U.P. Pt. Deen Dayal Upadhyaya Veterinary Science University and Cattle Research Institute, Mathura, India.
| | | | - C G Shashank
- ICAR-National Dairy Research Institute, Karnal, India
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13
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Ren Y, Ciwang R, Mehmood K, Li K. Effects of forages on the microbiota of crossed sheep on cold Plateau. Anim Biotechnol 2024; 35:2362639. [PMID: 38856695 DOI: 10.1080/10495398.2024.2362639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Diet is an important component to influence microbiota, there are less data available about the microbiome of Suffolk cross with Tibetan (SCT) animals with different fodders. The current study was conducted for comparing the fungi microbiota in SCT sheep fed with different forages. Sequencing of ileum samples from sheep groups of AH (alfalfa and oat grass), BH (mixture of grass and concentrated feeds), CH (concentrated feed I), DH (concentrated feed II) and EH (concentrated feed III) achieved 3,171,271 raw and 2,719,649 filtered sequences. Concentrated feeds changed fungi microbiota in SCT sheep with three phyla and 47 genera significantly different among the groups. Genera include positive genus of Scytalidium and negative fungi of Sarocladium, Kazachstania, Gibberella, Scytalidium, Candida, Wickerhamomyces. The findings of our study will contribute to efficient feeding of SCT sheep at cold plateau areas.
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Affiliation(s)
- Yue Ren
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, PR China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, PR China
| | - Renzeng Ciwang
- Institute of Livestock Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, PR China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa, PR China
| | - Khalid Mehmood
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, PR China
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14
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Cai H, Li X, Niu X, Li J, Lan X, Lei C, Huang Y, Xu H, Li M, Chen H. Copy number variations within fibroblast growth factor 13 gene influence growth traits and alternative splicing in cattle. Anim Biotechnol 2024; 35:2314104. [PMID: 38426908 DOI: 10.1080/10495398.2024.2314104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Previous researches revealed a copy number variation (CNV) region in the bovine fibroblast growth factor 13 (FGF13) gene. However, its effects remain unknown. This study detected the various copy number types in seven Chinese cattle breeds and analysed their population genetic characteristics and effects on growth traits and transcription levels. Copy number Loss was more frequent in Caoyuan Red cattle and Xianan cattle than in the other breeds. Association analysis between CNV and growth traits of Qinchuan indicated that the CNV was significantly related to chest depth, hip width and hucklebone width (P < 0.05). Additionally, the growth traits of individuals with copy number Loss were significantly inferior to those with copy number Gain or Median (P < 0.05). Besides, we found two splicing isoforms, AS1 and AS2, in FGF13 gene, which resulted from alternative 5' splicing sites of intron 1. These isoforms showed varied expression levels in various tissues. Moreover, CNV was significantly and negatively associated with the mRNA expression of AS1 (r = -0.525, P < 0.05). The CNVs in bovine FGF13 gene negatively regulated growth traits and gene transcription. These observations provide new insights into bovine FGF13 gene, delivering potentially useful information for future Chinese cattle breeding programs.
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Affiliation(s)
- Hanfang Cai
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Xin Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Xinran Niu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Jing Li
- Animal Health Supervision Institute of Biyang, Biyang, Henan, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agriculture University, Zhengzhou, China
| | - Hong Chen
- College of Animal Science, Xinjiang Agriculture University, Urumqi, China
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15
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Sawant S, Nandi SS, Gohil T, Jadhav A, Samudra P, Arora M, Rudra U, Deshpande J. A multiplex SNaPshot assay for the detection of single nucleotide polymorphism associated with clinical severity of enterovirus infections. Gene 2024; 926:148618. [PMID: 38821327 DOI: 10.1016/j.gene.2024.148618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Non-polio enterovirus infections are known to cause a variety of diseases and neurological complications. It is also known that the severity of these diseases largely differs among individuals with different genotypes and alleles. The Single Nucleotide Polymorphisms (SNPs) within specific genes have a considerable effect on the immune response to enteroviruses and on the outcome of disease, leading to variations in complications and infection susceptibility. Knowing the distribution of such SNPs can be valuable for individual case management and studying epidemiological parameters of enterovirus infections. In this feasibility study, a multiplex version of the primer extension-based technique called the SNaPshot Assay has been developed to examine SNPs in various relevant genes for predicting the clinical severity of enterovirus infections. It is already established that this technique is precise, consistent, scalable, and likely to exhibit high throughput. The multiplex SNaPshot can investigate multiple genetic susceptibility markers simultaneously, and the assay can be used to identify vulnerable populations, understand the epidemiology of infections, and manage the outbreaks of enteroviruses. Based on the literature, 15 SNPs were identified which are suspected for higher susceptibility to the worst outcomes after enterovirus infection and the assay was developed. Blood samples of 100 healthy volunteers were collected and tested for assay feasibility as well as to know the proportions of 15 selected SNPs. After the analysis, seven SNPs have been identified and suggested to be considered for future assays. Based on the pilot test results, it appears that positivity for any three out of the identified seven SNPs might indicate a higher risk, and future studies correlated with clinical studies among patients with and without severe diseases utilizing this assay will provide robust parameters to determine at-risk individuals more accurately.
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Affiliation(s)
- Sonali Sawant
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
| | - Shyam Sundar Nandi
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
| | - Trupti Gohil
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
| | - Abhijeet Jadhav
- Scientist E, National Institute of Virology, Pune 411001, India.
| | - Prasanna Samudra
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
| | - Meera Arora
- Dr. Babasaheb Ambedkar Memorial Hospital (Zonal) Byculla, Central Railway, Mumbai 400012, India.
| | - Ujjaini Rudra
- Dr. Balasaheb Vikhe Patil Rural Medical College, Loni 413736, India.
| | - Jagadish Deshpande
- National Institute of Virology Mumbai Unit, Haffkine Institute Compound, AD Marg, Parel, Mumbai 400012, India.
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16
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Lo WL, Huseby ES. The partitioning of TCR repertoires by thymic selection. J Exp Med 2024; 221:e20230897. [PMID: 39167074 DOI: 10.1084/jem.20230897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/22/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024] Open
Abstract
αβ T cells are critical components of the adaptive immune system; they maintain tissue and immune homeostasis during health, provide sterilizing immunity after pathogen infection, and are capable of eliminating transformed tumor cells. Fundamental to these distinct functions is the ligand specificity of the unique antigen receptor expressed on each mature T cell (TCR), which endows lymphocytes with the ability to behave in a cell-autonomous, disease context-specific manner. Clone-specific behavioral properties are initially established during T cell development when thymocytes use TCR recognition of major histocompatibility complex (MHC) and MHC-like ligands to instruct survival versus death and to differentiate into a plethora of inflammatory and regulatory T cell lineages. Here, we review the ligand specificity of the preselection thymocyte repertoire and argue that developmental stage-specific alterations in TCR signaling control cross-reactivity and foreign versus self-specificity of T cell sublineages.
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Affiliation(s)
- Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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17
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Royle JW, Hurwood D, Sadowski P, Dudley KJ. Non-CG DNA methylation marks the transition from pupa to adult in Helicoverpa armigera. INSECT MOLECULAR BIOLOGY 2024; 33:493-502. [PMID: 38668923 DOI: 10.1111/imb.12917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/10/2024] [Indexed: 08/20/2024]
Abstract
DNA methylation in insects is generally low in abundance, and its role is not well understood. It is often localised in protein coding regions and associated with the expression of 'housekeeping' genes. Few studies have explored DNA methylation dynamics during lifecycle stage transitions in holometabolous (metamorphosing) insects. Using targeted mass spectrometry, we have found a significant difference in global DNA methylation levels between larvae, pupae and adults of Helicoverpa armigera (Lepidoptera: Noctuidae) Hübner, a polyphagous pest of agricultural importance. Whole-genome bisulfite sequencing confirmed these observations and pointed to non-CG context being the primary explanation for the difference observed between pupa and adult. Non-CG methylation was enriched in genes specific to various signalling pathways (Hippo signalling, Hedgehog signalling and mitogen-activated protein kinase (MAPK) signalling) and ATP-dependent chromatin remodelling. Understanding the function of this epigenetic mark could be a target in future studies focusing on integrated pest management.
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Affiliation(s)
- Jack W Royle
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - David Hurwood
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Pawel Sadowski
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kevin J Dudley
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
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18
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Sun Y, Fan C, Lei D. Association between gut microbiota and postpartum depression: A bidirectional Mendelian randomization study. J Affect Disord 2024; 362:615-622. [PMID: 39029663 DOI: 10.1016/j.jad.2024.07.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 07/04/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUNDS Empirical investigations have shown an association between gut microbiota and postpartum depression (PPD); nevertheless, the precise cause-and-effect relationship between these two variables remains ambiguous. This research aimed to examine the possible reciprocal causal relationship between the gut microbiota and PPD. METHODS In this work, we used Mendelian randomization (MR) to analyze the relationship between the gut microbiota (n = 18,340) and PPD (n = 67,205). We obtained the relevant SNPs from publicly accessible genome-wide association studies (GWAS). The SNP estimations were combined by the inverse-variance weighted (IVW) method, including sensitivity analyses such as weighted median, MR Egger, and MR Pleiotropy Residual Sum and Outlier (PRESSO). RESULTS We have identified strong correlations between six bacterial characteristics and the likelihood of developing PPD. Our research revealed that the genus Ruminococcaceae UCG010, the family Veillonellaceae, and the class Clostridia had a beneficial effect on preventing PPD. The class Alphaproteobacteria, genus Slackia, and order NB1n were found to have a significant negative impact on PPD. The sensitivity studies conducted on these bacterial features consistently confirmed these finding. LIMITATIONS It is crucial to acknowledge that our study was conducted just within a European society, which may restrict its applicability to other groups. CONCLUSIONS The findings from our MR investigation indicate a potential causal relationship between certain kinds of gut bacteria and PPD. Additional investigation is required to elucidate the influence of gut microbiota on the advancement of PPD.
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Affiliation(s)
- Yonghao Sun
- Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, China
| | - Cuifang Fan
- Department of Obstetrics, Renmin Hospital of Wuhan University, Wuhan 430000, China.
| | - Di Lei
- Department of Obstetrics, Renmin Hospital of Wuhan University, Wuhan 430000, China.
