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Chrószcz M, Hajto J, Misiołek K, Szumiec Ł, Ziemiańska M, Radlicka-Borysewska A, Borczyk M, Zięba M, Gołda S, Siwiec M, Ziółkowska B, Piechota M, Korostyński M, Rodriguez Parkitna J. μ-Opioid receptor transcriptional variants in the murine forebrain and spinal cord. Gene 2025; 932:148890. [PMID: 39187136 DOI: 10.1016/j.gene.2024.148890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/14/2024] [Accepted: 08/22/2024] [Indexed: 08/28/2024]
Abstract
Oprm1, the gene encoding the μ-opioid receptor, has multiple reported transcripts, with a variable 3' region and many alternative sequences encoding the C-terminus of the protein. The functional implications of this variability remain mostly unexplored, though a recurring notion is that it could be exploited by developing selective ligands with improved clinical profiles. Here, we comprehensively examined Oprm1 transcriptional variants in the murine central nervous system, using long-read RNAseq as well as spatial and single-cell transcriptomics. The results were validated with RNAscope in situ hybridization. We found a mismatch between transcripts annotated in the mouse genome (GRCm38/mm10) and the RNA-seq results. Sequencing data indicated that the primary Oprm1 transcript has a 3' terminus located on chr10:6,860,027, which is ∼ 9.5 kilobases downstream of the longest annotated exon 4 end. Long-read sequencing confirmed that the final Oprm1 exon included a 10.2 kilobase long 3' untranslated region, and the presence of the long variant was unambiguously confirmed using RNAscope in situ hybridization in the thalamus, striatum, cortex and spinal cord. Conversely, expression of the Oprm1 reference transcript or alternative transcripts of the Oprm1 gene was absent or close to the detection limit. Thus, the primary transcript of the Oprm1 mouse gene is a variant with a long 3' untranslated region, which is homologous to the human OPRM1 primary transcript and encodes the same conserved C-terminal amino acid sequence.
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Affiliation(s)
- Magdalena Chrószcz
- Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Jacek Hajto
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Klaudia Misiołek
- Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Łukasz Szumiec
- Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Magdalena Ziemiańska
- Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Anna Radlicka-Borysewska
- Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Małgorzata Borczyk
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Mateusz Zięba
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Sławomir Gołda
- Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Marcin Siwiec
- Department of Physiology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Barbara Ziółkowska
- Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Marcin Piechota
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Michał Korostyński
- Laboratory of Pharmacogenomics, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland
| | - Jan Rodriguez Parkitna
- Department of Molecular Neuropharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, Krakow, Poland.
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2
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Diamantopoulos MA, Adamopoulos PG, Tsiakanikas P, Nisotakis T, Skourou PC, Scorilas A. Unraveling novel mRNA transcripts of the human DNA N-glycosylase 1 (NTHL1) gene with the implementation of an innovative targeted DNA-seq assay. Gene 2024; 930:148856. [PMID: 39147115 DOI: 10.1016/j.gene.2024.148856] [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: 02/15/2024] [Revised: 07/13/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
The human NTHL1 gene encodes a DNA glycosylase that plays a key role in the base excision repair (BER) pathway, repairing oxidative DNA damage and maintaining genome integrity. The physiological activity of NTHL1 is crucial in preventing genetic alterations that can lead to cancer. In this study, we employed an innovative targeted DNA sequencing (DNA-seq) methodology to explore the transcriptional landscape of the NTHL1 gene, revealing previously uncharacterized alternative splicing events and novel exons. Our designed approach provided significantly improved sequencing depth and coverage, enabling the identification of novel NTHL1 mRNA transcripts. Bioinformatics analysis confirmed all annotated splice junctions of the main NTHL1 transcripts (v.1 - v.3) and revealed novel mRNA transcripts (NTHL1 v.4 - v.9) derived from splicing events between annotated exons as well as mRNAs containing previously uncharacterized exons (NTHL1 v.10 - v.14). Quantitative PCR analysis highlighted a diverse expression pattern of these novel transcripts across different human cell lines, suggesting cell-specific roles and regulatory mechanisms. Notably, NTHL1 v.5 was overexpressed in luminal A breast cancer cells (MCF-7), while v.13 was prominent in triple negative (BT-20), HER2 + breast cancer (SK-BR-3), prostate, colorectal cancer cells and HEK-293 cells. Our findings suggest that specific novel NTHL1 transcripts may encode protein isoforms with distinct structural features, as indicated by ribosome profiling datasets, while others containing premature termination codons could function as long non-coding RNAs. These insights enhance our understanding of NTHL1 regulatory role and its potential as a biomarker and therapeutic target in human malignancies. This study underscores the importance of exploring the transcriptional diversity of NTHL1 to fully elucidate its role in cancer pathobiology.
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Affiliation(s)
- Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Tsiakanikas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Theodoros Nisotakis
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Paraskevi C Skourou
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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3
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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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4
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Nichols RA, Ide AD, Morrison CT, Anger AL, Buccilli MJ, Damer CK. Copine C plays a role in adhesion and streaming in Dictyostelium. Cell Adh Migr 2024; 18:1-19. [PMID: 38378453 PMCID: PMC10880500 DOI: 10.1080/19336918.2024.2315629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
Copines are a family of calcium-dependent membrane-binding proteins. To study these proteins, anull mutant for cpnC was created in Dictyostelium, which has six copines genes (cpnA-cpnF). During development, cpnC- cells were able to aggregate, but did not form streams. Once aggregated into mounds, they formed large ring structures. cpnC- cells were less adherent to plastic substrates, but more adherent to other cells. These phenotypes correlated with changes in adhesion protein expression with decreased expression of SibA and increased expression of CsaA in developing cpnC- cells. We also measured the expression of RegA, a cAMP phosphodiesterase, and found that cpnC- cells have reduced RegA expression. The reduced RegA expression in cpnC- cells is most likely responsible for the observed phenotypes.
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Affiliation(s)
- Rodney A. Nichols
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Amber D. Ide
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Cody T. Morrison
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | - Amber L. Anger
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| | | | - Cynthia K. Damer
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
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5
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Yao XQ, Chen JY, Garcia-Segura ME, Wen ZH, Yu ZH, Huang ZC, Hamel R, Liu JH, Shen X, Huang ZP, Lu YM, Zhou ZT, Liu CT, Shi JM, Zhu QA, Peruzzotti-Jametti L, Chen JT. Integrated multi-omics analysis reveals molecular changes associated with chronic lipid accumulation following contusive spinal cord injury. Exp Neurol 2024; 380:114909. [PMID: 39097074 DOI: 10.1016/j.expneurol.2024.114909] [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: 05/09/2024] [Revised: 06/23/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
Functional and pathological recovery after spinal cord injury (SCI) is often incomplete due to the limited regenerative capacity of the central nervous system (CNS), which is further impaired by several mechanisms that sustain tissue damage. Among these, the chronic activation of immune cells can cause a persistent state of local CNS inflammation and damage. However, the mechanisms that sustain this persistent maladaptive immune response in SCI have not been fully clarified yet. In this study, we integrated histological analyses with proteomic, lipidomic, transcriptomic, and epitranscriptomic approaches to study the pathological and molecular alterations that develop in a mouse model of cervical spinal cord hemicontusion. We found significant pathological alterations of the lesion rim with myelin damage and axonal loss that persisted throughout the late chronic phase of SCI. This was coupled by a progressive lipid accumulation in myeloid cells, including resident microglia and infiltrating monocyte-derived macrophages. At tissue level, we found significant changes of proteins indicative of glycolytic, tricarboxylic acid cycle (TCA), and fatty acid metabolic pathways with an accumulation of triacylglycerides with C16:0 fatty acyl chains in chronic SCI. Following transcriptomic, proteomic, and epitranscriptomic studies identified an increase of cholesterol and m6A methylation in lipid-droplet-accumulating myeloid cells as a core feature of chronic SCI. By characterizing the multiple metabolic pathways altered in SCI, our work highlights a key role of lipid metabolism in the chronic response of the immune and central nervous system to damage.
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Affiliation(s)
- Xin-Qiang Yao
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Ying Chen
- Comprehensive Medical Treatment Ward, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Monica Emili Garcia-Segura
- Department of Metabolism, Digestion and Reproduction, Imperial College London, United Kingdom; Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Zi-Han Wen
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zi-Han Yu
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zu-Cheng Huang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Regan Hamel
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jun-Hao Liu
- Division of Spine Surgery, Department of Orthopaedics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
| | - Xing Shen
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Ping Huang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan-Meng Lu
- Central Laboratory, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Tao Zhou
- Central Laboratory, Southern Medical University, Guangzhou, Guangdong, China
| | - Cui-Ting Liu
- Central Laboratory, Southern Medical University, Guangzhou, Guangdong, China
| | - Jun-Min Shi
- Central Laboratory, Southern Medical University, Guangzhou, Guangdong, China
| | - Qing-An Zhu
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Luca Peruzzotti-Jametti
- Department of Metabolism, Digestion and Reproduction, Imperial College London, United Kingdom; Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jian-Ting Chen
- Division of Spine Surgery, Department of Orthopaedics, Nanfang hospital, Southern Medical University, Guangzhou, Guangdong, China.
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6
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Giatti S, Cioffi L, Diviccaro S, Piazza R, Melcangi RC. Analysis of the finasteride treatment and its withdrawal in the rat hypothalamus and hippocampus at whole-transcriptome level. J Endocrinol Invest 2024; 47:2565-2574. [PMID: 38493246 PMCID: PMC11393021 DOI: 10.1007/s40618-024-02345-y] [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: 11/23/2023] [Accepted: 02/18/2024] [Indexed: 03/18/2024]
Abstract
PURPOSE As reported in patients treated for androgenetic alopecia with finasteride (i.e., a blocker of the enzyme 5 alpha-reductase) and in an animal model, side effects affecting sexual, psychiatric, neurological, and physical domains, may occur during the treatment and persist with drug suspension. The etiopathogenesis of these side effects has been poorly explored. Therefore, we performed a genome-wide analysis of finasteride effects in the brain of adult male rat. METHODS Animals were treated (i.e., for 20 days) with finasteride (1mg/rat/day). 24 h after the last treatment and 1 month after drug suspension, RNA sequencing analysis was performed in hypothalamus and hippocampus. Data were analyzed by differential expression analysis and Gene-Set Enrichment Analyses (GSEA). RESULTS Data obtained after finasteride treatment showed that 186 genes (i.e., 171 up- and 15 downregulated) and 19 (i.e., 17 up- and 2 downregulated) were differentially expressed in the hypothalamus and hippocampus, respectively. Differential expression analysis at the drug withdrawal failed to identify dysregulated genes. Several gene-sets were enriched in these brain areas at both time points. CONCLUSION Some of the genes reported to be differentially expressed (i.e., TTR, DIO2, CLDN1, CLDN2, SLC4A5, KCNE2, CROT, HCRT, MARCKSL1, VGF, IRF2BPL) and GSEA, suggest a potential link with specific side effects previously observed in patients and in the animal model, such as depression, anxiety, disturbance in memory and attention, and sleep disturbance. These data may provide an important background for future experiments aimed at confirming the pathological role of these genes.
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Affiliation(s)
- S Giatti
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - L Cioffi
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - S Diviccaro
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy
| | - R Piazza
- Dipartimento di Medicina e Chirurgia, Università di Milano-Bicocca, Milan, Italy
| | - R C Melcangi
- Dipartimento di Scienze Farmacologiche e Biomolecolari "Rodolfo Paoletti", Università degli Studi di Milano, Via Balzaretti 9, 20133, Milan, Italy.
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7
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Kumar KR, Cowley MJ, Davis RL. Next-Generation Sequencing and Emerging Technologies. Semin Thromb Hemost 2024; 50:1026-1038. [PMID: 38692283 DOI: 10.1055/s-0044-1786397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.
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Affiliation(s)
- Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, Australia
| | - Mark J Cowley
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Computational Biology Group, Children's Cancer Institute, University of New South Wales, Randwick, New South Wales, Australia
| | - Ryan L Davis
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
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8
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Chapus F, Giraud G, Huchon P, Rodà M, Grand X, Charre C, Goldsmith C, Roca Suarez AA, Martinez MG, Fresquet J, Diederichs A, Locatelli M, Polvèche H, Scholtès C, Chemin I, Hernandez Vargas H, Rivoire M, Bourgeois CF, Zoulim F, Testoni B. Helicases DDX5 and DDX17 promote heterogeneity in HBV transcription termination in infected human hepatocytes. J Hepatol 2024; 81:609-620. [PMID: 38782119 DOI: 10.1016/j.jhep.2024.05.016] [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: 10/16/2023] [Revised: 03/28/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND & AIMS Transcription termination fine-tunes gene expression and contributes to the specification of RNA function in eukaryotic cells. Transcription termination of HBV is subject to the recognition of the canonical polyadenylation signal (cPAS) common to all viral transcripts. However, the regulation of this cPAS and its impact on viral gene expression and replication is currently unknown. METHODS To unravel the regulation of HBV transcript termination, we implemented a 3' RACE (rapid amplification of cDNA ends)-PCR assay coupled to single molecule sequencing both in in vitro-infected hepatocytes and in chronically infected patients. RESULTS The detection of a previously unidentified transcriptional readthrough indicated that the cPAS was not systematically recognized during HBV replication in vitro and in vivo. Gene expression downregulation experiments demonstrated a role for the RNA helicases DDX5 and DDX17 in promoting viral transcriptional readthrough, which was, in turn, associated with HBV RNA destabilization and decreased HBx protein expression. RNA and chromatin immunoprecipitation, together with mutation of the cPAS sequence, suggested a direct role of DDX5 and DDX17 in functionally linking cPAS recognition to transcriptional readthrough, HBV RNA stability and replication. CONCLUSIONS Our findings identify DDX5 and DDX17 as crucial determinants of HBV transcriptional fidelity and as host restriction factors for HBV replication. IMPACT AND IMPLICATIONS HBV covalently closed circular (ccc)DNA degradation or functional inactivation remains the holy grail for the achievement of HBV cure. Transcriptional fidelity is a cornerstone in the regulation of gene expression. Here, we demonstrate that two helicases, DDX5 and DDX17, inhibit recognition of the HBV polyadenylation signal and thereby transcriptional termination, thus decreasing HBV RNA stability and acting as restriction factors for efficient cccDNA transcription and viral replication. The observation that DDX5 and DDX17 are downregulated in patients chronically infected with HBV suggests a role for these helicases in HBV persistence in vivo. These results open new perspectives for researchers aiming at identifying new targets to neutralise cccDNA transcription.