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19
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Singh R, Yadav D, Ingole PG, Ahn YH. Magnetic engineering nanoparticles: Versatile tools revolutionizing biomedical applications. BIOMATERIALS ADVANCES 2024; 163:213948. [PMID: 38959651 DOI: 10.1016/j.bioadv.2024.213948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/18/2024] [Accepted: 06/29/2024] [Indexed: 07/05/2024]
Abstract
The use of nanoparticles has increased significantly over the past few years in a number of fields, including diagnostics, biomedicine, environmental remediation, and water treatment, generating public interest. Among various types of nanoparticles, magnetic nanoparticles (MNPs) have emerged as an essential tool for biomedical applications due to their distinct physicochemical properties compared to other nanoparticles. This review article focuses on the recent growth of MNPs and comprehensively reviews the advantages, multifunctional approaches, biomedical applications, and latest research on MNPs employed in various biomedical techniques. Biomedical applications of MNPs hold on to their ability to rapidly switch magnetic states under an external field at room temperature. Ideally, these MNPs should be highly susceptible to magnetization when the field is applied and then lose that magnetization just as quickly once the field is removed. This unique property allows MNPs to generate heat when exposed to high-frequency magnetic fields, making them valuable tools in developing treatments for hyperthermia and other heat-related illnesses. This review underscores the role of MNPs as tools that hold immense promise in transforming various aspects of healthcare, from diagnostics and imaging to therapeutic treatments, with discussion on a wide range of peer-reviewed articles published on the subject. At the conclusion of this work, challenges and potential future advances of MNPs in the biomedical field are highlighted.
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Affiliation(s)
- Randeep Singh
- Department of Civil Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea.
| | - Diksha Yadav
- Chemical Engineering Group, Engineering Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam 785006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Pravin G Ingole
- Chemical Engineering Group, Engineering Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam 785006, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
| | - Young-Ho Ahn
- Department of Civil Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea.
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20
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Limavady A, Marlais M. The extent of kidney involvement in paediatric tuberous sclerosis complex. Pediatr Nephrol 2024; 39:2927-2937. [PMID: 38832977 PMCID: PMC11349837 DOI: 10.1007/s00467-024-06417-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Tuberous sclerosis (TSC)-associated kidney disease is a leading cause of mortality in adults with TSC. This study aimed to understand TSC features in children, particularly kidney involvement, to inform clinical care for this specific group. METHODS This retrospective cohort study included all paediatric (< 19 years) TSC cases at a large tertiary paediatric nephrology centre. Relevant data were collected from patients' records, statistical analyses were performed to identify associations between variables, survival probabilities were estimated with Kaplan‒Meier curves, and log-rank tests were conducted to assess survival differences among genetic mutations. RESULTS A total of 182 children with TSC were included. Among the 145 children with available kidney imaging data, 78.6% (114/145) exhibited kidney lesions. Angiomyolipomas (AMLs) were significantly more prevalent in the TSC2 mutation group (p = 0.018). Children with TSC2 mutations generally had poorer lesion-free survival than those with TSC1 mutations, but this difference was only significant for AMLs (p = 0.030). The change in size of largest AMLs increased with age and doubled in children above 9 years; a similar pattern was observed when stratified by genetic mutation. In contrast, kidney cysts exhibited two peaks: one in children under 5 years (2.31 mm/year) and the second in children between 15-19 years (2.82 mm/year). Chronic kidney disease was observed in 12.3% (10/81) of children, and high-risk AMLs above 3 cm were observed in 9% (13/145). CONCLUSIONS While TSC kidney disease emerges later in the disease course than neurological features, our findings emphasise the importance of kidney surveillance during childhood, including routine kidney imaging, kidney function, and blood pressure monitoring.
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Affiliation(s)
- Andrew Limavady
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Matko Marlais
- Great Ormond Street Institute of Child Health, University College London, London, UK.
- Department of Paediatric Nephrology, Great Ormond Street Hospital, London, UK.
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21
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Vassy JL, Brunette CA, Yi T, Harrison A, Cardellino MP, Assimes TL, Christensen KD, Devineni P, Gaziano JM, Gong X, Hui Q, Knowles JW, Muralidhar S, Natarajan P, Pyarajan S, Sears MG, Shi Y, Sturm AC, Whitbourne SB, Sun YV, Danowski ME. Design and pilot results from the Million Veteran Program Return Of Actionable Results (MVP-ROAR) Study. Am Heart J 2024; 276:99-109. [PMID: 38762090 DOI: 10.1016/j.ahj.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND As a mega-biobank linked to a national healthcare system, the Million Veteran Program (MVP) can directly improve the health care of participants. To determine the feasibility and outcomes of returning medically actionable genetic results to MVP participants, the program launched the MVP Return of Actionable Results (MVP-ROAR) Study, with familial hypercholesterolemia (FH) as an exemplar actionable condition. METHODS The MVP-ROAR Study consists of a completed single-arm pilot phase and an ongoing randomized clinical trial (RCT), in which MVP participants are recontacted and invited to receive clinical confirmatory gene sequencing testing and a telegenetic counseling intervention. The primary outcome of the RCT is 6-month change in low-density lipoprotein cholesterol (LDL-C) between participants receiving results at baseline and those receiving results after 6 months. RESULTS The pilot developed processes to identify and recontact participants nationally with probable pathogenic variants in low-density lipoprotein receptor (LDLR) on the MVP genotype array, invite them to clinical confirmatory gene sequencing, and deliver a telegenetic counseling intervention. Among participants in the pilot phase, 8 (100%) had active statin prescriptions after 6 months. Results were shared with 16 first-degree family members. Six-month ΔLDL-C (low-density lipoprotein cholesterol) after the genetic counseling intervention was -37 mg/dL (95% CI: -12 to -61; P = .03). The ongoing RCT will determine between-arm differences in this primary outcome. CONCLUSION While underscoring the importance of clinical confirmation of research results, the pilot phase of the MVP-ROAR Study marks a turning point in MVP and demonstrates the feasibility of returning genetic results to participants and their providers. The ongoing RCT will contribute to understanding how such a program might improve patient health care and outcomes. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov ID NCT04178122.
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Affiliation(s)
- Jason L Vassy
- VA Boston Healthcare System, Boston, MA; Departments of Medicine and Population Medicine, Harvard Medical School, Boston, MA.
| | - Charles A Brunette
- VA Boston Healthcare System, Boston, MA; Departments of Medicine and Population Medicine, Harvard Medical School, Boston, MA
| | - Thomas Yi
- VA Boston Healthcare System, Boston, MA
| | | | | | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA; VA Palo Alto Health Care System, Palo Alto, CA
| | - Kurt D Christensen
- Departments of Medicine and Population Medicine, Harvard Medical School, Boston, MA; PRecisiOn Medicine Translational Research Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA
| | | | - J Michael Gaziano
- VA Boston Healthcare System, Boston, MA; Departments of Medicine and Population Medicine, Harvard Medical School, Boston, MA
| | - Xin Gong
- VA Boston Healthcare System, Boston, MA
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA; VA Atlanta Healthcare System, Decatur, GA
| | - Joshua W Knowles
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Sumitra Muralidhar
- Veterans Health Administration, Office of Research and Development, Washington, DC
| | - Pradeep Natarajan
- Departments of Medicine and Population Medicine, Harvard Medical School, Boston, MA; Division of Cardiology, Massachusetts General Hospital, Boston, MA; Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | | | | | | | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA; VA Atlanta Healthcare System, Decatur, GA
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22
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Andrawus M, David GB, Terziyska I, Sharvit L, Bergman A, Barzilai N, Raj SM, Govindaraju DR, Atzmon G. Genome integrity as a potential index of longevity in Ashkenazi Centenarian's families. GeroScience 2024; 46:4147-4162. [PMID: 38724875 PMCID: PMC11335978 DOI: 10.1007/s11357-024-01178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/24/2024] [Indexed: 06/19/2024] Open
Abstract
The aging process, or senescence, is characterized by age-specific decline in physical and physiological function, and increased frailty and genomic changes, including mutation accumulation. However, the mechanisms through which changes in genomic architecture influence human longevity have remained obscure. Copy number variants (CNVs), an abundant class of genomic variants, offer unique opportunities for understanding age-related genomic changes. Here we report the spectrum of CNVs in a cohort of 670 Ashkenazi Jewish centenarians, their progeny, and unrelated controls. The average ages of these groups were 97.4 ± 2.8, 69.2 ± 9.2, and 66.5 ± 7.0 respectively. For the first time, we compared different size classes of CNVs, from 1 kB to 100 MB in size. Using a high-resolution custom Affymetrix array, targeting 44,639 genomic regions, we identified a total of 12,166, 22,188, and 10,285 CNVs in centenarians, their progeny, and control groups, respectively. Interestingly, the offspring group showed the highest number of unique CNVs, followed by control and centenarians. While both gains and losses were found in all three groups, centenarians showed a significantly higher average number of both total gains and losses relative to their controls (p < 0.0327, 0.0182, respectively). Moreover, centenarians showed a lower total length of genomic material lost, suggesting that they may maintain superior genomic integrity over time. We also observe a significance fold increase of CNVs among the offspring, implying greater genomic integrity and a putative mechanism for longevity preservation. Genomic regions that experienced loss or gains appear to be distributed across many sites in the genome and contain genes involved in DNA transcription, cellular transport, developmental pathways, and metabolic functions. Our findings suggest that the exceptional longevity observed in centenarians may be attributed to the prolonged maintenance of functionally important genes. These genes are intrinsic to specific genomic regions as well as to the overall integrity of the genomic architecture. Additionally, a strong association between longer CNVs and differential gene expression observed in this study supports the notion that genomic integrity could positively influence longevity.
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Affiliation(s)
| | - Gil Ben David
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., 3498838, Mount Carmel, Haifa, Israel
| | | | - Lital Sharvit
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Srilakshmi M Raj
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | | | - Gil Atzmon
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel.
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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23
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Kim AH, Sakin I, Viviano S, Tuncel G, Aguilera SM, Goles G, Jeffries L, Ji W, Lakhani SA, Kose CC, Silan F, Oner SS, Kaplan OI, Ergoren MC, Mishra-Gorur K, Gunel M, Sag SO, Temel SG, Deniz E. CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow. Life Sci Alliance 2024; 7:e202402708. [PMID: 39168639 PMCID: PMC11339347 DOI: 10.26508/lsa.202402708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Intellectual and developmental disabilities result from abnormal nervous system development. Over a 1,000 genes have been associated with intellectual and developmental disabilities, driving continued efforts toward dissecting variant functionality to enhance our understanding of the disease mechanism. This report identified two novel variants in CC2D1A in a cohort of four patients from two unrelated families. We used multiple model systems for functional analysis, including Xenopus, Drosophila, and patient-derived fibroblasts. Our experiments revealed that cc2d1a is expressed explicitly in a spectrum of ciliated tissues, including the left-right organizer, epidermis, pronephric duct, nephrostomes, and ventricular zone of the brain. In line with this expression pattern, loss of cc2d1a led to cardiac heterotaxy, cystic kidneys, and abnormal CSF circulation via defective ciliogenesis. Interestingly, when we analyzed brain development, mutant tadpoles showed abnormal CSF circulation only in the midbrain region, suggesting abnormal local CSF flow. Furthermore, our analysis of the patient-derived fibroblasts confirmed defective ciliogenesis, further supporting our observations. In summary, we revealed novel insight into the role of CC2D1A by establishing its new critical role in ciliogenesis and CSF circulation.
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Affiliation(s)
- Angelina Haesoo Kim
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Irmak Sakin
- Department of ENT, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Acibadem University School of Medicine, Istanbul, Turkey
| | - Stephen Viviano
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Gulten Tuncel
- https://ror.org/02x8svs93 DESAM Research Institute, Near East University, Nicosia, Cyprus
| | | | - Gizem Goles
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Lauren Jeffries
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Saquib A Lakhani
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Canan Ceylan Kose
- Canakkale 18 March University, Faculty of Medicine, Department of Medical Genetics, Canakkale, Turkey
| | - Fatma Silan
- Canakkale 18 March University, Faculty of Medicine, Department of Medical Genetics, Canakkale, Turkey
| | - Sukru Sadik Oner
- Department of Pharmacology, Goztepe Prof. Dr. Suleyman Yalcin City Hospital, Istanbul, Turkey
- Istanbul Medeniyet University, Science and Advanced Technologies Research Center (BILTAM), Istanbul, Turkey
| | - Oktay I Kaplan
- Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri, Turkey
| | - Mahmut Cerkez Ergoren
- https://ror.org/02x8svs93 Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Ketu Mishra-Gorur
- https://ror.org/03pnmqc26 Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Murat Gunel
- https://ror.org/03pnmqc26 Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Yale Program in Brain Tumor Research, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Sebnem Ozemri Sag
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Sehime G Temel
- Department of Medical Genetics, Faculty of Medicine, Uludag University, Bursa, Turkey
- Department of Histology and Embryology and Health Sciences Institute, Department of Translational Medicine, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Engin Deniz
- https://ror.org/03pnmqc26 Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
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24
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Zhang H, Liu B, Cheng J, Li Z, Jia M, Li M, Zhao L, Wang L, Xi Y. Characterization and integrated analysis of extrachromosomal DNA amplification in hematological malignancies. Neoplasia 2024; 56:101025. [PMID: 38996538 PMCID: PMC11301242 DOI: 10.1016/j.neo.2024.101025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
The study of extrachromosomal DNA (ecDNA), an element existing beyond classical chromosomes, contributes to creating a more comprehensive map of the cancer genome. In hematological malignancies, research on ecDNA has lacked comprehensive investigation into its frequency, structure, function, and mechanisms of formation. We re-analyzed WGS data from 208 hematological cancer samples across 11 types, focusing on ecDNA characteristics. Amplification of ecDNA was observed in 7 of these cancer types, with no instances found in normal blood cells. Patients with leukemia carrying ecDNA showed a low induction therapy remission rate (<30 %), a high relapse rate (75 %) among those who achieved complete remission, and a significantly lower survival rate compared to the general leukemia population, even those with complex chromosomal karyotypes. Among the 55 identified ecDNA amplicons, 268 genes were detected, of which 38 are known cancer-related genes exhibiting significantly increased copy numbers. By integrating RNA-Seq data, we discovered that the increased copy number, resulting in a higher amount of available DNA templates, indeed leads to the elevated expression of genes encoded on ecDNA. Additionally, through the integration of H3K4me3/H3K27ac chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin with sequencing, and high-throughput chromosome conformation capture data, we identified that ecDNA amplifications can also facilitate efficient, copy number-independent amplification of oncogenes. This process is linked to active histone modifications, improved chromatin accessibility, and enhancer hijacking, all of which are effects of ecDNA amplification. Mechanistically, chromothripsis and dysfunction of the DNA repair pathway can, to some extent, explain the origin of ecDNA.
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Affiliation(s)
- Hao Zhang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Bei Liu
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Juan Cheng
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Zijian Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Mingfeng Jia
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Ming Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Long Zhao
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lina Wang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yaming Xi
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China.
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25
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Wu C, Shazeeb MS, Mangkalaphiban K, Han G, Peker A, Rentiya ZS, Gounis MJ, Jacobson A. Investigating therapeutic nonsense suppression in a neurofibromatosis mouse model. Exp Neurol 2024; 380:114914. [PMID: 39106942 DOI: 10.1016/j.expneurol.2024.114914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/15/2024] [Accepted: 07/31/2024] [Indexed: 08/09/2024]
Abstract
Neurofibromatosis type 1 (NF1) is a human genetic disorder caused by variants in the NF1 gene. Plexiform neurofibromas, one of many NF1 manifestations, are benign peripheral nerve sheath tumors occurring in up to 50% of NF1 patients. A substantial fraction of NF1 pathogenetic variants are nonsense mutations, which result in the synthesis of truncated non-functional NF1 protein (neurofibromin). To date, no therapeutics have restored neurofibromin expression or addressed the consequences of this protein's absence in NF1 nonsense mutation patients, but nonsense suppression is a potential approach to the problem. Ataluren is a small molecule drug that has been shown to stimulate functional nonsense codon readthrough in several models of nonsense mutation diseases, as well as in Duchenne muscular dystrophy patients. To test ataluren's potential applicability in nonsense mutation NF1 patients, we evaluated its therapeutic effects using three treatment regimens in a previously established NF1 patient-derived (c.2041C > T; p.Arg681X) nonsense mutation mouse model. Collectively, our experiments indicate that: i) ataluren appeared to slow the growth of neurofibromas and alleviate some paralysis phenotypes, ii) female Nf1-nonsense mutation mice manifested more severe paralysis and neurofibroma phenotypes than male mice, iii) ataluren doses with apparent effectiveness were lower in female mice than in male mice, and iv) age factors also influenced ataluren's effectiveness.
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Affiliation(s)
- Chan Wu
- Department of Microbiology, UMass Chan Medical School, Worcester, MA, USA
| | | | | | - George Han
- Department of Radiology, UMass Chan Medical School, Worcester, MA, USA; Department of Medicine, Beth Israel Deaconess Medical Center, Brockton, MA, USA
| | - Ahmet Peker
- Department of Radiology, UMass Chan Medical School, Worcester, MA, USA; Koç University Hospital, Istanbul, Türkiye
| | - Zubir S Rentiya
- Department of Radiology, UMass Chan Medical School, Worcester, MA, USA; Department of Radiation Oncology & Radiology, University of Virginia, Charlottesville, VA, USA
| | - Matthew J Gounis
- Department of Radiology, UMass Chan Medical School, Worcester, MA, USA
| | - Allan Jacobson
- Department of Microbiology, UMass Chan Medical School, Worcester, MA, USA; Li Weibo Institute for Rare Disease Research, UMass Chan Medical School, Worcester, MA, USA.
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26
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Chaudhary R, Rehman M, Agarwal V, Kumar A, Kaushik AS, Srivastava S, Srivastava S, Verma R, Rajinikanth PS, Mishra V. Terra incognita of glial cell dynamics in the etiology of leukodystrophies: Broadening disease and therapeutic perspectives. Life Sci 2024; 354:122953. [PMID: 39122110 DOI: 10.1016/j.lfs.2024.122953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/09/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Neuroglial cells, also known as glia, are primarily characterized as auxiliary cells within the central nervous system (CNS). The recent findings have shed light on their significance in numerous physiological processes and their involvement in various neurological disorders. Leukodystrophies encompass an array of rare and hereditary neurodegenerative conditions that were initially characterized by the deficiency, aberration, or degradation of myelin sheath within CNS. The primary cellular populations that experience significant alterations are astrocytes, oligodendrocytes and microglia. These glial cells are either structurally or metabolically impaired due to inherent cellular dysfunction. Alternatively, they may fall victim to the accumulation of harmful by-products resulting from metabolic disturbances. In either situation, the possible replacement of glial cells through the utilization of implanted tissue or stem cell-derived human neural or glial progenitor cells hold great promise as a therapeutic strategy for both the restoration of structural integrity through remyelination and the amelioration of metabolic deficiencies. Various emerging treatment strategies like stem cell therapy, ex-vivo gene therapy, infusion of adeno-associated virus vectors, emerging RNA-based therapies as well as long-term therapies have demonstrated success in pre-clinical studies and show promise for rapid clinical translation. Here, we addressed various leukodystrophies in a comprehensive and detailed manner as well as provide prospective therapeutic interventions that are being considered for clinical trials. Further, we aim to emphasize the crucial role of different glial cells in the pathogenesis of leukodystrophies. By doing so, we hope to advance our understanding of the disease, elucidate underlying mechanisms, and facilitate the development of potential treatment interventions.
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Affiliation(s)
- Rishabh Chaudhary
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Mujeeba Rehman
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Vipul Agarwal
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Anand Kumar
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Arjun Singh Kaushik
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Siddhi Srivastava
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Sukriti Srivastava
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Rajkumar Verma
- University of Connecticut School of Medicine, 200 Academic Way, Farmington, CT 06032, USA
| | - P S Rajinikanth
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
| | - Vikas Mishra
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India.
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27
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Bahia W, Soltani I, Abidi A, Mahdhi A, Mastouri M, Ferchichi S, Almawi WY. Structural impact, ligand-protein interactions, and molecular phenotypic effects of TGF-β1 gene variants: In silico analysis with implications for idiopathic pulmonary fibrosis. Gene 2024; 922:148565. [PMID: 38762014 DOI: 10.1016/j.gene.2024.148565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Idiopathic Pulmonary Fibrosis (IPF) is a chronic interstitial lung disease resulting in progressively deteriorating lung function. Transforming growth factor-β1 (TGF-β1) belongs to the TGF superfamily and exerts a profibrotic role in promoting lung fibrosis by facilitating fibroblast infiltration and activity, extracellular matrix deposition, and inhibition of collagen breakdown, thus promoting tissue remodelling and IPF. MATERIALS AND METHODS We evaluated the link between pathogenic TGF-β1 SNPs and IPF pathogenesis and the structure-activity functional consequences of those SNPs on the TGF-β1 protein. Several computational algorithms were merged to address the functional consequences of TGF-β1 gene mutations to protein stability, putative post-translational modification sites, ligand-protein interactions, and molecular phenotypic effects. These included FATHMM, POLYPHEN2, PROVEAN, and SIFT tools (identifying deleterious nsSNPs in the TGF-β1 gene), along with Pmut, PhD-SNP, SNAP, MutPred and the related TMHMM, MARCOIL, and DisProt algorithms (predicting structural disorders). INPS-MD was also used to evaluate the mutation-induced TGF-β1 protein's stability and MODPRED for recognition of post-translational TGF-β1 modification. RESULTS In total, 14 major pathogenic variants markedly impact the destabilization of the TGF-β1 protein, with most of these high-risk mutations associated with decreased stability of the TGF-β1 protein as per the I-Mutant, MUpro, and INPS-MD tools. R205W, R185W, R180Q, D86Y, and I300T variants were proposed to participate in the post-translational modifications, thus affecting affect protein-ligand interactions. Furthermore, at-risk genetic variants appear to target conserved regions in the alpha helices, random coils, and extracellular loops, resulting in a varied composition of amino acids, charge, hydrophobicity, and spatial architecture. CONCLUSIONS This study manuscript comprehensively analyzes gene variants within the TGF-β1 gene, offering novel insights into their structural and functional implications in interacting with target sites. This study is significant for the development of targeted therapeutic strategies and personalized treatment approaches for patients with inflammatory lung diseases such as IPF.