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Affiliation(s)
- Fleur Chapus
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France
| | - Guillaume Giraud
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Pélagie Huchon
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Mélanie Rodà
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Xavier Grand
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Caroline Charre
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; Department of Virology, Croix Rousse Hospital, Hospices Civils de Lyon, Lyon, France
| | | | - Armando Andres Roca Suarez
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Maria-Guadalupe Martinez
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France
| | - Judith Fresquet
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - Audrey Diederichs
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Maëlle Locatelli
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France
| | - Hélène Polvèche
- CECS/AFM, I-Stem, Corbeil-Essonnes, 91100, France; University Claude Bernard of Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 69007, Lyon, France
| | - Caroline Scholtès
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; Department of Virology, Croix Rousse Hospital, Hospices Civils de Lyon, Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Isabelle Chemin
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | | | - Michel Rivoire
- INSERM U1032, Centre Léon Bérard (CLB), 69008 Lyon, France; The Lyon Hepatology Institute EVEREST, France
| | - Cyril F Bourgeois
- University Claude Bernard of Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 69007, Lyon, France
| | - Fabien Zoulim
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon, France; Department of Hepatology, Hospices Civils de Lyon, France; The Lyon Hepatology Institute EVEREST, France.
| | - Barbara Testoni
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France; The Lyon Hepatology Institute EVEREST, France.
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Abdelgawad A, Nascimento M, Prahl A, Flügger M, Szentiks CA, Holtze S, Hildebrandt TB, Trimpert J. Fatal infection caused by a genetically distinct elephant endotheliotropic herpesvirus type 5 in a captive Asian elephant in Germany. Virol J 2024; 21:221. [PMID: 39285293 PMCID: PMC11406788 DOI: 10.1186/s12985-024-02477-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
BACKGROUND Elephant endotheliotropic herpesvirus (EEHV) infection is the most common cause for lethal hemorrhagic disease in captive juvenile Asian elephants (Elephas maximus). Although EEHV1 is known as the most likely cause of fatal haemorrhagic disease in Asian elephants, EEHV5 was lately involved in lethal cases of haemorrhagic disease in captive elephants. CASE PRESENTATION Here we report the first death of a four-year old Asian elephant diagnosed with EEHV5 in Germany. Molecular diagnosis yielded detection of EEHV5 DNA in all tested tissues. Histopathological examination revealed typical features of hemorrhagic disease in all examined organs. EEHV5 was sequenced from total DNA isolated from heart tissue by Illumina and Nanopore sequencing. Sequencing data showed 3,881 variants, distributed across the entire genome, compared to the published EEHV5 sequence. CONCLUSIONS We have detected EEHV5 in a fatal disease case of a male Asian elephant. Whole genome sequencing revealed substantial differences of our DNA isolate compared to available EEHV5 sequences. This report of fatal haemorrhagic disease associated with EEHV5 infection should raise awareness for EEHV5 as an important elephant pathogen. Genome sequencing and downstream SNPs analysis will further encourage future research to understand genetic diversity, pathogenesis and virulence of EEHVs with respect to developing new diagnostic methods, prophylactic strategies, and implementation of surveillance and control measures.
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Affiliation(s)
- Azza Abdelgawad
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Mariana Nascimento
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Adriane Prahl
- Tierpark Hagenbeck Gem. GmbH, Lokstedter Grenzstraße 2, 22527, Hamburg, Germany
| | - Michael Flügger
- Tierpark Hagenbeck Gem. GmbH, Lokstedter Grenzstraße 2, 22527, Hamburg, Germany
| | - Claudia A Szentiks
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315, Berlin, Germany
| | - Susanne Holtze
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315, Berlin, Germany
| | - Thomas B Hildebrandt
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315, Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany.
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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10
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Pérez-Gómez A, González-Brusi L, Flores-Borobia I, Martínez De Los Reyes N, Toledano-Díaz A, López-Sebastián A, Santiago Moreno J, Ramos-Ibeas P, Bermejo-Álvarez P. PPARG is dispensable for bovine embryo development up to tubular stages†. Biol Reprod 2024; 111:557-566. [PMID: 38832705 PMCID: PMC11402522 DOI: 10.1093/biolre/ioae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/25/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024] Open
Abstract
Following blastocyst hatching, ungulate embryos undergo a prolonged preimplantation period termed conceptus elongation. Conceptus elongation constitutes a highly susceptible period for embryonic loss, and the embryonic requirements during this process are largely unknown, but multiple lipid compounds have been identified in the fluid nourishing the elongating conceptuses. Peroxisome proliferator-activated receptors mediate the signaling actions of prostaglandins and other lipids, and, between them, PPARG has been pointed out to play a relevant role in conceptus elongation by a functional study that depleted PPARG in both uterus and conceptus. The objective of this study has been to determine if embryonic PPARG is required for bovine embryo development. To that aim, we have generated bovine PPARG knock-out embryos in vitro using two independent gene ablation strategies and assessed their developmental ability. In vitro development to Day 8 blastocyst was unaffected by PPARG ablation, as total, inner cell mass, and trophectoderm cell numbers were similar between wild-type and knock-out D8 embryos. In vitro post-hatching development to D12 was also comparable between different genotypes, as embryo diameter, epiblast cell number, embryonic disk formation, and hypoblast migration rates were unaffected by the ablation. The development of tubular stages equivalent to E14 was assessed in vivo, following a heterologous embryo transfer experiment, observing that the development of extra-embryonic membranes and of the embryonic disk was not altered by PPARG ablation. In conclusion, PPARG ablation did not impaired bovine embryo development up to tubular stages.
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Affiliation(s)
- Alba Pérez-Gómez
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Leopoldo González-Brusi
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Inés Flores-Borobia
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Nuria Martínez De Los Reyes
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Adolfo Toledano-Díaz
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Antonio López-Sebastián
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Julián Santiago Moreno
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Priscila Ramos-Ibeas
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pablo Bermejo-Álvarez
- Animal Reproduction Department, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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11
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Fang J, Lin A, Yan H, Feng L, Lin S, Mason P, Zhou L, Xu X, Zhao K, Huang Y, Henry RJ. Cytoplasmic genomes of Jasminum sambac reveal divergent sub-mitogenomic conformations and a large nuclear chloroplast-derived insertion. BMC PLANT BIOLOGY 2024; 24:861. [PMID: 39272034 PMCID: PMC11401388 DOI: 10.1186/s12870-024-05557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND Jasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal ("SP"), double-petal ("DP"), and multi-petal ("MP"). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions. RESULTS Here, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, "SP", "DP", and "MP-hutou" ("HT"), with PacBio reads and the "HT" chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in "HT". We identified a 14.3 kb "HT"-specific insertion on Chr7 of the "HT" nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that "DP" and "HT" evolved from "SP", with "HT" being the most recent derivative of "DP". CONCLUSION The comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.
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Affiliation(s)
- Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, China.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
| | - Aiting Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hansong Yan
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, China
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Patrick Mason
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Linwei Zhou
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Xiuming Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Zhao
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yongji Huang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China.
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
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12
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Laflamme N, Triassi V, Martineau L, Toffa DH, Létourneau-Guillon L, Laplante A, Cossette P, Samarut É, Tétreault M, Nguyen DK. X-Linked Bilateral Polymicrogyria With Epilepsy and Intellectual Disability Associated With a Novel KIF4A Variant. Am J Med Genet A 2024:e63860. [PMID: 39268972 DOI: 10.1002/ajmg.a.63860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 07/19/2024] [Accepted: 08/18/2024] [Indexed: 09/15/2024]
Abstract
We studied three brothers and a maternal half-brother featuring global developmental delay, mild to moderate intellectual disability, epilepsy, microcephaly, and strabismus. All had bilateral perisylvian and perirolandic polymicrogyria, while some also had malformations of the hippocampus (malrotation and dysplasia), cerebellum (heterotopias and asymmetric aplasia), corpus callosum dysgenesis, and brainstem asymmetric dysplasia. Exome sequencing showed that all four patients had a novel variant (c.1597C>T:p.Leu533Phe) on the KIF4A gene on chromosome X. We discuss how this variant is possibly pathogenic and could explain the reported phenotype.
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Affiliation(s)
- Naomi Laflamme
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Valérie Triassi
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
- Bioinformatics Program, Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Laurence Martineau
- Neurology Division, Centre Hospitalier Universitaire de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Dènahin Hinnoutondji Toffa
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
| | | | - Annie Laplante
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Patrick Cossette
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
- Division of Radiology, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada
| | - Éric Samarut
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
| | - Martine Tétreault
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
| | - Dang Khoa Nguyen
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Université de Montréal, Montreal, Quebec, Canada
- Neurology Division, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada
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13
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Cheah HL, Citartan M, Lee LP, Ahmed SA, Salleh MZ, Teh LK, Tang TH. Exploring the transcription start sites and other genomic features facilitates the accurate identification and annotation of small RNAs across multiple stress conditions in Mycobacterium tuberculosis. Funct Integr Genomics 2024; 24:160. [PMID: 39264475 DOI: 10.1007/s10142-024-01437-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024]
Abstract
Mycobacterium tuberculosis (MTB) is a pathogen that is known for its ability to persist in harsh environments and cause chronic infections. Understanding the regulatory networks of MTB is crucial for developing effective treatments. Small regulatory RNAs (sRNAs) play important roles in gene expression regulation in all kingdoms of life, and their classification based solely on genomic location can be imprecise due to the computational-based prediction of protein-coding genes in bacteria, which often neglects segments of mRNA such as 5'UTRs, 3'UTRs, and intercistronic regions of operons. To address this issue, our study simultaneously discovered genomic features such as TSSs, UTRs, and operons together with sRNAs in the M. tuberculosis H37Rv strain (ATCC 27294) across multiple stress conditions. Our analysis identified 1,376 sRNA candidates and 8,173 TSSs in MTB, providing valuable insights into its complex regulatory landscape. TSS mapping enabled us to classify these sRNAs into more specific categories, including promoter-associated sRNAs, 5'UTR-derived sRNAs, 3'UTR-derived sRNAs, true intergenic sRNAs, and antisense sRNAs. Three of these sRNA candidates were experimentally validated using 3'-RACE-PCR: predictedRNA_0240, predictedRNA_0325, and predictedRNA_0578. Future characterization and validation are necessary to fully elucidate the functions and roles of these sRNAs in MTB. Our study is the first to simultaneously unravel TSSs and sRNAs in MTB and demonstrate that the identification of other genomic features, such as TSSs, UTRs, and operons, allows for more accurate and specific classification of sRNAs.
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Affiliation(s)
- Hong-Leong Cheah
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
- Monash University Malaysia Genomics Platform, School of Science, Monash University Malaysia, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia
| | - Marimuthu Citartan
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Li-Pin Lee
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Siti Aminah Ahmed
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM) Selangor, Bandar Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM) Selangor, Bandar Puncak Alam, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM) Selangor, Bandar Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM) Selangor, Bandar Puncak Alam, Selangor, Malaysia
| | - Thean-Hock Tang
- Advanced Medical and Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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14
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Martim DB, Brilhante AJVC, Lima AR, Paixão DAA, Martins-Junior J, Kashiwagi FM, Wolf LD, Costa MS, Menezes FF, Prata R, Gazolla MC, Aricetti JA, Persinoti GF, Rocha GJM, Giuseppe PO. Resolving the metabolism of monolignols and other lignin-related aromatic compounds in Xanthomonas citri. Nat Commun 2024; 15:7994. [PMID: 39266555 PMCID: PMC11393088 DOI: 10.1038/s41467-024-52367-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 09/03/2024] [Indexed: 09/14/2024] Open
Abstract
Lignin, a major plant cell wall component, has an important role in plant-defense mechanisms against pathogens and is a promising renewable carbon source to produce bio-based chemicals. However, our understanding of microbial metabolism is incomplete regarding certain lignin-related compounds like p-coumaryl and sinapyl alcohols. Here, we reveal peripheral pathways for the catabolism of the three main lignin precursors (p-coumaryl, coniferyl, and sinapyl alcohols) in the plant pathogen Xanthomonas citri. Our study demonstrates all the necessary enzymatic steps for funneling these monolignols into the tricarboxylic acid cycle, concurrently uncovering aryl aldehyde reductases that likely protect the pathogen from aldehydes toxicity. It also shows that lignin-related aromatic compounds activate transcriptional responses related to chemotaxis and flagellar-dependent motility, which might play an important role during plant infection. Together our findings provide foundational knowledge to support biotechnological advances for both plant diseases treatments and conversion of lignin-derived compounds into bio-based chemicals.
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Affiliation(s)
- Damaris B Martim
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Anna J V C Brilhante
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Augusto R Lima
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Douglas A A Paixão
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Joaquim Martins-Junior
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Fernanda M Kashiwagi
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Lucia D Wolf
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Mariany S Costa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Fabrícia F Menezes
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Rafaela Prata
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Matheus C Gazolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Juliana A Aricetti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - George J M Rocha
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Priscila O Giuseppe
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil.
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15
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Du P, Zhu K, Wang M, Sun Z, Tan J, Sun B, Sun B, Wang P, He G, Xiong J, Huang Z, Meng H, Sun C, Xie S, Wang B, Ge D, Ma Y, Sheng P, Ren X, Tao Y, Xu Y, Qin X, Allen E, Zhang B, Chang X, Wang K, Bao H, Yu Y, Wang L, Ma X, Du Z, Guo J, Yang X, Wang R, Ma H, Li D, Pan Y, Li B, Zhang Y, Zheng X, Han S, Jin L, Chen G, Li H, Wang CC, Wen S. Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic. Curr Biol 2024; 34:3996-4006.e11. [PMID: 39146937 DOI: 10.1016/j.cub.2024.07.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/05/2024] [Accepted: 07/17/2024] [Indexed: 08/17/2024]
Abstract
The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities.