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Affiliation(s)
- Wael Bahia
- Research Unit of Clinical and Molecular Biology (UR17ES29), Department of Biochemistry, Faculty of Pharmacy of Monastir, University of Monastir, Tunisia
| | - Ismael Soltani
- Research Unit of Clinical and Molecular Biology (UR17ES29), Department of Biochemistry, Faculty of Pharmacy of Monastir, University of Monastir, Tunisia
| | - Anouar Abidi
- Laboratory of Physiology, Faculty of Medicine of Tunis, la Rabta, 1007, Tunis, Tunisia; Laboratory of Functional Physiology and Valorization of Bioresources, High Institute of Biotechnology of Beja, University of Jendouba, Beja, Tunisia
| | - Abdelkarim Mahdhi
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environment and Products, Faculty of Pharmacy, University of Monastir, Tunisia
| | - Maha Mastouri
- Laboratory of Infectious Diseases and Biological Agents, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Salima Ferchichi
- Research Unit of Clinical and Molecular Biology (UR17ES29), Department of Biochemistry, Faculty of Pharmacy of Monastir, University of Monastir, Tunisia
| | - Wassim Y Almawi
- Faculty of Sciences, El Manar University, Tunis, Tunisia; Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada.
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28
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Maraqah HH, Aboubechara JP, Abu-Asab MS, Lee HS, Aboud O. Excessive lipid production shapes glioma tumor microenvironment. Ultrastruct Pathol 2024; 48:367-377. [PMID: 39157967 DOI: 10.1080/01913123.2024.2392728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/27/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024]
Abstract
Disrupted lipid metabolism is a characteristic of gliomas. This study utilizes an ultrastructural approach to characterize the prevalence and distribution of lipids within gliomas. This study made use of tissue from IDH1 wild type (IDH1-wt) glioblastoma (n = 18) and IDH1 mutant (IDH1-mt) astrocytoma (n = 12) tumors. We uncover a prevalent and intriguing surplus of lipids. The bulk of the lipids manifested as sizable cytoplasmic inclusions and extracellular deposits in the tumor microenvironment (TME); in some tumors the lipids were stored in the classical membraneless spheroidal lipid droplets (LDs). Frequently, lipids accumulated inside mitochondria, suggesting possible dysfunction of the beta-oxidation pathway. Additionally, the tumor vasculature have lipid deposits in their lumen and vessel walls; this lipid could have shifted in from the tumor microenvironment or have been produced by the vessel-invading tumor cells. Lipid excess in gliomas stems from disrupted beta-oxidation and dysfunctional oxidative phosphorylation pathways. The implications of this lipid-driven environment include structural support for the tumor cells and protection against immune responses, non-lipophilic drugs, and free radicals.
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Affiliation(s)
- Haitham H Maraqah
- Medicine & Health Science Faculty, School of Meidicine, An-Najah National University, Nablus, Palestine
| | - John Paul Aboubechara
- Department of Neurology, University of California Davis, Sacramento, CA, USA
- Comprehensive Cancer Center, University of California, Davis, Sacramento, CA, USA
| | - Mones S Abu-Asab
- Electron Microscopy Lab, Biological Imaging Core, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Han Sung Lee
- Department of Pathology and Laboratory Medicine, UC Davis Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Orwa Aboud
- Department of Neurology, University of California Davis, Sacramento, CA, USA
- Comprehensive Cancer Center, University of California, Davis, Sacramento, CA, USA
- Department of Neurosurgery, UC Davis Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
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29
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Yu F, Li X, Sheng C, Li L. DNA Nanotechnology Targeting Mitochondria: From Subcellular Molecular Imaging to Tailor-Made Therapeutics. Angew Chem Int Ed Engl 2024; 63:e202409351. [PMID: 38872505 DOI: 10.1002/anie.202409351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 06/15/2024]
Abstract
Mitochondria, one of the most important organelles, represent a crucial subcellular target for fundamental research and biomedical applications. Despite significant advances in the design of DNA nanotechnologies for a variety of bio-applications, the dearth of strategies that enable mitochondria targeting for subcellular molecular imaging and therapy remains an outstanding challenge in this field. In this Minireview, we summarize the recent progresses on the emerging design and application of DNA nanotechnology for mitochondria-targeted molecular imaging and tumor treatment. We first highlight the engineering of mitochondria-localized DNA nanosensors for in situ detection and imaging of diverse key molecules that are essential to maintain mitochondrial functions, including mitochondrial DNA and microRNA, enzymes, small molecules, and metal ions. Then, we compile the developments of DNA nanotechnologies for mitochondria-targeted anti-tumor therapy, including modularly designed DNA nanodevices for subcellular delivery of therapeutic agents, and programmed DNA assembly for mitochondrial interference. We will place an emphasis on clarification of the chemical principles of how DNA nanobiotechnology can be designed to target mitochondria for various biomedical applications. Finally, the remaining challenges and future directions in this emerging field will be discussed, hoping to inspire further development of advanced DNA toolkits for both academic and clinical research regarding mitochondria.
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Affiliation(s)
- Fangzhi Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangfei Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuangui Sheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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30
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Li R, Sone N, Gotoh S, Sun X, Hagood JS. Contemporary and emerging technologies for research in children's rare and interstitial lung disease. Pediatr Pulmonol 2024; 59:2349-2359. [PMID: 37204232 DOI: 10.1002/ppul.26490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/20/2023]
Abstract
Although recent decades have seen the identification, classification and discovery of the genetic basis of many children's interstitial and rare lung disease (chILD) disorders, detailed understanding of pathogenesis and specific therapies are still lacking for most of them. Fortunately, a revolution of technological advancements has created new opportunities to address these critical knowledge gaps. High-throughput sequencing has facilitated analysis of transcription of thousands of genes in thousands of single cells, creating tremendous breakthroughs in understanding normal and diseased cellular biology. Spatial techniques allow analysis of transcriptomes and proteomes at the subcellular level in the context of tissue architecture, in many cases even in formalin-fixed, paraffin-embedded specimens. Gene editing techniques allow creation of "humanized" animal models in a shorter time frame, for improved knowledge and preclinical therapeutic testing. Regenerative medicine approaches and bioengineering advancements facilitate the creation of patient-derived induced pluripotent stem cells and their differentiation into tissue-specific cell types which can be studied in multicellular "organoids" or "organ-on-a-chip" approaches. These technologies, singly and in combination, are already being applied to gain new biological insights into chILD disorders. The time is ripe to systematically apply these technologies to chILD, together with sophisticated data science approaches, to improve both biological understanding and disease-specific therapy.
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Affiliation(s)
- Rongbo Li
- Department of Pediatrics, Division of Respiratory Medicine, UC-San Diego, La Jolla, California, USA
| | - Naoyuki Sone
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Shimpei Gotoh
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Xin Sun
- Department of Pediatrics, Division of Respiratory Medicine, UC-San Diego, La Jolla, California, USA
| | - James S Hagood
- Department of Pediatrics, Pulmonology Division, Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Kasimoğlu N, Gürarslan Baş N. The relationship between parental attitude toward childhood epilepsy and spiritual orientation. Epilepsy Behav 2024; 158:109946. [PMID: 39002274 DOI: 10.1016/j.yebeh.2024.109946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/27/2024] [Accepted: 07/07/2024] [Indexed: 07/15/2024]
Abstract
AIM The aim of this study is to evaluate the relationship between parental attitudes toward childhood epilepsy and spiritual orientations. METHODS This descriptive study was conducted online between May and July 2022 with 417 parents residing in the eastern part of Turkey. Data were collected using a descriptive information form, the Social Attitudes Scale toward Childhood Epilepsies, and the Spiritual Orientation Scale. The obtained data were analyzed using the SPSS software package, employing descriptive statistics such as frequency, percentage, mean, standard deviation, as well as inferential statistics including independent samples t-test, ANOVA, multiple linear regression and correlation tests. RESULTS The Total Social Attitudes Scale Score toward Childhood Epilepsies was calculated as 45.10 ± 7.81, and the Spiritual Orientation Scale Score was 89.88 ± 30.30 for parents with an average age of 36.64 ± 8.26. It was found statistically significant and high (p > 0.05) for parents who are female, have a higher level of education, and have previously received education about epilepsy regarding both the Total Social Attitudes Scale Score toward Childhood Epilepsies and the Spiritual Orientation Scale Score. A statistically significant positive correlation was found between the Total Social Attitudes Scale Score toward Childhood Epilepsies and the Spiritual Orientation Scale Score. CONCLUSION According to the findings of the research, parents' attitudes towards childhood epilepsy are positive, and their spiritual orientation levels are high. As parents' spiritual orientation levels increase, their positive attitudes towards childhood epilepsy also increase.
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Affiliation(s)
- Necla Kasimoğlu
- Erzincan Binali Yıldırım University, Faculty of Health Sciences, Department of Child Health and Diseases Nursing, Erzincan, Turkey.
| | - Nazan Gürarslan Baş
- Munzur University, Faculty of Health Sciences, Nursing Department Tunceli, Turkey.
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Zhang Y, Xu W, Peng C, Ren S, Mustafe Hidig S, Zhang C. Exploring the role of m7G modification in Cancer: Mechanisms, regulatory proteins, and biomarker potential. Cell Signal 2024; 121:111288. [PMID: 38971569 DOI: 10.1016/j.cellsig.2024.111288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
The dysregulation of N(7)-methylguanosine (m7G) modification is increasingly recognized as a key factor in the pathogenesis of cancers. Aberrant expression of these regulatory proteins in various cancers, including lung, liver, and bladder cancers, suggests a universal role in tumorigenesis. Studies have established a strong correlation between the expression levels of m7G regulatory proteins, such as Methyltransferase like 1 (METTL1) and WD repeat domain 4 (WDR4), and clinical parameters including tumor stage, grade, and patient prognosis. For example, in hepatocellular carcinoma, high METTL1 expression is associated with advanced tumor stage and poor prognosis. Similarly, WDR4 overexpression in colorectal cancer correlates with increased tumor invasiveness and reduced patient survival. This correlation underscores the potential of these proteins as valuable biomarkers for cancer diagnosis and prognosis. Additionally, m7G modification regulatory proteins influence cancer progression by modulating the expression of target genes involved in critical biological processes, including cell proliferation, apoptosis, migration, and invasion. Their ability to regulate these processes highlights their significance in the intricate network of molecular interactions driving tumor development and metastasis. Given their pivotal role in cancer biology, m7G modification regulatory proteins are emerging as promising therapeutic targets. Targeting these proteins could offer a novel approach to disrupt the malignant behavior of cancer cells and enhance treatment outcomes. Furthermore, their diagnostic and prognostic value could aid in the early detection of cancer and the selection of appropriate therapeutic strategies, ultimately enhancing patient management and survival rates. This review aims to explore the mechanisms of action of RNA m7G modification regulatory proteins in tumors and their potential applications in cancer progression and treatment. By delving into the roles of these regulatory proteins, we intend to provide a theoretical foundation for the development of novel cancer treatment strategies.
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Affiliation(s)
- Yu Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weihao Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chuanhui Peng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Shenli Ren
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sakarie Mustafe Hidig
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Zhejiang University School of Medicine Fourth Affiliated Hospital, Yiwu, Zhejiang, China
| | - Cheng Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Hoepers AM, Heinemann JA, Zanatta CB, Chu P, Hiscox TC, Agapito-Tenfen SZ. Predicted multispecies unintended effects from outdoor genome editing. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116707. [PMID: 38996645 DOI: 10.1016/j.ecoenv.2024.116707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 07/02/2024] [Accepted: 07/07/2024] [Indexed: 07/14/2024]
Abstract
CRISPR/Cas9, a potent genetic engineering tool widely adopted in agriculture, is capable of introducing new characteristics into plants on a large scale and without conventional breeding methods. Despite its remarkable efficiency, concerns have arisen regarding unintended consequences in uncontrolled environments. Our aim was to assess potential activity in organisms that could be exposed to genome editing in uncontrolled environments. We developed three scenarios, using irrigation, fumigation and fertilization as delivery methods, based on outdoor uses in agriculture, namely pest and disease control. Using publicly available software (Cas-OFFinder, NCBI Genome Data Viewer and STRING), off-target effects were predicted in multiple species commonly found in the agroecosystem, including humans (16 of 38 (42 %) sampled). Metabolic enrichment analysis (gene IDs), by connecting off-target genes into a physiological network, predicted effects on the development of nervous and respiratory systems. Our findings emphasize the importance of exercising caution when considering the use of this genome editing in uncontrolled environments. Unintended genomic alterations may occur in unintended organisms, underscoring the significance of understanding potential hazards and implementing safety measures to protect human health and the environment.
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Affiliation(s)
- Aline Martins Hoepers
- Crop Science Department, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Jack A Heinemann
- Centre for Integrated Research in Biosafety and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Philomena Chu
- NORCE Norwegian Research Centre AS, Climate & Environment Division, Siva Innovasjonssenter, Sykehusvn 21, Tromsø 9019, Norway
| | - Tessa C Hiscox
- Centre for Integrated Research in Biosafety and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sarah Zanon Agapito-Tenfen
- NORCE Norwegian Research Centre AS, Climate & Environment Division, Siva Innovasjonssenter, Sykehusvn 21, Tromsø 9019, Norway.
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Billes A, Pujalte M, Jedraszak G, Amsallem D, Boudry-Labis E, Boute O, Bouquillon S, Brischoux-Boucher E, Callier P, Coutton C, Denizet ALA, Dieterich K, Kuentz P, Lespinasse J, Mazel B, Morin G, Amram F, Pennamen P, Rio M, Piard J, Putoux A, Rama M, Roze-Guillaumey V, Schluth-Bolard C, Till M, Trouvé C, Vieville G, Rooryck C, Sanlaville D, Chatron N. Possible incomplete penetrance of Xq28 int22h-1/int22h-2 duplication. Clin Genet 2024; 106:234-246. [PMID: 38561231 DOI: 10.1111/cge.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Xq28 int22h-1/int22h-2 duplication is the result of non-allelic homologous recombination between int22h-1/int22h-2 repeats separated by 0.5 Mb. It is responsible for a syndromic form of intellectual disability (ID), with recurrent infections and atopic diseases. Minor defects, nonspecific facial dysmorphic features, and overweight have also been described. Half of female carriers have been reported with ID, whereas all reported evaluated born males present mild to moderate ID, suggesting complete penetrance. We collected data on 15 families from eight university hospitals. Among them, 40 patients, 21 females (one fetus), and 19 males (two fetuses), were carriers of typical or atypical Xq28 int22h-1/int22h-2 duplication. Twenty-one individuals were considered asymptomatic (16 females and 5 males), without significantly higher rate of recurrent infections, atopia, overweight, or facial dysmorphism. Approximately 67% live-born males and 23% live-born female carriers of the typical duplication did not have obvious signs of intellectual disability, suggesting previously undescribed incomplete penetrance or low expression in certain carriers. The possibility of a second-hit or modifying factors to this possible susceptibility locus is yet to be studied but a possible observational bias should be considered in assessing such challenging X-chromosome copy number gains. Additional segregation studies should help to quantify this newly described incomplete penetrance.
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Affiliation(s)
- Alexis Billes
- CHU Amiens Picardie, Service de Génétique Clinique, Amiens, France
- CHU Amiens Picardie, Laboratoire de Génétique Constitutionnelle, Amiens, France
| | - Mathilde Pujalte
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Guillaume Jedraszak
- CHU Amiens Picardie, Laboratoire de Génétique Constitutionnelle, Amiens, France
- CHU Amiens Picardie, Département de génétique, UR4666 HEMATIM, CURS, Université Picardie Jules Verne, Amiens, France
| | - Daniel Amsallem
- Service de Neuropédiatrie, CHU de Besançon, Besançon, France
| | - Elise Boudry-Labis
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Odile Boute
- Génétique Clinique, Centre Hospitalier Universitaire de Lille, Hôpital Jeanne de Flandre, Lille, France
| | - Sonia Bouquillon
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine - CHU de Besançon, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Patrick Callier
- Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France
- Unité Fonctionnelle Innovation diagnostique dans les maladies rares, laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon Bourgogne, Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France
| | - Charles Coutton
- Service de Génétique, Génomique, et Procréation, Centre Hospitalier Universitaire Grenoble Alpes, La Tronche, France
- INSERM 1209, CNRS UMR 5309, Institut pour l'Avancée des Biosciences (IAB), Université Grenoble Alpes, Grenoble, France
| | - Anne-Laude Avice Denizet
- Centre de Génétique Humaine - CHU de Besançon, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Klaus Dieterich
- Université Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, Medical Genetics, Grenoble Institute of Neurosciences, Grenoble, France
- CHU Grenoble, UM Génétique Chromosomique, Grenoble, France
| | - Paul Kuentz
- Oncobiologie Génétique Bioinformatique, PCBio, CHU de Besançon, Besançon, France
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD "Génétique des Anomalies du Développement", FHUTRANSLAD, Dijon, France
| | - James Lespinasse
- Centre Hospitalier de Chambéry, Service de Cytogénétique, Chambéry, France
| | - Benoît Mazel
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHUTRANSLAD - CHU Dijon Bourgogne, Dijon, France
| | - Gilles Morin
- CHU Amiens Picardie, Service de Génétique Clinique, Amiens, France
| | - Florence Amram
- CHU Amiens Picardie, Service de Génétique Clinique, Amiens, France
| | - Perrine Pennamen
- CHU Bordeaux, Laboratoire de Génétique Biologique, Bordeaux, France
| | - Marlène Rio
- Université Paris Cité, Institut Imagine, Inserm U1163, Paris, France
- Service de Médecine Génomique des maladies rares, AP-HP, Centre Hôpital Necker-Enfants Malades, Paris, France
| | - Juliette Piard
- Centre de Génétique Humaine - CHU de Besançon, Université de Bourgogne-Franche-Comté, Besançon, France
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche Comté, Dijon, France
| | - Audrey Putoux
- Hospices Civils de Lyon, Service de Génétique, Groupement Hospitalier Est, Bron, France
- Equipe GENDEV, Centre de Recherche en Neurosciences de Lyon, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Mélanie Rama
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, Centre Hospitalier Universitaire de Lille, Lille, France
| | | | - Caroline Schluth-Bolard
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261-INSERM U1315, Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Marianne Till
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Chloé Trouvé
- Centre de Génétique Humaine - CHU de Besançon, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Gaëlle Vieville
- Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble-Alpes, Grenoble, France
| | - Caroline Rooryck
- CHU de Bordeaux, Service de Génétique Médicale, Bordeaux, France
- Univ. Bordeaux, Maladies Rares: Génétique et Métabolisme (MRGM), U 1211 INSERM, Bordeaux, France
| | - Damien Sanlaville
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261-INSERM U1315, Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
| | - Nicolas Chatron
- Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261-INSERM U1315, Université de Lyon - Université Claude Bernard Lyon 1, Lyon, France
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Nawaz K, Alifah N, Hussain T, Hameed H, Ali H, Hamayun S, Mir A, Wahab A, Naeem M, Zakria M, Pakki E, Hasan N. From genes to therapy: A comprehensive exploration of congenital heart disease through the lens of genetics and emerging technologies. Curr Probl Cardiol 2024; 49:102726. [PMID: 38944223 DOI: 10.1016/j.cpcardiol.2024.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Congenital heart disease (CHD) affects approximately 1 % of live births worldwide, making it the most common congenital anomaly in newborns. Recent advancements in genetics and genomics have significantly deepened our understanding of the genetics of CHDs. While the majority of CHD etiology remains unclear, evidence consistently indicates that genetics play a significant role in its development. CHD etiology holds promise for enhancing diagnosis and developing novel therapies to improve patient outcomes. In this review, we explore the contributions of both monogenic and polygenic factors of CHDs and highlight the transformative impact of emerging technologies on these fields. We also summarized the state-of-the-art techniques, including targeted next-generation sequencing (NGS), whole genome and whole exome sequencing (WGS, WES), single-cell RNA sequencing (scRNA-seq), human induced pluripotent stem cells (hiPSCs) and others, that have revolutionized our understanding of cardiovascular disease genetics both from diagnosis perspective and from disease mechanism perspective in children and young adults. These molecular diagnostic techniques have identified new genes and chromosomal regions involved in syndromic and non-syndromic CHD, enabling a more defined explanation of the underlying pathogenetic mechanisms. As our knowledge and technologies continue to evolve, they promise to enhance clinical outcomes and reduce the CHD burden worldwide.