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Affiliation(s)
- Panxin Du
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Minghui Wang
- Institute of Archaeology, Academy of Social Sciences, Beijing 100101, China
| | | | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Bo Sun
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Bo Sun
- Linyi Museum, Linyi 276000, China
| | | | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China; Center for Archaeological Science, Sichuan University, Chengdu 610000, China
| | - Jianxue Xiong
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Zixiao Huang
- Department of History, Fudan University, Shanghai 200433, China
| | - Hailiang Meng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chang Sun
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Shouhua Xie
- Department of History, Fudan University, Shanghai 200433, China
| | - Bangyan Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Dong Ge
- Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, Shanghai 200041, China
| | | | - Pengfei Sheng
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Xiaoying Ren
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Yichen Tao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Xiaoli Qin
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Edward Allen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Baoshuai Zhang
- USTC Archaeometry Laboratory, University of Science and Technology of China, Hefei 230026, China
| | - Xin Chang
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Ke Wang
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Haoquan Bao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yao Yu
- Department of History, Fudan University, Shanghai 200433, China
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China
| | - Xiaolin Ma
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Zhenyuan Du
- Shandong Provincial Institute of Cultural Relics and Archaeology, Jinan 250012, China
| | - Jianxin Guo
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Xiaomin Yang
- Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hao Ma
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Dapeng Li
- Yantai Municipal Museum, Yantai 264001, China
| | - Yiling Pan
- Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, Shanghai 200041, China
| | - Bicheng Li
- Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, Shanghai 200041, China
| | - Yunfei Zhang
- Shanghai Natural History Museum, Branch of the Shanghai Science & Technology Museum, Shanghai 200041, China
| | - Xiaoqu Zheng
- School of Cultural Heritage and Information Management, Shanghai University, Shanghai 200444, China
| | - Sheng Han
- Department of History, Fudan University, Shanghai 200433, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Gang Chen
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha 410083, China.
| | - Hui Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China.
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, Fujian Provincial Key Laboratory of Philosophy and Social Sciences in Bioanthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China; Center for the Belt and Road Archaeology and Ancient Civilizations, Shanghai 200433, China.
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16
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Tian Y, Zhang C, Tian X, Zhang L, Yin T, Dang Y, Liu Y, Lou H, He Q. H3T11 phosphorylation by CKII is required for heterochromatin formation in Neurospora. Nucleic Acids Res 2024; 52:9536-9550. [PMID: 39106166 PMCID: PMC11381320 DOI: 10.1093/nar/gkae664] [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: 01/30/2024] [Revised: 06/19/2024] [Accepted: 07/22/2024] [Indexed: 08/09/2024] Open
Abstract
Heterochromatin is a key feature of eukaryotic genomes and is crucial for maintaining genomic stability. In fission yeast, heterochromatin nucleation is mainly mediated by DNA-binding proteins or the RNA interference (RNAi) pathway. In the filamentous fungus Neurospora crassa, however, the mechanism that causes the initiation of heterochromatin at the relics of repeat-induced point mutation is unknown and independent of the classical RNAi pathway. Here, we show that casein kinase II (CKII) and its kinase activity are required for heterochromatin formation at the well-defined 5-kb heterochromatin of the 5H-cat-3 region and transcriptional repression of its adjacent cat-3 gene. Similarly, mutation of the histone H3 phosphorylation site T11 also impairs heterochromatin formation at the same locus. The catalytic subunit CKA colocalizes with H3T11 phosphorylation (H3pT11) within the 5H-cat-3 domain and the deletion of cka results in a significant decrease in H3T11 phosphorylation. Furthermore, the loss of kinase activity of CKII results in a significant reduction of H3pT11, H3K9me3 (histone H3 lysine 9 trimethylation) and DNA methylation levels, suggesting that CKII regulates heterochromatin formation by promoting H3T11 phosphorylation. Together, our results establish that histone H3 phosphorylation by CKII is a critical event required for heterochromatin formation.
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Affiliation(s)
- Yuan Tian
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chengcheng Zhang
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiang Tian
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lu Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Tong Yin
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Huiqiang Lou
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qun He
- MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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17
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Li H, Li B, Liu Y, Yang F, Cao Y, Xie J, Liu X, Zhao Z, Li C. Characterization of sequence variations in the extended flanking regions using massively parallel sequencing in 21 A-STRs and 21 Y-STRs. BMC Genomics 2024; 25:841. [PMID: 39244600 PMCID: PMC11380771 DOI: 10.1186/s12864-024-10762-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024] Open
Abstract
In forensic genetics, utilizing massively parallel sequencing (MPS) to analyze short tandem repeats (STRs) has demonstrated several advantages compared to conventional capillary electrophoresis (CE). Due to the current technical limitations, although flanking region polymorphisms had been mentioned in several previous studies, most studies focused on the core repeat regions of STRs or the variations in the adjacent flanking regions. In this study, we developed an MPS system consisting of two sets of multiplex PCR systems to detect not only the STR core repeat regions but also to observe variants located at relatively distant positions in the flanking regions. The system contained 42 commonly used forensic STRs, including 21 autosomal STRs (A-STRs) and 21 Y-chromosomal STRs (Y-STRs), and a total of 350 male individuals from a Chinese Han population were genotyped. The length and sequence variants per locus were tallied and categorized based on length (length-based, LB), sequence without flanking region (core repeat regions sequence-based, RSB), and sequence with flanking region (core repeat and flanking regions sequence-based, FSB), respectively. Allele frequencies, Y-haplotype frequencies, and forensic parameters were calculated based on LB, RSB, and FSB, respectively, to evaluate the improvement in discrimination power, heterozygosity, and effectiveness of forensic systems. The results suggested the sequence variations have more influence on A-STRs and could improve the identification ability of MPS-STR genotyping. Concordance between MPS and CE methods was confirmed by using commercial CE-based STR kits. The impact of flanking region variations on STR genotype analysis and potential factors contributing to discordances were discussed. A total of 58 variations in the flanking regions (53 SNPs/SNVs and 5 InDels) were observed and most variations (48/58) were distributed in A-STRs. In summary, this study delved deeper into the genetic information of forensic commonly used STR and advanced the application of massively parallel sequencing in forensic genetics.
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Affiliation(s)
- Hui Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Beixu Li
- School of Policing Studies, Shanghai University of Political Science and Law, Shanghai, 201701, China
| | - Yanan Liu
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China
- Ministry of Education's Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Fan Yang
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai, 200083, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China
| | - Zhenmin Zhao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Key Laboratory of Forensic Science, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, China.
| | - Chengtao Li
- Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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18
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Ararat-Sarria M, Curtidor H, Patarroyo MA. Characterisation of the erythrocyte invasion phenotype of FCB-2: A South American P. falciparum reference strain. Acta Trop 2024; 260:107379. [PMID: 39245156 DOI: 10.1016/j.actatropica.2024.107379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/12/2024] [Accepted: 09/02/2024] [Indexed: 09/10/2024]
Abstract
The extent of parasite adaptive capability involved in erythrocyte invasion represents a significant challenge for the development of a Plasmodium falciparum vaccine. The parasite's geographical and populational origin may influence such adaptive behaviour; in vitro culture-adapted parasite strains are typically used for such studies. Previous studies have reported invasion phenotypes in strains from Africa and Asia and, to a lesser extent, from Latin America. This study was aimed at expanding the pool of characterised parasite strains from Latin America by describing the invasion phenotype of the P. falciparum Colombia Bogotá 2 (FCB2) strain. The FCB2 genome was sequenced and erythrocyte invasion ligand sequences were analysed and compared to other previously reported ones. RT-PCR was used for assessing Pfeba family erythrocyte invasion ligands and reticulocyte binding homologue (Pfrh) gene transcription. A flow cytometry-based erythrocyte invasion assay (using enzymatically-treated erythrocytes) was used for determining the FCB2 strain's invasion phenotype. The P. falciparum FCB2 genome sequence was analysed, bearing in mind that prolonged in vitro parasite culture may affect its genome sequence and, in some cases, lead to the deletion of certain genes; it was demonstrated that all erythrocyte invasion ligand gene sequences studied here were preserved. Comparative analysis showed that the target genome sequences were conserved whereas transcriptional analysis highlighted Pfebas and Pfrhs gene expression. Erythrocyte invasion analysis demonstrated that the FCB2 strain has a sialic acid-resistant invasion phenotype.
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Affiliation(s)
- Monica Ararat-Sarria
- Receptor-Ligand Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C. 111321, Colombia; PhD programme in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá D.C. 111221, Colombia; Health Sciences Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá D.C. 111166, Colombia.
| | - Hernando Curtidor
- The Vice-rector's Office for Research, Universidad ECCI, Bogotá D.C. 111311, Colombia.
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá D.C. 111321, Colombia; Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá D.C. 111321, Colombia.
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19
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Cardoso-Sichieri R, Oliveira LS, Lopes-Caitar VS, Silva DCGD, Lopes IDON, Oliveira MFD, Arias CA, Abdelnoor RV, Marcelino-Guimarães FC. Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by Xanthomonas citri pv. glycines in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:2484. [PMID: 39273969 PMCID: PMC11397087 DOI: 10.3390/plants13172484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024]
Abstract
Bacterial pustule (BP), caused by Xanthomonas citri pv. glycines, is an important disease that, under favorable conditions, can drastically affect soybean production. We performed a genome-wide association study (GWAS) with a panel containing Brazilian and American cultivars, which were screened qualitatively and quantitatively against two Brazilian X. citri isolates (IBS 333 and IBS 327). The panel was genotyped using a genotyping by sequencing (GBS) approach, and we identified two main new regions in soybeans associated with X. citri resistance on chromosomes 6 (IBS 333) and 18 (IBS 327), different from the traditional rxp gene located on chromosome 17. The region on chromosome 6 was also detected by QTL mapping using a biparental cross between Williams 82 (R) and PI 416937 (S), showing that Williams 82 has another recessive resistance gene besides rxp, which was also detected in nine BP-resistant ancestors of the Brazilian cultivars (including CNS, S-100), based on haplotype analysis. Furthermore, we identified additional SNPs in strong LD (0.8) with peak SNPs by exploring variation available in WGS (whole genome sequencing) data among 31 soybean accessions. In these regions in strong LD, two candidate resistance genes were identified (Glyma.06g311000 and Glyma.18g025100) for chromosomes 6 and 18, respectively. Therefore, our results allowed the identification of new chromosomal regions in soybeans associated with BP disease, which could be useful for marker-assisted selection and will enable a reduction in time and cost for the development of resistant cultivars.
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Affiliation(s)
- Rafaella Cardoso-Sichieri
- Center for Biological Sciences, Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina 86057-970, PR, Brazil
| | - Liliane Santana Oliveira
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Alberto Carazzai Avenue, 1640, Cornélio Procópio 86300-000, PR, Brazil
| | | | | | - Ivani de O N Lopes
- Brazilian Agricultural Research Corporation (Embrapa Soja), Carlos João Strass Road, Warta County 86085-981, PR, Brazil
| | - Marcelo Fernandes de Oliveira
- Brazilian Agricultural Research Corporation (Embrapa Soja), Carlos João Strass Road, Warta County 86085-981, PR, Brazil
| | - Carlos Arrabal Arias
- Brazilian Agricultural Research Corporation (Embrapa Soja), Carlos João Strass Road, Warta County 86085-981, PR, Brazil
| | - Ricardo Vilela Abdelnoor
- Brazilian Agricultural Research Corporation (Embrapa Soja), Carlos João Strass Road, Warta County 86085-981, PR, Brazil
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20
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Torres-Berrío A, Estill M, Patel V, Ramakrishnan A, Kronman H, Minier-Toribio A, Issler O, Browne CJ, Parise EM, van der Zee YY, Walker DM, Martínez-Rivera FJ, Lardner CK, Durand-de Cuttoli R, Russo SJ, Shen L, Sidoli S, Nestler EJ. Mono-methylation of lysine 27 at histone 3 confers lifelong susceptibility to stress. Neuron 2024; 112:2973-2989.e10. [PMID: 38959894 PMCID: PMC11377169 DOI: 10.1016/j.neuron.2024.06.006] [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: 07/31/2023] [Revised: 02/05/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024]
Abstract
Histone post-translational modifications are critical for mediating persistent alterations in gene expression. By combining unbiased proteomics profiling and genome-wide approaches, we uncovered a role for mono-methylation of lysine 27 at histone H3 (H3K27me1) in the enduring effects of stress. Specifically, mice susceptible to early life stress (ELS) or chronic social defeat stress (CSDS) displayed increased H3K27me1 enrichment in the nucleus accumbens (NAc), a key brain-reward region. Stress-induced H3K27me1 accumulation occurred at genes that control neuronal excitability and was mediated by the VEFS domain of SUZ12, a core subunit of the polycomb repressive complex-2, which controls H3K27 methylation patterns. Viral VEFS expression changed the transcriptional profile of the NAc, led to social, emotional, and cognitive abnormalities, and altered excitability and synaptic transmission of NAc D1-medium spiny neurons. Together, we describe a novel function of H3K27me1 in the brain and demonstrate its role as a "chromatin scar" that mediates lifelong stress susceptibility.