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Affiliation(s)
- Khalid Nawaz
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Nur Alifah
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Talib Hussain
- Women Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Hameed
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Haider Ali
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Awal Mir
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Mohammad Zakria
- Advanced Center for Genomic Technologies, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Ermina Pakki
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia.
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Sang X, Zhang S. Mucus provisioning as milk in an amphibian. Integr Zool 2024; 19:1014-1016. [PMID: 38798139 DOI: 10.1111/1749-4877.12854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Two examples of vertebrates that feed young with mucus. Left: A female cichlid fish Symphysodon aequifasciatus; Right: A female caecilian Siphonops annulatus.
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Affiliation(s)
- Xiaohan Sang
- Centre for Behavioral Ecology and Evolution, State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Shichang Zhang
- Centre for Behavioral Ecology and Evolution, State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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Tay HW, Tay KS. Future directions for early detection of fracture related infections. J Orthop 2024; 55:64-68. [PMID: 38655538 PMCID: PMC11035015 DOI: 10.1016/j.jor.2024.03.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Fracture related infection (FRI) refers to pathogens infecting a fracture site and hence impeding fracture healing. It is a significant complication that carries substantial disease burden and socio-economic costs, but has had limited scientific development. Hence, this paper will review the existing strategies for early detection of FRI, in the form of serum markers, molecular diagnostics and imaging modalities, and further discuss potential future directions for improved detection of FRI. Existing Strategies for Diagnosis of FRI The Anti-infection Global Expert Committee (AIGEC) developed a consensus definition for FRI in 2017, which includes confirmatory and suggestive criteria for diagnosis of FRI. Existing strategies for diagnosis include clinical, laboratory, histopathological, microbiological and radiological investigations. Future Directions for Early Detection of FRI With increasing recognition of FRI, early detection is crucial for early treatment to be enforced. We have identified potential areas for future development in diagnostics for early detection of FRI, which are discussed in this manuscript. They include inflammatory cytokines, serum calcium levels, platelet count, improved management of histopathological and microbiological specimens, metagenomics, wound biomarkers, gut microbiota analysis, and novel imaging technologies.
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Affiliation(s)
- Hui Wen Tay
- Singapore General Hospital Department of Orthopaedic Surgery, Singapore
| | - Kae Sian Tay
- Singapore General Hospital Department of Orthopaedic Surgery, Singapore
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Guo D, Sheng W, Cai Y, Shu J, Cai C. Genetic Association of Lipids and Lipid-Lowering Drug Target Genes With Attention Deficit Hyperactivity Disorder. J Atten Disord 2024; 28:1425-1436. [PMID: 38166458 DOI: 10.1177/10870547231222219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
BACKGROUND Lipid metabolism plays an essential role in nervous system development. Cholesterol deficiency leads to a variety of neurodevelopmental disorders, such as autism spectrum disorder and fragile X syndrome. There have been a lot of efforts to search for biological markers associated with and causal to ADHD, among which lipid is one possible etiological factor that is quite widely studied. We aimed to evaluate the causal relationship between lipids traits, lipid-lowering drugs, and attention deficit hyperactivity disorder (ADHD) outcomes using Mendelian randomization (MR) studies. METHODS We used summary data from genome-wide association studies to explore the causal relationships between circulating lipid-related traits and ADHD. Then, quantitative trait loci for the expression of lipid-lowering drug target genes and genetic variants associated with lipid traits were extracted. Summary-data-based MR and inverse-variance-weighted MR (IVW-MR) were used to investigate the correlation between the expression of these drug-target genes and ADHD. RESULTS After rigorous screening, 939 instrumental variables were finally included for univariable mendelian randomization analysis. However, there is no correlation between lipid profile and ADHD risk. Drug target analysis by IVW-MR method observed that APOB-mediated low-density lipoprotein cholesterol was associated with lower ADHD risk (odds ratio [OR] = 0.90, 95% confidence interval [CI] [0.84, 0.97]; p = .007), whereas LPL-mediated triglycerides levels were associated with a higher risk of ADHD (OR = 1.13, 95% CI [1.06, 1.21]; p < .001). CONCLUSION Our results suggest that APOB gene and LPL gene may be candidate drug target genes for the treatment of ADHD.
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Affiliation(s)
- Detong Guo
- Tianjin Children's Hospital (Tianjin University Children's Hospital), China
- Tianjin Medical University, China
| | - Wenchao Sheng
- Tianjin Children's Hospital (Tianjin University Children's Hospital), China
- Tianjin Medical University, China
| | | | - Jianbo Shu
- Tianjin Children's Hospital (Tianjin University Children's Hospital), China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, China
| | - Chunquan Cai
- Tianjin Children's Hospital (Tianjin University Children's Hospital), China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, China
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MacCarrick G, Aradhya S, Bailey M, Chu D, Hunt A, Izzo E, Krakow D, Mackenzie W, Poll S, Raggio C, Shediac R, White KK, McLaughlin HM, Seratti G. Clinical utility of comprehensive gene panel testing for common and rare causes of skeletal dysplasia and other skeletal disorders: Results from the largest cohort to date. Am J Med Genet A 2024; 194:e63646. [PMID: 38702915 DOI: 10.1002/ajmg.a.63646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024]
Abstract
Molecular genetics enables more precise diagnoses of skeletal dysplasia and other skeletal disorders (SDs). We investigated the clinical utility of multigene panel testing for 5011 unrelated individuals with SD in the United States (December 2019-April 2022). Median (range) age was 8 (0-90) years, 70.5% had short stature and/or disproportionate growth, 27.4% had a positive molecular diagnosis (MDx), and 30 individuals received two MDx. Genes most commonly contributing to MDx were FGFR3 (16.9%), ALPL (13.0%), and COL1A1 (10.3%). Most of the 112 genes associated with ≥1 MDx were primarily involved in signal transduction (n = 35), metabolism (n = 23), or extracellular matrix organization (n = 17). There were implications associated with specific care/treatment options for 84.4% (1158/1372) of MDx-positive individuals; >50% were linked to conditions with targeted therapy approved or in clinical development, including osteogenesis imperfecta, achondroplasia, hypophosphatasia, and mucopolysaccharidosis. Forty individuals with initially inconclusive results became MDx-positive following family testing. Follow-up mucopolysaccharidosis enzyme activity testing was positive in 14 individuals (10 of these were not MDx-positive). Our findings showed that inclusion of metabolic genes associated with SD increased the clinical utility of a gene panel and confirmed that integrated use of comprehensive gene panel testing with orthogonal testing reduced the burden of inconclusive results.
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Affiliation(s)
- Gretchen MacCarrick
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mitch Bailey
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Dorna Chu
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Abigail Hunt
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Emanuela Izzo
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Deborah Krakow
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - William Mackenzie
- Department of Orthopaedic Surgery, Nemours Children's Hospital, Wilmington, Delaware, USA
| | - Sarah Poll
- Invitae Corporation, San Francisco, California, USA
| | - Cathleen Raggio
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, New York, USA
| | - Renée Shediac
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Klane K White
- Department of Pediatric Orthopedic Surgery, Children's Hospital Colorado, Aurora, Colorado, USA
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Zivotic I, Kolic I, Cvetkovic M, Spasojevic-Dimitrijeva B, Zivkovic M, Stankovic A, Jovanovic I. Copy number variation analysis identifies MIR9-3 and MIR1299 as novel miRNA candidate genes for CAKUT. Pediatr Nephrol 2024; 39:2655-2665. [PMID: 38656454 DOI: 10.1007/s00467-024-06381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) represent a frequent cause of pediatric kidney failure. CNVs, as a major class of genomic variations, can also affect miRNA regions. Common CNV corresponding miRNAs (cCNV-miRNAs) are functional variants regulating crucial processes which could affect urinary system development. Thus, we hypothesize that cCNV-miRNAs are associated with CAKUT occurrence and its expressivity. METHODS The extraction and filtering of common CNVs, identified in control samples deposited in publicly available databases gnomAD v2.1 and dbVar, were coupled with mapping of miRNA sequences using UCSC Genome Browser. After verification of the mapped miRNAs using referent miRBase V22.1, prioritization of cCNV-miRNA candidates has been performed using bioinformatic annotation and literature research. Genotyping of miRNA gene copy numbers for MIR9-3, MIR511, and MIR1299, was conducted on 221 CAKUT patients and 192 controls using TaqMan™ technology. RESULTS We observed significantly different MIR9-3 and MIR1299 gene copy number distribution between CAKUT patients and controls (Chi-square, P = 0.006 and P = 0.0002, respectively), while difference of MIR511 copy number distribution showed nominal significance (Chi-square, P = 0.027). The counts of less and more than two of MIR1299 copy numbers were more frequent within CAKUT patients compared to controls (P = 0.01 and P = 0.008, respectively) and also in cohort of patients with anomalies of the urinary tract compared to controls (P = 0.016 and P = 0.003, respectively). CONCLUSIONS Copy number variations of miRNA genes represent a novel avenue in clarification of the inheritance complexity in CAKUT and provide potential evidence about the association of common genetic variation with CAKUT phenotypes.
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Affiliation(s)
- Ivan Zivotic
- Department of Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia
| | - Ivana Kolic
- Department of Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia
| | - Mirjana Cvetkovic
- Nephrology and Urology Departments, University Children's Hospital, Belgrade, Serbia
- Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Brankica Spasojevic-Dimitrijeva
- Nephrology and Urology Departments, University Children's Hospital, Belgrade, Serbia
- Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Maja Zivkovic
- Department of Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia
| | - Aleksandra Stankovic
- Department of Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia
| | - Ivan Jovanovic
- Department of Radiobiology and Molecular Genetics, Vinča Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, P.O. Box 522, 11001, Belgrade, Serbia.
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Liu F, Li R, Zhu Z, Yang Y, Lu F. Current developments of gene therapy in human diseases. MedComm (Beijing) 2024; 5:e645. [PMID: 39156766 PMCID: PMC11329757 DOI: 10.1002/mco2.645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 08/20/2024] Open
Abstract
Gene therapy has witnessed substantial advancements in recent years, becoming a constructive tactic for treating various human diseases. This review presents a comprehensive overview of these developments, with a focus on their diverse applications in different disease contexts. It explores the evolution of gene delivery systems, encompassing viral (like adeno-associated virus; AAV) and nonviral approaches, and evaluates their inherent strengths and limitations. Moreover, the review delves into the progress made in targeting specific tissues and cell types, spanning the eye, liver, muscles, and central nervous system, among others, using these gene technologies. This targeted approach is crucial in addressing a broad spectrum of genetic disorders, such as inherited lysosomal storage diseases, neurodegenerative disorders, and cardiovascular diseases. Recent clinical trials and successful outcomes in gene therapy, particularly those involving AAV and the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins, are highlighted, illuminating the transformative potentials of this approach in disease treatment. The review summarizes the current status of gene therapy, its prospects, and its capacity to significantly ameliorate patient outcomes and quality of life. By offering comprehensive analysis, this review provides invaluable insights for researchers, clinicians, and stakeholders, enriching the ongoing discourse on the trajectory of disease treatment.
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Affiliation(s)
- Fanfei Liu
- Department of OphthalmologyWest China HospitalChengduSichuanChina
| | - Ruiting Li
- State Key Laboratory of BiotherapyWest China HospitalChengduSichuanChina
| | - Zilin Zhu
- College of Life SciencesSichuan UniversityChengduSichuanChina
| | - Yang Yang
- Department of OphthalmologyWest China HospitalChengduSichuanChina
- State Key Laboratory of BiotherapyWest China HospitalChengduSichuanChina
| | - Fang Lu
- Department of OphthalmologyWest China HospitalChengduSichuanChina
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Attallah A, Ardourel M, Gallazzini F, Lesne F, De Oliveira A, Togbé D, Briault S, Perche O. Lack of FMRP in the retina: Evidence of a retinal specific transcriptomic profile. Exp Eye Res 2024; 246:110015. [PMID: 39089568 DOI: 10.1016/j.exer.2024.110015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/11/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Fragile X Syndrome (FXS), the most common inherited form of human intellectual disability, is a monogenic neurodevelopmental disorder caused by a loss-of-function mutation of the FMR1 gene. FMR1 is encoding the Fragile X Messenger Ribonucleo Protein (FMRP) an RNA-binding protein that regulates the translation of synaptic proteins. The absence of FMRP expression has many important consequences on synaptic plasticity and function, leading to the FXS clinical phenotype. Over the last decade, a visual neurosensorial phenotype had been described in the FXS patients as well as in the murine model (Fmr1-/ymice), characterized by retinal deficits associated to retinal perception alterations. However, although the transcriptomic profile in the absence of FMRP has been studied in the cerebral part of the central nervous system (CNS), there are no actual data for the retina which is an extension of the CNS. Herein, we investigate the transcriptomic profile of mRNA from whole retinas of Fmr1-/ymice. Interestingly, we found a specific signature of Fmrp absence on retinal mRNA expression with few common genes compared to other brain studies. Gene Ontology on these retinal specific genes demonstrated an enrichment in retinal development genes as well as in synaptic genes. These alterations could be linked to the reported retinal phenotype of the FXS condition. In conclusion, we describe for the first time, retinal-specific transcriptomic changes in the absence of FMRP.
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Affiliation(s)
- Amir Attallah
- Orléans University, University Hospital Center of Orleans, LI(2)RSO, 14, Avenue de l'hôpital, 45100, Orléans, France; Orleans University, CNRS, laboratoire INEM, UMR7355, 3b Rue de la Férollerie, F-45071, Orléans, Cedex 2, France; ART ARNm US55, 14 Avenue de l'Hôpital, 45100, Orléans, France
| | - Maryvonne Ardourel
- Orléans University, University Hospital Center of Orleans, LI(2)RSO, 14, Avenue de l'hôpital, 45100, Orléans, France; ART ARNm US55, 14 Avenue de l'Hôpital, 45100, Orléans, France
| | - Felix Gallazzini
- University Hospital Center of Orleans, Genetic Department, 14 Avenue de l'Hôpital, 45100, Orléans, France
| | - Fabien Lesne
- University Hospital Center of Orléans CAR&IB, Pôle Biopatholgie, 14 Avenue de l'Hôpital, 45100, Orléans, France
| | - Anthony De Oliveira
- University Hospital Center of Orléans CAR&IB, Pôle Biopatholgie, 14 Avenue de l'Hôpital, 45100, Orléans, France
| | - Dieudonnée Togbé
- Orleans University, CNRS, laboratoire INEM, UMR7355, 3b Rue de la Férollerie, F-45071, Orléans, Cedex 2, France
| | - Sylvain Briault
- Orléans University, University Hospital Center of Orleans, LI(2)RSO, 14, Avenue de l'hôpital, 45100, Orléans, France; ART ARNm US55, 14 Avenue de l'Hôpital, 45100, Orléans, France; University Hospital Center of Orleans, Genetic Department, 14 Avenue de l'Hôpital, 45100, Orléans, France
| | - Olivier Perche
- Orléans University, University Hospital Center of Orleans, LI(2)RSO, 14, Avenue de l'hôpital, 45100, Orléans, France; ART ARNm US55, 14 Avenue de l'Hôpital, 45100, Orléans, France; University Hospital Center of Orleans, Genetic Department, 14 Avenue de l'Hôpital, 45100, Orléans, France.
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Akaike T, Morita M, Ogata S, Yoshitake J, Jung M, Sekine H, Motohashi H, Barayeu U, Matsunaga T. New aspects of redox signaling mediated by supersulfides in health and disease. Free Radic Biol Med 2024; 222:539-551. [PMID: 38992395 DOI: 10.1016/j.freeradbiomed.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Oxygen molecules accept electrons from the respiratory chain in the mitochondria and are responsible for energy production in aerobic organisms. The reactive oxygen species formed via these oxygen reduction processes undergo complicated electron transfer reactions with other biological substances, which leads to alterations in their physiological functions and cause diverse biological and pathophysiological consequences (e.g., oxidative stress). Oxygen accounts for only a small proportion of the redox reactions in organisms, especially under aerobic or hypoxic conditions but not under anaerobic and hypoxic conditions. This article discusses a completely new concept of redox biology, which is governed by redox-active supersulfides, i.e., sulfur-catenated molecular species. These species are present in abundance in all organisms but remain largely unexplored in terms of redox biology and life science research. In fact, accumulating evidence shows that supersulfides have extensive redox chemical properties and that they can be readily ionized or radicalized to participate in energy metabolism, redox signaling, and oxidative stress responses in cells and in vivo. Thus, pharmacological intervention and medicinal modulation of supersulfide activities have been shown to benefit the regulation of disease pathogenesis as well as disease control.
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Affiliation(s)
- Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan.
| | - Masanobu Morita
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Seiryo Ogata
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Jun Yoshitake
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Minkyung Jung
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Hiroki Sekine
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Hozumi Motohashi
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Uladzimir Barayeu
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan; Max-Planck-Institute for Polymer Research, Mainz, 55128, Germany.
| | - Tetsuro Matsunaga
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan; Center for Integrated Control, Epidemiology and Molecular Pathophysiology of Infectious Diseases, Akita University, Akita, 010-8543, Japan.
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Wang B, Mount S. Latent Dirichlet allocation mixture models for nucleotide sequence analysis. NAR Genom Bioinform 2024; 6:lqae099. [PMID: 39131816 PMCID: PMC11310860 DOI: 10.1093/nargab/lqae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 06/13/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024] Open
Abstract
Strings of nucleotides carrying biological information are typically described as sequence motifs represented by weight matrices or consensus sequences. However, many signals in DNA or RNA are recognized by multiple factors in temporal sequence, consist of distinct alternative motifs, or are best described by base composition. Here we apply the latent Dirichlet allocation (LDA) mixture model to nucleotide sequences. Using positions in an alignment of human or Drosophila splice sites as samples, we show that LDA readily identifies motifs, including such elusive cases as the intron branch site. Using whole sequences with positional k-mers as features, LDA can identify sequence subtypes enriched in long vs. short introns. LDA with bulk k-mers can reliably distinguish reading frame and species of origin in coding sequences from humans and Drosophila. We find that LDA is a useful model for describing heterogeneous signals, for assigning individual sequences to subtypes, and for identifying and characterizing sequences that do not fit recognized subtypes. Because LDA topic models are interpretable, they also aid the discovery of new motifs, even those present in a small fraction of samples. In summary, LDA can identify and characterize signals in nucleotide sequences, including candidate regulatory factors involved in biological processes.
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Affiliation(s)
- Bixuan Wang
- Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen M Mount
- Dept. of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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Li X, Chen L, Wang H, Li Y, Wu H, Guo F. Germacrone, isolated from Curcuma wenyujin, inhibits melanin synthesis through the regulation of the MAPK signaling pathway. J Nat Med 2024; 78:863-875. [PMID: 38809333 DOI: 10.1007/s11418-024-01818-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Abnormal melanin synthesis causes hyperpigmentation disorders, such as chloasma, freckles, and melanoma, which are highly multiple and prevalent. There were few reports on the anti-melanogenic effect of Curcuma wenyujin Y.H. Chen et C. Ling, and the bioactive compound has not been elucidated as well. The study aims to investigate the anti-melanogenic effect of C. wenyujin, and identify the bioactive compound, and further explore its underlying mechanism. Our results showed that the Petroleum ether fraction extracted from C. wenyujin rhizome had a significant anti-melanogenic effect, and germacrone isolated from it was confirmed as the major bioactive compound. To our data, germacrone significantly inhibited tyrosinase (TYR) activity, reduced melanosome synthesis, reduced dendrites formation of B16F10 cells, and melanosome transport to keratinocytes. Moreover, germacrone effectively decreased the hyperpigmentation in zebrafish and the skin of guinea pigs in vivo. Western-blot analysis showed that germacrone down-regulated the expression of TYR, TRP-1, TRP-2, Rab27a, Cdc42, and MITF proteins via the activation of the MAPK signaling pathway. Taken together, germacrone is an effective bioactive compound for melanogenesis inhibition. Our studies suggest that germacrone may be considered a potential candidate for skin whitening.