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Affiliation(s)
- Angélica Torres-Berrío
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Lurie Center for Autism, Massachusetts General Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Molly Estill
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vishwendra Patel
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hope Kronman
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Angélica Minier-Toribio
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Orna Issler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caleb J Browne
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Parise
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yentl Y van der Zee
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Deena M Walker
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Freddyson J Martínez-Rivera
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Casey K Lardner
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romain Durand-de Cuttoli
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott J Russo
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Freeman KG, Lauer MJ, Jiang D, Roscher J, Sandler S, Mercado N, Fryberger R, Kovalski J, Lutz AR, Hughes LE, VanDemark AP, Hatfull GF. Characterization of mycobacteriophage Adephagia cytotoxic proteins. G3 (BETHESDA, MD.) 2024; 14:jkae166. [PMID: 39031590 PMCID: PMC11373665 DOI: 10.1093/g3journal/jkae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 04/29/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
Mycobacterium phage Adephagia is a cluster K phage that infects Mycobacterium smegmatis and some strains of Mycobacterium pathogens. Adephagia has a siphoviral virion morphology and is temperate. Its genome is 59,646 bp long and codes for one tRNA gene and 94 predicted protein-coding genes; most genes not associated with virion structure and assembly are functionally ill-defined. Here, we determined the Adephagia gene expression patterns in lytic and lysogenic growth and used structural predictions to assign additional gene functions. We characterized 66 nonstructural genes for their toxic phenotypes when expressed in M. smegmatis, and we show that 25 of these (38%) are either toxic or strongly inhibit growth, resulting in either reduced viability or small colony sizes. Some of these genes are predicted to be involved in DNA metabolism or regulation, but others are of unknown function. We also characterize the HicAB-like toxin-antitoxin (TA) system encoded by Adephagia (gp91 and gp90, respectively) and show that the gp90 antitoxin is lysogenically expressed, abrogates gp91 toxicity, and is required for normal lytic and lysogenic growth.
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Affiliation(s)
- Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael J Lauer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Danny Jiang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Jennifer Roscher
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Sterling Sandler
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicholas Mercado
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Robert Fryberger
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Julia Kovalski
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Abigail R Lutz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lee E Hughes
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Andrew P VanDemark
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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22
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Shin Y, Park CM, Kim DE, Kim S, Lee SY, Lee JY, Jeon WH, Kim HG, Bae S, Yoon CH. Discovery of new acetamide derivatives of 5-indole-1,3,4-oxadiazol-2-thiol as inhibitors of HIV-1 Tat-mediated viral transcription. Antimicrob Agents Chemother 2024:e0064324. [PMID: 39230310 DOI: 10.1128/aac.00643-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/09/2024] [Indexed: 09/05/2024] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) encodes a transcriptional factor called Tat, which is critical for viral transcription. Tat-mediated transcription is highly ordered apart from the cellular manner; therefore, it is considered a target for developing anti-HIV-1 drugs. However, drugs targeting Tat-mediated viral transcription are not yet available. Our high-throughput screen of a compound library employing a dual-reporter assay identified a 1,3,4-oxadiazole scaffold against Tat and HIV-1 infection. Furthermore, a serial structure-activity relation (SAR) study performed with biological assays found 1,3,4-oxadiazole derivatives (9 and 13) containing indole and acetamide that exhibited potent inhibitory effects on HIV-1 infectivity, with half-maximal effective concentrations (EC50) of 0.17 (9) and 0.24 µM (13), respectively. The prominent derivatives specifically interfered with the viral transcriptional step without targeting other infection step(s) and efficiently inhibited the HIV-1 replication cycle in the T cell lines and peripheral blood mononuclear cells infected with HIV-1. Additionally, compared to the wild type, the compounds exhibited similar potency against anti-retroviral drug-resistant HIV-1 strains. In a series of mode-of-action studies, the compounds inhibited the ejection of histone H3 for facilitating viral transcription on the long-terminal repeat (LTR) promoter. Furthermore, SAHA (a histone deacetylase inhibitor) treatment abolished the compound potency, revealing that the compounds can possibly target Tat-regulated epigenetic modulation of LTR to inhibit viral transcription. Overall, our screening identified novel 1,3,4-oxadiazole compounds that inhibited HIV-1 Tat, and subsequent SAR-based optimization led to the derivatives 9 and 13 development that could be a promising scaffold for developing a new class of therapeutic agents for HIV-1 infection.
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Affiliation(s)
- YoungHyun Shin
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Chul Min Park
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
- Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Dong-Eun Kim
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Sungmin Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Sang-Yeop Lee
- Research Center for Bioconvergence Analysis, Ochang Center, Korea Basic Science Institute, Cheongju-si, Republic of Korea
| | - Jun Young Lee
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Won-Hui Jeon
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Hong Gi Kim
- Infectious Diseases Therapeutic Research Center, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
- Medicinal Chemistry and Pharmacology, Korea University of Science and Technology, Daejeon, Republic of Korea
| | - Songmee Bae
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Cheol-Hee Yoon
- Division of Chronic Viral Diseases, Center for Emerging Virus Research, Korea National Institute of Health, Cheongju, Republic of Korea
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23
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Zhou X, Hilk A, Solis NV, Scott N, Beach A, Soisangwan N, Billings CL, Burrack LS, Filler SG, Selmecki A. Single-cell detection of copy number changes reveals dynamic mechanisms of adaptation to antifungals in Candida albicans. Nat Microbiol 2024:10.1038/s41564-024-01795-7. [PMID: 39227665 DOI: 10.1038/s41564-024-01795-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 07/24/2024] [Indexed: 09/05/2024]
Abstract
Genomic copy number changes are associated with antifungal drug resistance and virulence across diverse fungal pathogens, but the rate and dynamics of these genomic changes in the presence of antifungal drugs are unknown. Here we optimized a dual-fluorescent reporter system in the diploid pathogen Candida albicans to quantify haplotype-specific copy number variation (CNV) and loss of heterozygosity (LOH) at the single-cell level with flow cytometry. We followed the frequency and dynamics of CNV and LOH at two distinct genomic locations in the presence and absence of antifungal drugs in vitro and in a murine model of candidiasis. Copy number changes were rapid and dynamic during adaptation to fluconazole and frequently involved competing subpopulations with distinct genotypes. This study provides quantitative evidence for the rapid speed at which diverse genotypes arise and undergo dynamic population-level fluctuations during adaptation to antifungal drugs in vitro and in vivo.
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Affiliation(s)
- Xin Zhou
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Audrey Hilk
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Norma V Solis
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
| | - Nancy Scott
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Annette Beach
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Natthapon Soisangwan
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Clara L Billings
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Laura S Burrack
- Gustavus Adolphus College, Department of Biology, Saint Peter, MN, USA
| | - Scott G Filler
- Division of Infectious Diseases, Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anna Selmecki
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA.
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24
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Li J, Yang A, Carneiro BA, Gamsiz Uzun ED, Massingham L, Uzun A. Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants. BMC Bioinformatics 2024; 25:288. [PMID: 39227781 PMCID: PMC11370019 DOI: 10.1186/s12859-024-05875-7] [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: 01/22/2024] [Accepted: 07/18/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND The variant call format (VCF) file is a structured and comprehensive text file crucial for researchers and clinicians in interpreting and understanding genomic variation data. It contains essential information about variant positions in the genome, along with alleles, genotype calls, and quality scores. Analyzing and visualizing these files, however, poses significant challenges due to the need for diverse resources and robust features for in-depth exploration. RESULTS To address these challenges, we introduce variant graph craft (VGC), a VCF file visualization and analysis tool. VGC offers a wide range of features for exploring genetic variations, including extraction of variant data, intuitive visualization, and graphical representation of samples with genotype information. VGC is designed primarily for the analysis of patient cohorts, but it can also be adapted for use with individual probands or families. It integrates seamlessly with external resources, providing insights into gene function and variant frequencies in sample data. VGC includes gene function and pathway information from Molecular Signatures Database (MSigDB) for GO terms, KEGG, Biocarta, Pathway Interaction Database, and Reactome. Additionally, it dynamically links to gnomAD for variant information and incorporates ClinVar data for pathogenic variant information. VGC supports the Human Genome Assembly Hg37 and Hg38, ensuring compatibility with a wide range of data sets, and accommodates various approaches to exploring genetic variation data. It can be tailored to specific user needs with optional phenotype input data. CONCLUSIONS In summary, VGC provides a comprehensive set of features tailored to researchers working with genomic variation data. Its intuitive interface, rapid filtering capabilities, and the flexibility to perform queries using custom groups make it an effective tool in identifying variants potentially associated with diseases. VGC operates locally, ensuring data security and privacy by eliminating the need for cloud-based VCF uploads, making it a secure and user-friendly tool. It is freely available at https://github.com/alperuzun/VGC .
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Affiliation(s)
- Jennifer Li
- Department of Computer Science, Brown University, Providence, RI, 02912, USA
| | - Andy Yang
- Department of Chemistry, Brown University, Providence, RI, 02912, USA
| | - Benedito A Carneiro
- Lifespan Cancer Institute, Providence, RI, 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI, 02912, USA
| | - Ece D Gamsiz Uzun
- Legorreta Cancer Center, Brown University, Providence, RI, 02912, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI, 02912, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA
- Department of Pathology and Laboratory Medicine, Alpert Medical School, Brown University, Providence, RI, 02912, USA
- Center for Clinical Cancer Informatics and Data Science (CCIDS), Brown/Lifespan, Providence, RI, 02912, USA
| | - Lauren Massingham
- Department of Pediatrics, Division of Genetics, Warren Alpert Medical School, Brown University, Providence, RI, 02912, USA
| | - Alper Uzun
- Legorreta Cancer Center, Brown University, Providence, RI, 02912, USA.
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI, 02912, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.
- Department of Pathology and Laboratory Medicine, Alpert Medical School, Brown University, Providence, RI, 02912, USA.
- Center for Clinical Cancer Informatics and Data Science (CCIDS), Brown/Lifespan, Providence, RI, 02912, USA.
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI, 02912, USA.
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25
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Liang Z, Zhu T, Yu Y, Wu C, Huang Y, Hao Y, Song X, Fu W, Yuan L, Cui Y, Huang S, Li C. PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation. Mol Cell 2024:S1097-2765(24)00692-0. [PMID: 39232583 DOI: 10.1016/j.molcel.2024.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 06/19/2024] [Accepted: 08/12/2024] [Indexed: 09/06/2024]
Abstract
Spreading of H3K27me3 is crucial for the maintenance of mitotically inheritable Polycomb-mediated chromatin silencing in animals and plants. However, how Polycomb repressive complex 2 (PRC2) accesses unmodified nucleosomes in spreading regions for spreading H3K27me3 remains unclear. Here, we show in Arabidopsis thaliana that the chromatin remodeler PICKLE (PKL) plays a specialized role in H3K27me3 spreading to safeguard cell identity during differentiation. PKL specifically localizes to H3K27me3 spreading regions but not to nucleation sites and physically associates with PRC2. Loss of PKL disrupts the occupancy of the PRC2 catalytic subunit CLF in spreading regions and leads to aberrant dedifferentiation. Nucleosome density increase endowed by the ATPase function of PKL ensures that unmodified nucleosomes are accessible to PRC2 catalytic activity for H3K27me3 spreading. Our findings demonstrate that PKL-dependent nucleosome compaction is critical for PRC2-mediated H3K27me3 read-and-write function in H3K27me3 spreading, thus revealing a mechanism by which repressive chromatin domains are established and propagated.
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Affiliation(s)
- Zhenwei Liang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Caihong Wu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yisui Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuanhao Hao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbing Yuan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China.
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26
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Wallace AD, Blue NR, Morgan T, Workalemahu T, Silver RM, Quinlan AR. Placental somatic mutation in human stillbirth and live birth: A pilot case-control study of paired placental, fetal, and maternal whole genomes. Placenta 2024; 154:137-144. [PMID: 38972082 PMCID: PMC11368634 DOI: 10.1016/j.placenta.2024.06.017] [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: 01/11/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION A high frequency of single nucleotide somatic mutations in the placenta has been recently described, but its relationship to placental dysfunction is unknown. METHODS We performed a pilot case-control study using paired fetal, maternal, and placental samples collected from healthy live birth controls (n = 10), live births with fetal growth restriction (FGR) due to placental insufficiency (n = 7), and stillbirths with FGR and placental insufficiency (n = 11). We quantified single nucleotide and structural somatic variants using bulk whole genome sequencing (30-60X coverage) in four biopsies from each placenta. We also assessed their association with clinical and histological evidence of placental dysfunction. RESULTS Seventeen pregnancies had sufficiently high-quality placental, fetal, and maternal DNA for analysis. Each placenta had a median of 473 variants (range 111-870), with 95 % arising in just one biopsy within each placenta. In controls, live births with FGR, and stillbirths, the median variant counts per placenta were 514 (IQR 381-779), 582 (450-735), and 338 (245-441), respectively. After adjusting for depth of sequencing coverage and gestational age at birth, the somatic mutation burden was similar between groups (FGR live births vs. controls, adjusted diff. 59, 95 % CI -218 to +336; stillbirths vs controls, adjusted diff. -34, -351 to +419), and with no association with placental dysfunction (p = 0.7). DISCUSSION We confirmed the high prevalence of somatic mutation in the human placenta and conclude that the placenta is highly clonal. We were not able to identify any relationship between somatic mutation burden and clinical or histologic placental insufficiency.
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Affiliation(s)
- Amelia D Wallace
- University of Utah Health, Department of Human Genetics, 15 N 2030 E, Eccles Institute of Human Genetics Rm 7160B, Salt Lake City, UT, 84112, USA; Utah Center for Genetic Discovery, 15 N 2030 E, #2100, Salt Lake City, UT, 4112, USA
| | - Nathan R Blue
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA
| | - Terry Morgan
- Oregon Health & Science University, Departments of Pathology and Obstetrics and Gynecology, 3181 SW Sam Jackson Park Rd, L-113, Portland, OR, 97239, USA
| | - Tsegaselassie Workalemahu
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA
| | - Robert M Silver
- University of Utah Health, Department of Obstetrics and Gynecology, 30 N Mario Capecchi Dr, Level 5 South, Salt Lake City, UT, 84132, USA.
| | - Aaron R Quinlan
- University of Utah Health, Department of Human Genetics, 15 N 2030 E, Eccles Institute of Human Genetics Rm 7160B, Salt Lake City, UT, 84112, USA; Utah Center for Genetic Discovery, 15 N 2030 E, #2100, Salt Lake City, UT, 4112, USA.