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Affiliation(s)
- Xiaoye Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Lijia Chen
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hong Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yiming Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Huali Wu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Fujiang Guo
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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Ferrari A, Pennestrì F, Bonciani M, Banfi G, Vainieri M, Tomaiuolo R. The role of patient-reported experiences in disclosing genetic prenatal testing: Findings from a large-scale survey on pregnant women. Eur J Obstet Gynecol Reprod Biol X 2024; 23:100327. [PMID: 39130210 PMCID: PMC11315116 DOI: 10.1016/j.eurox.2024.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024] Open
Abstract
Introduction Pregnant women can choose from different prenatal genetic tests throughout their maternity journey. We aim to investigate the clinical, societal, and economic determinants influencing the selection of different options (non-invasive, invasive, or both). Methods A systematic survey focusing on maternity pathways was launched by the Region of Tuscany, Italy, to collect data on pregnant women's experience, outcomes and satisfaction levels. Drawing from this survey, we retrospectively analyzed data on women who filled out the second-trimester questionnaire between March 2019 and February 2023 (n = 27,337), providing complete data on relevant variables. Logistic regression models were applied to identify the factors contributing to a higher likelihood of opting for non-invasive prenatal testing (NIPT) and invasive testing. Results Among the participants, 42.7 % chose only NIPT, 3.8 % opted for invasive tests exclusively, 1.3 % underwent both tests, and 52.2 % did not pursue any genetic testing. NIPT was more often chosen by older, Italian, highly educated, nulliparous women, who perceived better health, were employed (versus unemployed), had higher economic status, planned pregnancy, received hospital-based care (versus counseling center), under gynecologist supervision (versus midwife), not opted for combined testing and received pregnancy vaccinations. Conversely, invasive testing was more prevalent among older women but less common among those who were nulliparous, had Italian nationality, and had a perceived better health status. This group also tended to experience unplanned and high-risk pregnancy, did not take folate during pregnancy, received public hospital-based assistance, less frequently chose combined tests or NIPT, and had frequent delays in examinations. Conclusions Various factors beyond clinical considerations influence the selection of a prenatal test. Therefore, NIPT pathways should include balanced, high-quality information about benefits and limitations, ensuring laboratory specialists' active and integrated involvement in decision-making.
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Affiliation(s)
- Amerigo Ferrari
- Institute of Management, MeS (Management and Health) Laboratory, Scuola Superiore Sant’Anna, Pisa, Italy
- Department of Clinical and Experimental Medicine, Division of Obstetrics and Gynecology, University of Pisa, Pisa, Italy
| | | | - Manila Bonciani
- Institute of Management, MeS (Management and Health) Laboratory, Scuola Superiore Sant’Anna, Pisa, Italy
- Meyer Center for Health and Happiness, A. Meyer Children's Hospital, Florence, Italy
| | - Giuseppe Banfi
- IRCCS Ospedale Galeazzi Sant’Ambrogio, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Milena Vainieri
- Institute of Management, MeS (Management and Health) Laboratory, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Rossella Tomaiuolo
- IRCCS Ospedale Galeazzi Sant’Ambrogio, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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Herrera-Luis E, Martin-Almeida M, Pino-Yanes M. Asthma-Genomic Advances Toward Risk Prediction. Clin Chest Med 2024; 45:599-610. [PMID: 39069324 PMCID: PMC11284279 DOI: 10.1016/j.ccm.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Asthma is a common complex airway disease whose prediction of disease risk and most severe outcomes is crucial in clinical practice for adequate clinical management. This review discusses the latest findings in asthma genomics and current obstacles faced in moving forward to translational medicine. While genome-wide association studies have provided valuable insights into the genetic basis of asthma, there are challenges that must be addressed to improve disease prediction, such as the need for diverse representation, the functional characterization of genetic variants identified, variant selection for genetic testing, and refining prediction models using polygenic risk scores.
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Affiliation(s)
- Esther Herrera-Luis
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205, USA.
| | - Mario Martin-Almeida
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez, s/n. Facultad de Ciencias, San Cristóbal de La Laguna, S/C de Tenerife La Laguna 38200, Tenerife, Spain
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), Avenida Astrofísico Francisco Sánchez, s/n. Facultad de Ciencias, San Cristóbal de La Laguna, S/C de Tenerife La Laguna 38200, Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain; Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), San Cristóbal de La Laguna 38200, Tenerife, Spain
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LoPresti M, Igarashi A, Sonohara Y, Bowditch S. The emotional burden of caring for patients with Lennox-Gastaut syndrome, Dravet syndrome, and tuberous sclerosis complex-associated epilepsy: A qualitative study in Japan. Epilepsy Behav 2024; 158:109932. [PMID: 39029305 DOI: 10.1016/j.yebeh.2024.109932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 06/05/2024] [Accepted: 06/29/2024] [Indexed: 07/21/2024]
Abstract
INTRODUCTION Lennox-Gastaut syndrome (LGS) and Dravet syndrome (DS) are rare, childhood-onset conditions associated with severe, treatment-resistant epilepsy and developmental issues, including motor and cognitive impairment. Tuberous sclerosis complex (TSC) is a rare genetic disease commonly associated with epilepsy and other neuropsychiatric disorders. This cross-sectional, interview-based study examined the qualitative impact of caring for patients with LGS, DS, and TSC-associated epilepsy on caregivers in Japan, from the perspective of both caregivers and physicians. METHODS The survey included a pre-interview worksheet to describe caregivers' emotional journeys, followed by a ≤ 60-minute one-on-one interview. Eligible participants were Japanese caregivers of patients with LGS, DS, or TSC treated for epilepsy symptoms, and Japan-residing pediatricians or neurologists treating ≥ 3 patients with LGS, DS, and/or TSC. Interview question responses were subjected to content analysis to identify the most common response tendencies and themes. RESULTS Twenty-six caregivers responded (mean [standard deviation (SD)] age, 45.9 [9.5] years; age range 29-68; 92 % female), caring for patients with LGS (n = 5), DS (n = 10), and TSC (n = 11); patient mean (SD) age, 13.6 (10.0) years; age range 2-44; 27 % adults; 50 % female. Nineteen physicians, treating patients with LGS (n = 9), DS (n = 7), and TSC (n = 10), participated. Caregivers and physicians generally aligned on the factors affecting caregivers' emotional states / quality of life (QoL). The most frequently reported caregiver emotions at the time of diagnosis were shock and discouragement, anxiety for the future, and relief at receiving a diagnosis. Negative emotions throughout disease progression up until the time of survey were mainly caused by worsening of seizures, burden of constant caregiving / lack of free time, and patient's developmental issues. Positive emotions were linked to effective treatment / reduced seizures; more free time owing to the use of facilities, services, or other caregiving support; and developmental progress. Physicians acknowledged that caregivers required consultation services to support their emotional needs. In terms of unmet needs, caregiver and physician responses were aligned on the insufficient availability of services/facilities, the lack of effective treatments, and the uncertainties of adult patient care. CONCLUSIONS Caregivers of patients with LGS, DS, or TSC-associated epilepsy in Japan reported a high degree of emotional burden related to frequent seizures, developmental issues, and constant caregiving. The burden of suboptimal treatment effectiveness, limited access to support services, and uncertainties in long-term care emphasize important unmet treatment needs.
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Affiliation(s)
- Michael LoPresti
- Value & Access Department, INTAGE Healthcare Inc., Ochanomizu Sola City 13F Kanda Surugadai 4-6 Chiyoda-ku, Tokyo 101-0062, Japan.
| | - Ataru Igarashi
- Department of Public Health, School of Medicine, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan; Department of Health Economics and Outcomes Research, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yaoki Sonohara
- Value & Access Department, INTAGE Healthcare Inc., Ochanomizu Sola City 13F Kanda Surugadai 4-6 Chiyoda-ku, Tokyo 101-0062, Japan.
| | - Sally Bowditch
- Department of Patient Access and Value, Jazz Pharmaceuticals UK Ltd., Spires House, 5700 John Smith Drive, Oxford Business Park, South, Oxford OX4 2RW, UK.
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Azhuvalappil S, Prasad R, Sahadevan P, Chatterjee P, Pradhan H, Rai P, Gupta A, Kommaddi RP, Issac TG, Sundarakumar JS. Association between APOE genotypes and metabolic syndrome in a middle aged and elderly Urban South Indian population. Metabol Open 2024; 23:100301. [PMID: 39148663 PMCID: PMC11325077 DOI: 10.1016/j.metop.2024.100301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 08/17/2024] Open
Abstract
Background This study examines the association between apolipoprotein E (APOE) genotypes and metabolic syndrome (MetS) in an older urban population in South India, as part of the Tata Longitudinal Study on Aging. Methods A total of 618 participants aged 45 and above were analyzed cross-sectionally for the association between APOE carrier status and MetS (based on both NCEP ATP III and Consensus criteria). Results Despite the high prevalence of MetS observed in this cohort (51.62 % by NCEP-ATP III and 61.33 % by Consensus criteria), multivariable logistic regression revealed no significant association between APOE genotypes and MetS under both criteria. However, specific associations were noted in age and sex-stratified analyses; notably, E2 carriers under 60 showed 0.42-fold decreased odds (95%CI:0.20,0.89, p-value-0.023) for an increased waist circumference, and E4 carriers above 60 were at 1.85 times increased odds (95 % CI:1.04,3.28, p-value<0.05) for decreased HDL. Conclusion These findings suggest that while APOE genotypes influence certain metabolic parameters, their impact on MetS may be limited in this urban setting, possibly overshadowed by environmental factors and lifestyle influences, which was highlighted by the differences seen in its sister rural cohort.
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Affiliation(s)
- Shilna Azhuvalappil
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
- Indian Institute of Science Education and Research (IISER), Kolkata, 741246, India
| | - Raghav Prasad
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
| | - Pravin Sahadevan
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
- Department of Biostatistics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore, India
| | - Priya Chatterjee
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
| | - Hitesh Pradhan
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
| | - Pooja Rai
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
| | - Anant Gupta
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
- Manipal Academy of Higher Education, Manipal, India
| | - Reddy Peera Kommaddi
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
| | - Thomas G Issac
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
| | - Jonas S Sundarakumar
- Centre for Brain Research, Indian Institute of Science, Bangalore, 560012, India
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50
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Bai S, Wang G, Song R, Liu Y, Hua L, Yang J, Zhang L, Ur Rehman S, Hao X, Hou L, Zhang C, Li H, Liang Y, Zhao L, Xue Y, Wang Z, Chen S. Mutations in wheat TaAPA2 gene result in pleiotropic effects on plant architecture. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2039-2042. [PMID: 38842650 DOI: 10.1007/s11427-024-2620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Affiliation(s)
- Shengsheng Bai
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Rui Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Yanna Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Jinwei Yang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Lijun Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Shams Ur Rehman
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Xiaohua Hao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Lifeng Hou
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Chaozhong Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Yanyan Liang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Lihua Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Yan Xue
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China
| | - Zheng Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, China.
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