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27
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Kaymak I, Watson MJ, Oswald BM, Ma S, Johnson BK, DeCamp LM, Mabvakure BM, Luda KM, Ma EH, Lau K, Fu Z, Muhire B, Kitchen-Goosen SM, Vander Ark A, Dahabieh MS, Samborska B, Vos M, Shen H, Fan ZP, Roddy TP, Kingsbury GA, Sousa CM, Krawczyk CM, Williams KS, Sheldon RD, Kaech SM, Roy DG, Jones RG. ACLY and ACSS2 link nutrient-dependent chromatin accessibility to CD8 T cell effector responses. J Exp Med 2024; 221:e20231820. [PMID: 39150482 PMCID: PMC11329787 DOI: 10.1084/jem.20231820] [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: 10/06/2023] [Revised: 04/02/2024] [Accepted: 07/03/2024] [Indexed: 08/17/2024] Open
Abstract
Coordination of cellular metabolism is essential for optimal T cell responses. Here, we identify cytosolic acetyl-CoA production as an essential metabolic node for CD8 T cell function in vivo. We show that CD8 T cell responses to infection depend on acetyl-CoA derived from citrate via the enzyme ATP citrate lyase (ACLY). However, ablation of ACLY triggers an alternative, acetate-dependent pathway for acetyl-CoA production mediated by acyl-CoA synthetase short-chain family member 2 (ACSS2). Mechanistically, acetate fuels both the TCA cycle and cytosolic acetyl-CoA production, impacting T cell effector responses, acetate-dependent histone acetylation, and chromatin accessibility at effector gene loci. When ACLY is functional, ACSS2 is not required, suggesting acetate is not an obligate metabolic substrate for CD8 T cell function. However, loss of ACLY renders CD8 T cells dependent on acetate (via ACSS2) to maintain acetyl-CoA production and effector function. Together, ACLY and ACSS2 coordinate cytosolic acetyl-CoA production in CD8 T cells to maintain chromatin accessibility and T cell effector function.
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Affiliation(s)
- Irem Kaymak
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - McLane J Watson
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Brandon M Oswald
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Shixin Ma
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies , La Jolla, CA, USA
| | - Benjamin K Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Lisa M DeCamp
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Batsirai M Mabvakure
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Katarzyna M Luda
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen , København, Denmark
| | - Eric H Ma
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Kin Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute , Grand Rapids, MI, USA
| | - Zhen Fu
- Bioinformatics and Biostatistics Core, Van Andel Institute , Grand Rapids, MI, USA
| | - Brejnev Muhire
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Susan M Kitchen-Goosen
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Alexandra Vander Ark
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Michael S Dahabieh
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
| | - Bozena Samborska
- Goodman Cancer Institute, Faculty of Medicine, McGill University , Montréal, Canada
| | - Matthew Vos
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | | | | | | | | | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Kelsey S Williams
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
| | - Ryan D Sheldon
- Mass Spectrometry Core Facility, Van Andel Institute , Grand Rapids, MI, USA
| | - Susan M Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies , La Jolla, CA, USA
| | - Dominic G Roy
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal , Montréal, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
- Institut du Cancer de Montréal , Montréal, Canada
| | - Russell G Jones
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, USA
- Metabolism and Nutrition (MeNu) Program, Van Andel Institute , Grand Rapids, MI, USA
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28
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Bennis NX, Bieseman J, Daran JMG. Unlocking lager's flavour palette by metabolic engineering of Saccharomyces pastorianus for enhanced ethyl ester production. Metab Eng 2024; 85:180-193. [PMID: 39134117 DOI: 10.1016/j.ymben.2024.08.002] [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: 05/02/2024] [Revised: 07/11/2024] [Accepted: 08/05/2024] [Indexed: 08/26/2024]
Abstract
Despite being present in trace amounts, ethyl esters play a crucial role as flavour compounds in lager beer. In yeast, ethyl hexanoate, ethyl octanoate and ethyl decanoate, responsible for fruity and floral taste tones, are synthesized from the toxic medium chain acyl-CoA intermediates released by the fatty acid synthase complex during the fatty acid biosynthesis, as a protective mechanism. The aim of this study was to enhance the production of ethyl esters in the hybrid lager brewing yeast Saccharomyces pastorianus by improving the medium chain acyl-CoA precursor supply. Through CRISPR-Cas9-based genetic engineering, specific FAS1 and FAS2 genes harbouring mutations in domains of the fatty acid synthesis complex were overexpressed in a single and combinatorial approach. These mutations in the ScFAS genes led to specific overproduction of the respective ethyl esters: overexpression of ScFAS1I306A and ScFAS2G1250S significantly improved ethyl hexanoate production and ScFAS1R1834K boosted the ethyl octanoate production. Combinations of ScFAS1 mutant genes with ScFAS2G1250S greatly enhanced predictably the final ethyl ester concentrations in cultures grown on full malt wort, but also resulted in increased levels of free medium chain fatty acids causing alterations in flavour profiles. Finally, the elevated medium chain fatty acid pool was directed towards the ethyl esters by overexpressing the esterase ScEEB1. The genetically modified S. pastorianus strains were utilized in lager beer production, and the resulting beverage exhibited significantly altered flavour profiles, thereby greatly expanding the possibilities of the flavour palette of lager beers.
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Affiliation(s)
- Nicole X Bennis
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - Jimme Bieseman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
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29
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Demir S, Tastan C, Ulu ZO, Canbaz EN, Unlen L, Sahin F. Comparison of strain specific pathogenicity of Herpes Simplex Virus Type 1 by high-throughput sequencing. J Virol Methods 2024; 329:114994. [PMID: 38971379 DOI: 10.1016/j.jviromet.2024.114994] [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: 04/24/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Herpes Simplex Virus Type 1 (HSV-1) is a widespread human pathogen known for causing a spectrum of clinical manifestations, ranging from mild cold sores to severe complications like encephalitis. Understanding the strain-specific variations of HSV-1 is crucial for elucidating its pathogenesis and developing targeted therapeutic interventions. In this multifaceted study, we investigated the strain-specific characteristics of HSV-1 using an in vivo rat model. Firstly, a pilot study was conducted to assess the capacity of three HSV-1 strains (Fisher (F), KOS (K), and MacIntyre (M)) to induce cold sores in rats. Remarkably, the F strain exhibited pronounced pathogenicity, inducing erythema, swelling, and disrupted epidermis with ulceration, distinguishing it from the K and M strains. Subsequently, the treatment capability of intravenous acyclovir injection in HSV-1 F strain-infected rats was evaluated. Acyclovir treatment resulted in a significant reduction in HSV-1 viral copy numbers in serum and dissected neuronal tissues, particularly in the spinal cord, brain, and lower lip. Lastly, whole genome sequencing data revealed that high-impact mutations occurred in the K and M strains within the UL49, US2, and US3 genes. These mutations may play a pivotal role in influencing viral replication, dissemination, pathogenesis, and infectivity. In contrast, the moderate missense variant mutations detected in the US12, US8, UL3, UL30, UL31, and UL36 genes appeared to have no effect on viral pathogenesis and infectivity, based on RT-PCR data for spinal cord, trigeminal nerve, brain, and the lower lip. These strain-specific mutations underscore the dynamic nature of HSV-1 evolution. Collectively, our findings contribute to a deeper understanding of HSV-1 strain diversity and pave the way for the development of targeted therapeutic strategies against this medically significant virus.
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Affiliation(s)
- Sevda Demir
- Department of Genetic and Bioengineering, Faculty of Engineering, Yeditepe University, Ataşehir, İstanbul, Turkey.
| | - Cihan Tastan
- Transgenic Cell Technologies and Epigenetic Application and Research Center (TRGENMER), Üsküdar University, Istanbul, Turkey; Molecular Biology and Genetics Department, Faculty of Engineering and Natural Science, Üsküdar University, Istanbul, Turkey.
| | - Zehra Omeroglu Ulu
- Department of Genetic and Bioengineering, Faculty of Engineering, Yeditepe University, Ataşehir, İstanbul, Turkey.
| | - Eda Nur Canbaz
- Department of Genetic and Bioengineering, Faculty of Engineering, Yeditepe University, Ataşehir, İstanbul, Turkey.
| | - Lara Unlen
- Department of Genetic and Bioengineering, Faculty of Engineering, Yeditepe University, Ataşehir, İstanbul, Turkey.
| | - Fikrettin Sahin
- Department of Genetic and Bioengineering, Faculty of Engineering, Yeditepe University, Ataşehir, İstanbul, Turkey.
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30
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Dong J, Li J, Zuo Y, Wang J, Chen Y, Tu W, Wang H, Li C, Shan Y, Wang Y, Song B, Cai X. Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii. HORTICULTURE RESEARCH 2024; 11:uhae181. [PMID: 39247882 PMCID: PMC11374536 DOI: 10.1093/hr/uhae181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/01/2024] [Indexed: 09/10/2024]
Abstract
Solanum commersonii (2n = 2x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55 Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16 Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25 Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.
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Affiliation(s)
- Jianke Dong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwen Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Yingtao Zuo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Jin Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Ye Chen
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Tu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang 438000, China
| | - Haibo Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi 445000, China
| | - Chenxi Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Yacheng Shan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Botao Song
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Xingkui Cai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
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31
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He X, Chen J, Li Z. Complete organelle genomes of the threatened aquatic species Scheuchzeria palustris (Scheuchzeriaceae): Insights into adaptation and phylogenomic placement. Ecol Evol 2024; 14:e70248. [PMID: 39219575 PMCID: PMC11364858 DOI: 10.1002/ece3.70248] [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: 07/21/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Scheuchzeria palustris, the only species in the Scheuchzeriaceae family, plays a crucial role in methane production and transportation, influencing the global carbon cycle and maintaining ecosystem stability. However, it is now threatened by human activities and global warming. In this study, we generated new organelle genomes for S. palustris, with the plastome (pt) measuring 158,573 bp and the mitogenome (mt) measuring 420,724 bp. We predicted 296 RNA editing sites in mt protein-coding genes (PCGs) and 142 in pt-PCGs. Notably, abundant RNA editing sites in pt-PCGs likely originated from horizontal gene transfer between the plastome and mitogenome. Additionally, we identified positive selection signals in four mt-PCGs (atp4, ccmB, nad3, and sdh4) and one pt-PCG (rps7), which may contribute to the adaptation of S. palustris to low-temperature and high-altitude environments. Furthermore, we identified 35 mitochondrial plastid DNA (MTPT) segments totaling 58,479 bp, attributed to dispersed repeats near most MTPT. Phylogenetic trees reconstructed from mt- and pt-PCGs showed topologies consistent with the APG IV system. However, the conflicting position of S. palustris can be explained by significant differences in the substitution rates of its mt- and pt-PCGs (p < .001). In conclusion, our study provides vital genomic resources to support future conservation efforts and explores the adaptation mechanisms of S. palustris.
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Affiliation(s)
- Xiang‐Yan He
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in WanjiangBasin Co‐Funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- Aquatic Plant Research Center, Wuhan Botanical GardenChinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jin‐Ming Chen
- Aquatic Plant Research Center, Wuhan Botanical GardenChinese Academy of SciencesWuhanChina
| | - Zhi‐Zhong Li
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in WanjiangBasin Co‐Funded by Anhui Province and Ministry of Education of the People's Republic of China, School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
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Kervarrec T, Appenzeller S, Gramlich S, Coyaud E, Bachiri K, Appay R, Macagno N, Tallet A, Bonenfant C, Lecorre Y, Kapfer J, Kettani S, Srinivas N, Lei KC, Lange A, Becker JC, Sarosi EM, Sartelet H, von Deimling A, Touzé A, Guyétant S, Samimi M, Schrama D, Houben R. Analyses of combined Merkel cell carcinomas with neuroblastic components suggests that loss of T antigen expression in Merkel cell carcinoma may result in cell cycle arrest and neuroblastic transdifferentiation. J Pathol 2024; 264:112-124. [PMID: 39049595 DOI: 10.1002/path.6304] [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: 01/02/2024] [Revised: 02/28/2024] [Accepted: 05/08/2024] [Indexed: 07/27/2024]
Abstract
Merkel cell carcinoma (MCC) is an aggressive skin cancer frequently caused by genomic integration of the Merkel cell polyomavirus (MCPyV). MCPyV-negative cases often present as combined MCCs, which represent a distinctive subset of tumors characterized by association of an MCC with a second tumor component, mostly squamous cell carcinoma. Up to now, only exceptional cases of combined MCC with neuroblastic differentiation have been reported. Herein we describe two additional combined MCCs with neuroblastic differentiation and provide comprehensive morphologic, immunohistochemical, transcriptomic, genetic and epigenetic characterization of these tumors, which both arose in elderly men and appeared as an isolated inguinal adenopathy. Microscopic examination revealed biphasic tumors combining a poorly differentiated high-grade carcinoma with a poorly differentiated neuroblastic component lacking signs of proliferation. Immunohistochemical investigation revealed keratin 20 and MCPyV T antigen (TA) in the MCC parts, while neuroblastic differentiation was confirmed in the other component in both cases. A clonal relation of the two components can be deduced from 20 and 14 shared acquired point mutations detected by whole exome analysis in both combined tumors, respectively. Spatial transcriptomics demonstrated a lower expression of stem cell marker genes such as SOX2 and MCM2 in the neuroblastic component. Interestingly, although the neuroblastic part lacked TA expression, the same genomic MCPyV integration and the same large T-truncating mutations were observed in both tumor parts. Given that neuronal transdifferentiation upon TA repression has been reported for MCC cell lines, the most likely scenario for the two combined MCC/neuroblastic tumors is that neuroblastic transdifferentiation resulted from loss of TA expression in a subset of MCC cells. Indeed, DNA methylation profiling suggests an MCC-typical cellular origin for the combined MCC/neuroblastomas. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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MESH Headings
- Humans
- Carcinoma, Merkel Cell/pathology
- Carcinoma, Merkel Cell/virology
- Carcinoma, Merkel Cell/genetics
- Carcinoma, Merkel Cell/metabolism
- Male
- Skin Neoplasms/pathology
- Skin Neoplasms/genetics
- Skin Neoplasms/virology
- Skin Neoplasms/metabolism
- Antigens, Viral, Tumor/genetics
- Antigens, Viral, Tumor/metabolism
- Cell Transdifferentiation
- Merkel cell polyomavirus/genetics
- Cell Cycle Checkpoints/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Aged, 80 and over
- Aged
- Neoplasms, Complex and Mixed/pathology
- Neoplasms, Complex and Mixed/genetics
- Neoplasms, Complex and Mixed/metabolism
- Neuroblastoma/pathology
- Neuroblastoma/genetics
- Neuroblastoma/metabolism
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Affiliation(s)
- Thibault Kervarrec
- Department of Pathology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
- "Biologie des infections à polyomavirus" team, UMR INRAE ISP 1282, Université de Tours, Tours, France
- CARADERM Network
| | - Silke Appenzeller
- Comprehensive Cancer Center Mainfranken, University Hospital of Würzburg, Würzburg, Germany
| | - Susanne Gramlich
- Institute of Pathology, University of Würzburg, Würzburg, Germany
| | | | - Kamel Bachiri
- PRISM INSERM U1192, Université de Lille, Lille, France
| | - Romain Appay
- Department of Pathology, Université de Marseille, Assistance publique des Hopitaux de Marseille, Marseille, France
| | - Nicolas Macagno
- CARADERM Network
- Department of Pathology, Université de Marseille, Assistance publique des Hopitaux de Marseille, Marseille, France
| | - Anne Tallet
- Platform of Somatic Tumor Molecular Genetics, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Christine Bonenfant
- Platform of Somatic Tumor Molecular Genetics, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Yannick Lecorre
- Dermatology Department, LUNAM Université, CHU Angers, Angers, France
| | | | | | - Nalini Srinivas
- Department of Translational Skin Cancer Research and Dermatology, University Hospital Essen, Essen, Germany
| | - Kuan Cheok Lei
- Department of Translational Skin Cancer Research and Dermatology, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anja Lange
- Bioinformatics & Computational Biophysics, University Duisburg-Essen, Essen, Germany
| | - Jürgen C Becker
- Department of Translational Skin Cancer Research and Dermatology, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eva Maria Sarosi
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Hervé Sartelet
- Laboratoire de Biopathologie, CHRU de Nancy, Nancy, France
- INSERM U1256, Université de Lorraine, Nancy, France
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Antoine Touzé
- "Biologie des infections à polyomavirus" team, UMR INRAE ISP 1282, Université de Tours, Tours, France
| | - Serge Guyétant
- Department of Pathology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
- "Biologie des infections à polyomavirus" team, UMR INRAE ISP 1282, Université de Tours, Tours, France
| | - Mahtab Samimi
- "Biologie des infections à polyomavirus" team, UMR INRAE ISP 1282, Université de Tours, Tours, France
- CARADERM Network
- Department of Dermatology, Université de Tours, Centre Hospitalier Universitaire de Tours, Tours, France
| | - David Schrama
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Roland Houben
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
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Hossain Mollah J, Hatimuria A, Kumar Chauhan V. Transcriptomic analysis of Bombyx mori in its early larval stage (2 nd instar) of development upon Nosema bombycis transovarial infection. J Invertebr Pathol 2024; 206:108157. [PMID: 38908473 DOI: 10.1016/j.jip.2024.108157] [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: 01/01/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
The infection caused by Nosema bombycis often known as pebrine, is a devastating sericulture disease. The infection can be transmitted to the next generation through eggs laid by infected female Bombyx mori moths (transovarial) as well as with N. bombycis contaminated food (horizontal). Most diagnoses were carried out in the advanced stages of infection until the time that infection might spread to other healthy insects. Hence, early diagnosis of pebrine is of utmost importance to quarantine infected larvae from uninfected silkworm batches and stop further spread of the infection. The findings of our study provide an insight into how the silkworm larval host defence system was activated against early N. bombycis transovarial infection. The results obtained from transcriptome analysis of infected 2nd instar larvae revealed significant (adjusted P-value < 0.05) expression of 1888 genes of which 801 genes were found to be upregulated and 1087 genes were downregulated when compared with the control. Pathway analysis indicated activation of the immune deficiency (IMD) pathway, which shows a potential immune defence response against pebrine infection as well as suppression of the melanin synthesis pathway due to lower expression of prophenoloxidase activating enzyme (PPAE). Liquid chromatography mass spectrometry (LC-MS/MS) analysis of haemolymph from infected larvae shows the secretion of serpin binding protein of N. bombycis which might be involved in the suppression of the melanization pathway. Moreover, among the differentially expressed genes, we found that LPMC-61, yellow-y, gasp and osiris 9 can be utilised as potential markers for early diagnosis of transovarial pebrine infection in B. mori. Physiological as well as biochemical roles and functions of many of the essential genes are yet to be established, and enlightened research will be required to characterize the products of these genes.
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Affiliation(s)
- Jahid Hossain Mollah
- Department of Zoology, Siksha Bhavana (Institute of Science), Visva-Bharati, Santiniketan, West Bengal-731235, India
| | - Arindam Hatimuria
- Department of Zoology, Siksha Bhavana (Institute of Science), Visva-Bharati, Santiniketan, West Bengal-731235, India
| | - Vinod Kumar Chauhan
- Department of Zoology, Siksha Bhavana (Institute of Science), Visva-Bharati, Santiniketan, West Bengal-731235, India.
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Liu C, Fu S, Yi C, Liu Y, Huang Y, Guo X, Zhang K, Liu Q, Birchler JA, Han F. Unveiling the distinctive traits of functional rye centromeres: minisatellites, retrotransposons, and R-loop formation. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1989-2002. [PMID: 38805064 DOI: 10.1007/s11427-023-2524-0] [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: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 05/29/2024]
Abstract
Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments. Despite their conserved functionality, centromeric DNA sequences exhibit rapid evolution, presenting diverse sizes and compositions across species. The functional significance of rye centromeric DNA sequences, particularly in centromere identity, remains unclear. In this study, we comprehensively characterized the sequence composition and organization of rye centromeres. Our findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons (LTR-RTs) and interspersed minisatellites. We systematically classified LTR-RTs into five categories, highlighting the prevalence of younger CRS1, CRS2, and CRS3 of CRSs (centromeric retrotransposons of Secale cereale) were primarily located in the core centromeres and exhibited a higher association with CENH3 nucleosomes. The minisatellites, mainly derived from retrotransposons, along with CRSs, played a pivotal role in establishing functional centromeres in rye. Additionally, we observed the formation of R-loops at specific regions of CRS1, CRS2, and CRS3, with both rye pericentromeres and centromeres exhibiting enrichment in R-loops. Notably, these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres, suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere specification. Our work provides insights into the DNA sequence composition, distribution, and potential function of R-loops in rye centromeres. This knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres, offering implications for the development of synthetic centromeres in future plant modifications and beyond.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulan Fu
- Key Laboratory for Plant Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Congyang Yi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianrui Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaibiao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - James A Birchler
- Division of Biological Science, University of Missouri, Columbia, 65211-7400, USA
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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35
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Wright CF, Sharp LN, Jackson L, Murray A, Ware JS, MacArthur DG, Rehm HL, Patel KA, Weedon MN. Guidance for estimating penetrance of monogenic disease-causing variants in population cohorts. Nat Genet 2024; 56:1772-1779. [PMID: 39075210 DOI: 10.1038/s41588-024-01842-3] [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: 12/15/2023] [Accepted: 06/24/2024] [Indexed: 07/31/2024]
Abstract
Penetrance is the probability that an individual with a pathogenic genetic variant develops a specific disease. Knowing the penetrance of variants for monogenic disorders is important for counseling of individuals. Until recently, estimates of penetrance have largely relied on affected individuals and their at-risk family members being clinically referred for genetic testing, a 'phenotype-first' approach. This approach substantially overestimates the penetrance of variants because of ascertainment bias. The recent availability of whole-genome sequencing data in individuals from very-large-scale population-based cohorts now allows 'genotype-first' estimates of penetrance for many conditions. Although this type of population-based study can underestimate penetrance owing to recruitment biases, it provides more accurate estimates of penetrance for secondary or incidental findings. Here, we provide guidance for the conduct of penetrance studies to ensure that robust genotypes and phenotypes are used to accurately estimate penetrance of variants and groups of similarly annotated variants from population-based studies.
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Affiliation(s)
- Caroline F Wright
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK.
| | - Luke N Sharp
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Leigh Jackson
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Anna Murray
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - James S Ware
- National Heart and Lung Institute and MRC Laboratory of Medical Sciences, Imperial College London, London, UK
- Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kashyap A Patel
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, Medical School, University of Exeter, Exeter, UK.
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Greene SE, Huang Y, Fischer K, Rosa BA, Martin J, Mitreva M, Yates D, Wanji S, Kamgno J, Budge PJ, Weil GJ, Fischer PU. A novel antigen biomarker for detection of high-level of Loa loa microfilaremia. PLoS Negl Trop Dis 2024; 18:e0012461. [PMID: 39226306 PMCID: PMC11398663 DOI: 10.1371/journal.pntd.0012461] [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: 02/19/2024] [Revised: 09/13/2024] [Accepted: 08/17/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Loiasis is a disease caused by the nematode Loa loa. Serious adverse events sometimes occur in people with heavy L. loa microfilaremia after ivermectin treatment. In regions of Central Africa where loiasis is endemic, this significantly impedes global elimination programs for lymphatic filariasis and onchocerciasis that use mass distribution of ivermectin. Improved diagnostic tests to identify individuals at increased risk of serious adverse events could facilitate efforts to eliminate lymphatic filariasis and onchocerciasis in this region. METHODS AND FINDINGS We previously identified the L. loa protein Ll-Bhp-1 in loiasis patient sera. Here, we further characterize Ll-Bhp-1 and report development of an antigen capture ELISA to detect this antigen. This assay detected Ll-Bhp-1 in 74 of 116 (63.8%) loiasis patient sera. Ll-Bhp-1 levels were significantly correlated with L. loa microfilarial counts, and the sensitivity of the assay was highest for samples from people with high counts, (94% and 100% in people with ≥20,000 and ≥50,000 microfilaria per milliliter of blood, respectively). The antigen was not detected in 112 sera from people with other filarial infections, or in 34 control sera from the USA. CONCLUSIONS This Ll-Bhp-1 antigen assay is specific for loiasis, and highly sensitive for identifying people with high L. loa microfilarial counts who are at increased risk for serious adverse events after ivermectin treatment. L. loa antigen detection has the potential to facilitate loiasis mapping efforts and programs to eliminate lymphatic filariasis and onchocerciasis in Central Africa.
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Affiliation(s)
- Sarah E Greene
- Infectious Diseases Division, Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, United States of America
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Yuefang Huang
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Bruce A Rosa
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - John Martin
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Makedonka Mitreva
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri, United States of America
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Devyn Yates
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Samuel Wanji
- Parasites and Vector Biology research unit (PAVBRU), Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
- Research Foundation for Tropical Diseases and the Environment (REFOTDE), Buea, Cameroon
| | - Joseph Kamgno
- Higher Institute for Scientific and Medical Research (ISM), Yaoundé, Cameroon
- Department of Public Health, Faculty of Medicine and Biomedical Sciences, Department of Public Health, University of Yaoundé I, Yaoundé, Cameroon
| | - Philip J Budge
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Gary J Weil
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Peter U Fischer
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
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37
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Li F, Wang Y, Mostafa HHA, Wang T, Zhu S, Yuan M, Gao S, Liu T. Genome-wide association analysis identifies candidates of three bulb traits in garlic. PHYSIOLOGIA PLANTARUM 2024; 176:e14523. [PMID: 39262285 DOI: 10.1111/ppl.14523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/14/2024] [Accepted: 08/28/2024] [Indexed: 09/13/2024]
Abstract
Garlic bulbs generally possess several swelling cloves, and the swelling degree of the bulbs determines its yield and appearance quality. However, the genetic basis underlying bulb traits remains poorly known. To address this issue, we performed a genome-wide association analysis for three bulb traits: bulb weight, diameter, and height. It resulted in the identification of 51 significant associated signals from 38 genomic regions. Twelve genes from the associated regions, whose transcript abundances in the developmental bulb showed significant correlations with the investigated traits in 81 garlic accessions, were considered the candidates of the corresponding locus. We focused on five of these candidates and their variations and revealed that the promoter variations of fructose-bisphosphate aldolase-encoding Asa8G05696.1 and beta-fructofuranosidase-encoding Asa6G01167.1 are responsible for the functional diversity of these two genes in garlic population. Interestingly, our results revealed that all candidates we focused on experienced a degree of selection during garlic evolutionary history, and different genotypes of them were retained in two China-cultivated garlic groups. Taken together, these results suggest a potential involvement of those candidates in the parallel evolution of garlic bulb organs in two China-cultivated garlic groups. This study provides important insights into the genetic basis of garlic bulb traits and their evolution.
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Affiliation(s)
- Fu Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Hassan H A Mostafa
- Central Laboratory of Organic Agriculture, Agricultural Research Center, Giza, Egypt
| | - Taotao Wang
- Shandong Dongyun Research Center of garlic Engineering, JinXiang, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Meng Yuan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Song Gao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Touming Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
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38
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Duppala SK, Poleboyina PK, Kour B, Bale G, Vyas A, Pawar SC, Suravajhala PN, Vuree S. A Pilot Study Based on the Correlation Between Whole Exome and Transcriptome Reveals Potent Variants in the Indian Population of Cervical Cancer. Indian J Microbiol 2024; 64:1222-1245. [PMID: 39282199 PMCID: PMC11399378 DOI: 10.1007/s12088-024-01295-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/19/2024] [Indexed: 09/18/2024] Open
Abstract
Cervical malignancy (CC) is the 2nd most prevalent malignancy among females, leading to cancer mortality. Primary detection of CC tumors results in an improved prognosis. CC is a malignant gynecological tumor, with few treatment options. New diagnostic and therapeutic agents are required to expand patient survival and quality of life. If CC tumors can be found at an early stage, the prognosis is much brighter. New diagnostic and therapeutic agents are needed to increase patient survival and quality of life. In this work, we performed whole-exome sequencing utilizing V5 (Illumina platform) 10 samples, 5 control and 5 CC tumour tissue, and we compared the results with transcriptome studies. KMT2C variations were shown to be among the most vicious in this analysis. From an Indian viewpoint, we found a plethora of SNVs and mutations, including those with known, unknown, and possible effects on health. Based on our findings, we know that the KMT2C gene is on chr. Seven and in exon 8, all three recognized variants are missense, synonymous, coding synonymous, non-coding variants, and GnomAD MAF (- 0.05). The variation at position (7:152265091, T > A, SNV 62478356) in KMT2C is unique, potent, and pathogenic. The missense coding transcript CIQTNF maps to chromosome 7 and displays T > C SNV. In addition, we performed single strand conformational polymorphism analysis on 64 samples and further confirmed them using Sanger sequencing to understand and verify the mutations. KMT2C shows a log FC value of - 1.16. Understanding emerging harmful mutations from an Indian viewpoint is facilitated by our bioinformatics-based, extensive correlation studies of WES analysis. Potentially harmful and new mutations were found in our preliminary analysis; among these ten top mutated genes, KMT2C and CIQTNF were altered in ten cases of CC with an Indian phenotype.
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Affiliation(s)
- Santosh Kumari Duppala
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Jalandhar, India
| | - Pavan Kumar Poleboyina
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana 500007 India
| | - Bhumandeep Kour
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Jalandhar, India
| | - Govardhan Bale
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana 500007 India
| | - Ashish Vyas
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Jalandhar, India
| | - Smita C Pawar
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, Telangana 500007 India
| | - Prashanth N Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana, Kerala 690525 India
- Bioclues.org, Hyderabad, Telangana India
| | - Sugunakar Vuree
- GenepoweRx, K&H Personalized Medicine Clinic, Jubilee Hills, Hyderabad, Telangana 500033 India
- Bioclues.org, Hyderabad, Telangana India
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39
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Helsen J, Reza MH, Carvalho R, Sherlock G, Dey G. Spindle architecture constrains karyotype evolution. Nat Cell Biol 2024; 26:1496-1503. [PMID: 39117795 PMCID: PMC11392806 DOI: 10.1038/s41556-024-01485-w] [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: 11/14/2023] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
The eukaryotic cell division machinery must rapidly and reproducibly duplicate and partition the cell's chromosomes in a carefully coordinated process. However, chromosome numbers vary dramatically between genomes, even on short evolutionary timescales. We sought to understand how the mitotic machinery senses and responds to karyotypic changes by using a series of budding yeast strains in which the native chromosomes have been successively fused. Using a combination of cell biological profiling, genetic engineering and experimental evolution, we show that chromosome fusions are well tolerated up until a critical point. Cells with fewer than five centromeres lack the necessary number of kinetochore-microtubule attachments needed to counter outward forces in the metaphase spindle, triggering the spindle assembly checkpoint and prolonging metaphase. Our findings demonstrate that spindle architecture is a constraining factor for karyotype evolution.
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Affiliation(s)
- Jana Helsen
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Md Hashim Reza
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Ricardo Carvalho
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany.
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40
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Dong C, Meng X, Zhang T, Guo Z, Liu Y, Wu P, Chen S, Zhou F, Ma Y, Xiong H, Shu S, He A. Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome. Nat Methods 2024; 21:1624-1633. [PMID: 39025969 PMCID: PMC11399096 DOI: 10.1038/s41592-024-02360-0] [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: 08/13/2023] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
Studies of molecular and cellular functions of small-molecule inhibitors in cancer treatment, eliciting effects by targeting genome and epigenome associated proteins, requires measurement of drug-target engagement in single-cell resolution. Here we present EpiChem for in situ single-cell joint mapping of small molecules and multimodal epigenomic landscape. We demonstrate single-cell co-assays of three small molecules together with histone modifications, chromatin accessibility or target proteins in human colorectal cancer (CRC) organoids. Integrated multimodal analysis reveals diverse drug interactions in the context of chromatin states within heterogeneous CRC organoids. We further reveal drug genomic binding dynamics and adaptive epigenome across cell types after small-molecule drug treatment in CRC organoids. This method provides a unique tool to exploit the mechanisms of cell type-specific drug actions.
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Affiliation(s)
- Chao Dong
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaoxuan Meng
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Tong Zhang
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhifang Guo
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
- Peking University International Cancer Institute, Beijing, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China
| | - Yaxi Liu
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Peihuang Wu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shiwei Chen
- Peking University International Cancer Institute, Beijing, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China
| | - Fanqi Zhou
- State Key Laboratory of Medical Molecular Biology, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Haiqing Xiong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Shaokun Shu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China.
- Peking University International Cancer Institute, Beijing, China.
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China.
| | - Aibin He
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Key laboratory of Carcinogenesis and Translational Research of Ministry of Education of China, Peking University Cancer Hospital & Institute, Beijing, China.
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China.
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41
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Togi S, Ura H, Niida Y. Qualitative and quantitative analysis of MED12 c.887G>A causing both missense and splicing variants in X-linked Ohdo syndrome. Am J Med Genet A 2024; 194:e63628. [PMID: 38655688 DOI: 10.1002/ajmg.a.63628] [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: 12/05/2023] [Revised: 03/24/2024] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
The phenotypes associated with MED12 pathogenic variants are diverse. Male patients usually have missense variants, but the effects of base substitutions on mRNA splicing have not been investigated. Here, we report a Japanese brother with intellectual disability, characteristic facial appearance with blepharophimosis, cleft palate, Fallot tetralogy, vesicoureteral reflux, and deafness. A known missense pathogenic variant was detected in MED12, NM_005120.3:c.887G>A p.(Arg296Gln), and X-linked Ohdo syndrome was diagnosed in combination with their phenotype. mRNA splicing of MED12 was evaluated qualitatively and quantitatively using long-range PCR-based targeted RNA sequencing (reverse transcribed long amplicon sequencing), and it was shown that this missense variant simultaneously causes aberrant splicing of the 42-bp in-frame deletion in exon 7, r.847_888del, which accounts for approximately 30% of the mRNAs in both siblings. The X chromosome inactivation study showed that the X chromosome carrying the mutant allele was 100% inactivated in the carrier mothers. mRNA level analysis is essential for the accurate interpretation of the effects of variants. In this case, the MED12 protein function may be reduced by more than just an amino acid substitution, resulting in the patients with the most severe phenotype of MED12-related syndrome in males.
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Affiliation(s)
- Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
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Guan P, Chen J, Mo C, Fukawa T, Zhang C, Cai X, Li M, Hong JH, Chan JY, Ng CCY, Lee JY, Wong SF, Liu W, Zeng X, Wang P, Xiao R, Rajasegaran V, Myint SS, Lim AMS, Yeong JPS, Tan PH, Ong CK, Xu T, Du Y, Bai F, Yao X, Teh BT, Tan J. Comprehensive molecular characterization of collecting duct carcinoma for therapeutic vulnerability. EMBO Mol Med 2024; 16:2132-2145. [PMID: 39122888 PMCID: PMC11393068 DOI: 10.1038/s44321-024-00102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/24/2024] [Accepted: 07/01/2024] [Indexed: 08/12/2024] Open
Abstract
Collecting duct carcinoma (CDC) is an aggressive rare subtype of kidney cancer with unmet clinical needs. Little is known about its underlying molecular alterations and etiology, primarily due to its rarity, and lack of preclinical models. This study aims to comprehensively characterize molecular alterations in CDC and identify its therapeutic vulnerabilities. Through whole-exome and transcriptome sequencing, we identified KRAS hotspot mutations (G12A/D/V) in 3/13 (23%) of the patients, in addition to known TP53, NF2 mutations. 3/13 (23%) patients carried a mutational signature (SBS22) caused by aristolochic acid (AA) exposures, known to be more prevalent in Asia, highlighting a geologically specific disease etiology. We further discovered that cell cycle-related pathways were the most predominantly dysregulated pathways. Our drug screening with our newly established CDC preclinical models identified a CDK9 inhibitor LDC000067 that specifically inhibited CDC tumor growth and prolonged survival. Our study not only improved our understanding of oncogenic molecular alterations of Asian CDC, but also identified cell-cycle machinery as a therapeutic vulnerability, laying the foundation for clinical trials to treat patients with such aggressive cancer.
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Affiliation(s)
- Peiyong Guan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Jianfeng Chen
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Chengqiang Mo
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, PR China
| | - Tomoya Fukawa
- Department of Urology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Chao Zhang
- Department of Genitourinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, P. R. China
| | - Xiuyu Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Mei Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jing Han Hong
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Jason Yongsheng Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Jing Yi Lee
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Suet Far Wong
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Wei Liu
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Xian Zeng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Peili Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Rong Xiao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Vikneswari Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Abner Ming Sun Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Republic of Singapore
| | - Puay Hoon Tan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Republic of Singapore
- Division of Pathology, Singapore General Hospital, Singapore, Republic of Singapore
- Luma Medical Centre, Singapore, Republic of Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Tao Xu
- Department of Urology, Peking University People's Hospital, Beijing, 100044, China
| | - Yiqing Du
- Department of Urology, Peking University People's Hospital, Beijing, 100044, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xin Yao
- Department of Genitourinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, P. R. China.
| | - Bin Tean Teh
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore.
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore, Republic of Singapore.
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore.
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore, Republic of Singapore.
| | - Jing Tan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Republic of Singapore.
- Hainan Academy of Medical Science, Hainan Medical University, Haikou, PR China.
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Wang F, Xi Z, Wang M, Wang L, Wang J. Genome-wide chromatin accessibility reveals transcriptional regulation of heterosis in inter-subspecific hybrid rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:2331-2348. [PMID: 38976378 DOI: 10.1111/tpj.16920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/21/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
The utilization of rice heterosis is essential for ensuring global food security; however, its molecular mechanism remains unclear. In this study, comprehensive analyses of accessible chromatin regions (ACRs), DNA methylation, and gene expression in inter-subspecific hybrid and its parents were performed to determine the potential role of chromatin accessibility in rice heterosis. The hybrid exhibited abundant ACRs, in which the gene ACRs and proximal ACRs were directly related to transcriptional activation rather than the distal ACRs. Regarding the dynamic accessibility contribution of the parents, paternal ZHF1015 transmitted a greater number of ACRs to the hybrid. Accessible genotype-specific target genes were enriched with overrepresented transcription factors, indicating a unique regulatory network of genes in the hybrid. Compared with its parents, the differentially accessible chromatin regions with upregulated chromatin accessibility were much greater than those with downregulated chromatin accessibility, reflecting a stronger regulation in the hybrid. Furthermore, DNA methylation levels were negatively correlated with ACR intensity, and genes were strongly affected by CHH methylation in the hybrid. Chromatin accessibility positively regulated the overall expression level of each genotype. ACR-related genes with maternal Z04A-bias allele-specific expression tended to be enriched during carotenoid biosynthesis, whereas paternal ZHF1015-bias genes were more active in carbohydrate metabolism. Our findings provide a new perspective on the mechanism of heterosis based on chromatin accessibility in inter-subspecific hybrid rice.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zengde Xi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengyao Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Linyou Wang
- Zhejiang Academy of Agricultural Sciences, Institute of Crop and Nuclear Technology Utilization, Hangzhou, 310021, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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de Oliveira BCD, Shiburah ME, Assis LHC, Fontes VS, Bisetegn H, Passos ADO, de Oliveira LS, Alves CDS, Ernst E, Martienssen R, Gallo-Francisco PH, Giorgio S, Batista MM, Soeiro MDNC, Menna-Barreto RFS, Aoki JI, Coelho AC, Cano MIN. Leishmania major telomerase RNA knockout: From altered cell proliferation to decreased parasite infectivity. Int J Biol Macromol 2024; 279:135150. [PMID: 39218181 DOI: 10.1016/j.ijbiomac.2024.135150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/14/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
This study focuses on the biological impacts of deleting the telomerase RNA from Leishmania major (LeishTER), a parasite responsible for causing leishmaniases, for which no effective treatment or prevention is available. TER is a critical player in the telomerase ribonucleoprotein complex, containing the template sequence copied by the reverse transcriptase component during telomere elongation. The success of knocking out both LeishTER alleles was confirmed, and no off-targets were detected. LmTER-/- cells share similar characteristics with other TER-depleted eukaryotes, such as altered growth patterns and partial G0/G1 cell cycle arrest in early passages, telomere shortening, and elevated TERRA expression. They also exhibit increased γH2A phosphorylation, suggesting that the loss of LeishTER induces DNA damage signaling. Moreover, pro-survival autophagic signals and mitochondrion alterations were shown without any detectable plasma membrane modifications. LmTER-/- retained the ability to transform into metacyclics, but their infectivity capacity was compromised. Furthermore, the overexpression of LeishTER was also deleterious, inducing a dominant negative effect that led to telomere shortening and growth impairments. These findings highlight TER's vital role in parasite homeostasis, opening discussions about its potential as a drug target candidate against Leishmania.
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Affiliation(s)
- Beatriz Cristina Dias de Oliveira
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Mark Ewusi Shiburah
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil; Animal Research Institute, Council for Scientific and Industrial Research (CSIR-ARI), Accra, Ghana
| | - Luiz Henrique Castro Assis
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Veronica Silva Fontes
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Habtye Bisetegn
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil; Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Arthur de Oliveira Passos
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | - Leilane S de Oliveira
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil
| | | | - Evan Ernst
- Howard Hughes Medical Institute/Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rob Martienssen
- Howard Hughes Medical Institute/Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Selma Giorgio
- Department of Animal Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
| | - Marcos Meuser Batista
- Cellular Biology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Juliana Ide Aoki
- Department of Animal Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
| | - Adriano Cappellazzo Coelho
- Department of Animal Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Sao Paulo, Brazil
| | - Maria Isabel Nogueira Cano
- Department of Chemical and Biological Sciences, Biosciences Institute, São Paulo State University (UNESP), Botucatu, Sao Paulo, Brazil.
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Lu G, Ye ZX, Qi YH, Lu JB, Mao QZ, Zhuo JC, Huang HJ, He YJ, Li YY, Xu ZT, Chen JP, Zhang CX, Li JM. Endogenous nege-like viral elements in arthropod genomes reveal virus-host coevolution and ancient history of two plant virus families. J Virol 2024:e0099724. [PMID: 39212930 DOI: 10.1128/jvi.00997-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/03/2024] [Indexed: 09/04/2024] Open
Abstract
Negevirus is a recently proposed taxon of arthropod-infecting virus, which is associated with plant viruses of two families (Virgaviridae and Kitaviridae). Nevertheless, the evolutionary history of negevirus-host and its relationship with plant viruses remain poorly understood. Endogenous nege-like viral elements (ENVEs) are ancient nege-like viral sequences integrated into the arthropod genomes, which can serve as the molecular fossil records of previous viral infection. In this study, 292 ENVEs were identified in 150 published arthropod genomes, revealing the evolutionary history of nege-like viruses and two related plant virus families. We discovered three novel and eight strains of nege-like viruses in 11 aphid species. Further analysis indicated that 10 ENVEs were detected in six aphid genomes, and they were divided into four types (ENVE1-ENVE4). Orthologous integration and phylogenetic analyses revealed that nege-like viruses had a history of infection of over 60 My and coexisted with aphid ancestors throughout the Cenozoic Era. Moreover, two nege-like viral proteins (CP and SP24) were highly homologous to those of plant viruses in the families Virgaviridae and Kitaviridae. CP- and SP24-derived ENVEs were widely integrated into numerous arthropod genomes. These results demonstrate that nege-like viruses have a long-term coexistence with arthropod hosts and plant viruses of the two families, Virgaviridae and Kitaviridae, which may have evolved from the nege-like virus ancestor through horizontal virus transfer events. These findings broaden our perspective on the history of viral infection in arthropods and the origins of plant viruses. IMPORTANCE Although negevirus is phylogenetically related to plant virus, the evolutionary history of negevirus-host and its relationship with plant virus remain largely unknown. In this study, we used endogenous nege-like viral elements (ENVEs) as the molecular fossil records to investigate the history of nege-like viral infection in arthropod hosts and the evolution of two related plant virus families (Virgaviridae and Kitaviridae). Our results showed the infection of nege-like viruses for over 60 My during the arthropod evolution. ENVEs highly homologous to viral sequences in Virgaviridae and Kitaviridae were present in a wide range of arthropod genomes but were absent in plant genomes, indicating that plant viruses in these two families possibly evolved from the nege-like virus ancestor through cross-species horizontal virus transmission. Our findings provide a new perspective on the virus-host coevolution and the origins of plant viruses.
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Affiliation(s)
- Gang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yu-Hua Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jia-Bao Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Qian-Zhuo Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yu-Juan He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yi-Yuan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zhong-Tian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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Elhassan YS, Appenzeller S, Landwehr LS, Lippert J, Popat D, Gilligan LC, Abdi L, Goh E, Diaz-Cano S, Kircher S, Gramlich S, Sutcliffe RP, Thangaratinam S, Chan LF, Fassnacht M, Arlt W, Ronchi CL. Primary unilateral macronodular adrenal hyperplasia with concomitant glucocorticoid and androgen excess and KDM1A inactivation. Eur J Endocrinol 2024; 191:334-344. [PMID: 39171930 PMCID: PMC11378072 DOI: 10.1093/ejendo/lvae106] [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: 03/20/2024] [Revised: 07/20/2024] [Accepted: 08/20/2024] [Indexed: 08/23/2024]
Abstract
BACKGROUND Primary bilateral macronodular adrenal hyperplasia (PBMAH) is a rare cause of Cushing's syndrome. Individuals with PBMAH and glucose-dependent insulinotropic polypeptide (GIP)-dependent Cushing's syndrome due to ectopic expression of the GIP receptor (GIPR) typically harbor inactivating KDM1A sequence variants. Primary unilateral macronodular adrenal hyperplasia (PUMAH) with concomitant glucocorticoid and androgen excess has never been encountered or studied. METHODS We investigated a woman with a large, heterogeneous adrenal mass and severe adrenocorticotropic hormone-independent glucocorticoid and androgen excess, a biochemical presentation typically suggestive of adrenocortical carcinoma. The patient presented during pregnancy (22nd week of gestation) and reported an 18-month history of oligomenorrhea, hirsutism, and weight gain. We undertook an exploratory study with detailed histopathological and genetic analysis of the resected adrenal mass and leukocyte DNA collected from the patient and her parents. RESULTS Histopathology revealed benign macronodular adrenal hyperplasia. Imaging showed a persistently normal contralateral adrenal gland. Whole-exome sequencing of 4 representative nodules detected KDM1A germline variants, benign NM_001009999.3:c.136G > A:p.G46S, and likely pathogenic NM_001009999.3:exon6:c.865_866del:p.R289Dfs*7. Copy number variation analysis demonstrated an additional somatic loss of the KDM1A wild-type allele on chromosome 1p36.12 in all nodules. RNA sequencing of a representative nodule showed low/absent KDM1A expression and increased GIPR expression compared with 52 unilateral sporadic adenomas and 4 normal adrenal glands. Luteinizing hormone/chorionic gonadotropin receptor expression was normal. Sanger sequencing confirmed heterozygous KDM1A variants in both parents (father: p.R289Dfs*7 and mother: p.G46S) who showed no clinical features suggestive of glucocorticoid or androgen excess. CONCLUSIONS We investigated the first PUMAH associated with severe Cushing's syndrome and concomitant androgen excess, suggesting pathogenic mechanisms involving KDM1A.
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Affiliation(s)
- Yasir S Elhassan
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
- Centre for Endocrinology, Diabetes and Metabolism, University Hospitals Birmingham NHS Foundation Trust, Birmingham Health Partners, Birmingham, United Kingdom
| | - Silke Appenzeller
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Laura-Sophie Landwehr
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Juliane Lippert
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Dillon Popat
- Faculty of Medicine and Dentistry, Centre for Endocrinology, William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Lorna C Gilligan
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
| | - Lida Abdi
- MRC Laboratory of Medical Sciences, London, United Kingdom
| | - Edwina Goh
- Birmingham Women's Hospital, Birmingham, United Kingdom
| | - Salvador Diaz-Cano
- Department of Pathology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Stefan Kircher
- Department of Pathology, University of Würzburg, Würzburg, Germany
| | - Susanne Gramlich
- Department of Pathology, University of Würzburg, Würzburg, Germany
| | - Robert P Sutcliffe
- The Liver Unit, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Shakila Thangaratinam
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
- Birmingham Women's Hospital, Birmingham, United Kingdom
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, United Kingdom
| | - Li F Chan
- Faculty of Medicine and Dentistry, Centre for Endocrinology, William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
| | - Martin Fassnacht
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Wiebke Arlt
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
- MRC Laboratory of Medical Sciences, London, United Kingdom
- Faculty of Medicine, Institute of Clinical Sciences, Imperial College London, London, United Kingdom
| | - Cristina L Ronchi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom
- Centre for Endocrinology, Diabetes and Metabolism, University Hospitals Birmingham NHS Foundation Trust, Birmingham Health Partners, Birmingham, United Kingdom
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47
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Rodríguez-Varela R, Yaka R, Pochon Z, Sanchez-Pinto I, Solaun JL, Naidoo T, Guinet B, Pérez-Ramallo P, Lagerholm VK, de Anca Prado V, Valdiosera C, Krzewińska M, Herrasti L, Azkarate A, Götherström A. Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis. SCIENCE ADVANCES 2024; 10:eadp8625. [PMID: 39196943 PMCID: PMC11352919 DOI: 10.1126/sciadv.adp8625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/19/2024] [Indexed: 08/30/2024]
Abstract
Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Reyhan Yaka
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Iban Sanchez-Pinto
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - José Luis Solaun
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Stockholm, Sweden
| | - Benjamin Guinet
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Cristina Valdiosera
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Lourdes Herrasti
- Departamento de Antropología, Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain
| | - Agustín Azkarate
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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48
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Shi Y, Li X, Xue Y, Hu D, Song X. Cell cycle-regulated transcription factor AP2XII-9 is a key activator for asexual division and apicoplast inheritance in Toxoplasma gondii tachyzoite. mBio 2024:e0133624. [PMID: 39207100 DOI: 10.1128/mbio.01336-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Toxoplasma gondii is an intracellular parasitic protozoan that poses a significant risk to the fetus carried by a pregnant woman or to immunocompromised individuals. T. gondii tachyzoites duplicate rapidly in host cells during acute infection through endodyogeny. This highly regulated division process is accompanied by complex gene regulation networks. TgAP2XII-9 is a cell cycle-regulated transcription factor, but its specific role in the parasite cell cycle is not fully understood. In this study, we demonstrate that TgAP2XII-9 is identified as a nuclear transcription factor and is dominantly expressed during the S/M phase of the tachyzoite cell cycle. Cleavage Under Targets and Tagmentation (CUT&Tag) results indicate that TgAP2XII-9 targets key genes for the moving junction machinery (RON2, 4, and 8) and daughter cell inner membrane complex (IMC). TgAP2XII-9 deficiency resulted in a significant downregulation of rhoptry proteins and rhoptry neck proteins, leading to a severe defect in the invasion and egress efficiency of tachyzoites. Additionally, the loss of TgAP2XII-9 correlated with a substantial downregulation of multiple IMC and apicoplast proteins, leading to disorders of daughter bud formation and apicoplast inheritance and further contributing to the inability of cell division and intracellular proliferation. Our study reveals that TgAP2XII-9 acts as a critical S/M-phase regulator that orchestrates the endodyogeny and apicoplast division in T. gondii tachyzoites. This study contributes to a broader understanding of the complexity of the parasite's cell cycle and its key regulators. IMPORTANCE The intracellular apicoplast parasite Toxoplasma gondii poses a great threat to the public health. The acute infection of T. gondii tachyzoites relies on efficient invasion by forming a moving junction structure and also fast replication by highly regulated endodyogeny. This study shows that an ApiAP2 transcription factor, TgAP2XII-9, acts as an activator for the S/M-phase gene expression, including genes related to daughter buds and moving junction formation. Loss of TgAP2XII-9 results in significant growth defects and disorders in endodyogeny and apicoplast inheritance of the parasites. Our results provide valuable insights into the transcriptional regulation of the parasite cell cycle and invading machinery in T. gondii.
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Affiliation(s)
- Yuehong Shi
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xuan Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yingying Xue
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Dandan Hu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
| | - Xingju Song
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, China
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49
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Lv Y, Li J, Wang Z, Liu Y, Jiang Y, Li Y, Lv Z, Huang X, Peng X, Cao Y, Yang H. Polycomb proteins RING1A/B promote H2A monoubiquitination to regulate female gametophyte development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4822-4836. [PMID: 38717070 DOI: 10.1093/jxb/erae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/07/2024] [Indexed: 08/29/2024]
Abstract
A functional female gametophyte is the basis of successful sexual reproduction in flowering plants. During female gametophyte development, the megaspore mother cell (MMC), which differentiates from a single subepidermal somatic cell in the nucellus, undergoes meiosis to produce four megaspores; only the one at the chalazal end, referred to as the functional megaspore (FM), then undergoes three rounds of mitosis and develops into a mature embryo sac. Here, we report that RING1A and RING1B (RING1A/B), two functionally redundant Polycomb proteins in Arabidopsis, are critical for female gametophyte development. Mutations of RING1A/B resulted in defects in the specification of the MMC and the FM, and in the subsequent mitosis of the FM, thereby leading to aborted ovules. Detailed analysis revealed that several genes essential for female gametophyte development were ectopically expressed in the ring1a ring1b mutant, including Argonaute (AGO) family genes and critical transcription factors. Furthermore, RING1A/B bound to some of these genes to promote H2A monoubiquitination (H2Aub). Taken together, our study shows that RING1A/B promote H2Aub modification at key genes for female gametophyte development, suppressing their expression to ensure that the development progresses correctly.
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Affiliation(s)
- Yanfang Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jian Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Zheng Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Yue Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yili Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanzhuo Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhaopeng Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaoyi Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiongbo Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ying Cao
- College of Life Sciences, RNA Center, Capital Normal University, Beijing 100048, China
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- RNA Institute, Wuhan University, Wuhan 430072, China
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50
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Dehaene N, Boussardon C, Andrey P, Charif D, Brandt D, Gilouppe Taillefer C, Nietzel T, Ricou A, Simon M, Tran J, Vezon D, Camilleri C, Arimura SI, Schwarzländer M, Budar F. The mitochondrial orf117Sha gene desynchronizes pollen development and causes pollen abortion in Arabidopsis Sha cytoplasmic male sterility. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4851-4872. [PMID: 38733289 DOI: 10.1093/jxb/erae214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024]
Abstract
Cytoplasmic male sterility (CMS) is of major agronomical relevance in hybrid breeding. In gametophytic CMS, abortion of pollen is determined by the grain genotype, while in sporophytic CMS, it is determined by the mother plant genotype. While several CMS mechanisms have been dissected at the molecular level, gametophytic CMS has not been straightforwardly accessible. We used the gametophytic Sha-CMS in Arabidopsis to characterize the cause and process of pollen abortion by implementing in vivo biosensing in single pollen and mitoTALEN mutagenesis. We obtained conclusive evidence that orf117Sha is the CMS-causing gene, despite distinct characteristics from other CMS genes. We measured the in vivo cytosolic ATP content in single pollen, followed pollen development, and analyzed pollen mitochondrial volume in two genotypes that differed only by the presence of the orf117Sha locus. Our results showed that the Sha-CMS is not triggered by ATP deficiency. Instead, we observed desynchronization of a pollen developmental program. Pollen death occurred independently in pollen grains at diverse stages and was preceded by mitochondrial swelling. We conclude that pollen death is grain-autonomous in Sha-CMS and propose that mitochondrial permeability transition, which was previously described as a hallmark of developmental and environmental-triggered cell death programs, precedes pollen death in Sha-CMS.
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Affiliation(s)
- Noémie Dehaene
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Clément Boussardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Philippe Andrey
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Delphine Charif
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Dennis Brandt
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Clémence Gilouppe Taillefer
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Thomas Nietzel
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Anthony Ricou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Matthieu Simon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Joseph Tran
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Daniel Vezon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Christine Camilleri
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany
| | - Françoise Budar
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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