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Ho T, Eichner N, Sathapondecha P, Nantapojd T, Meister G, Udomkit A. Ago4-piRNA complex is a key component of genomic immune system against transposon expression in Penaeus monodon. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109693. [PMID: 38878913 DOI: 10.1016/j.fsi.2024.109693] [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: 01/10/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Argonaute proteins are key constituents of small RNA-guided regulatory pathways. In crustaceans, members of the AGO subfamily of Argonaute proteins that play vital roles in immune defense are well studied, while proteins of the PIWI subfamily are less established. PmAgo4 of the black tiger shrimp, Penaeus monodon, though phylogenetically clustered with the AGO subfamily, has distinctive roles of the PIWI subfamily in safeguarding the genome from transposon invasion and controlling germ cell development. This study explored a molecular mechanism by which PmAgo4 regulates transposon expression in the shrimp germline. PmAgo4-associated small RNAs were co-immunoprecipitated from shrimp testis lysate using a PmAgo4-specific polyclonal antibody. RNA-seq revealed a majority of 26-27 nt long small RNAs in the PmAgo4-IP fraction suggesting that PmAgo4 is predominantly associated with piRNAs. Mapping of these piRNAs on nucleotide sequences of two gypsy and a mariner-like transposons of P. monodon suggested that most piRNAs were originated from the antisense strand of transposons. Suppression of PmAgo4 expression by a specific dsRNA elevated the expression levels of the three transposons while decreasing the levels of transposon-related piRNAs. Taken together, these results imply that PmAgo4 exerts its suppressive function on transposons by controlling the biogenesis of transposon-related piRNAs and thus, provides a defense mechanism against transposon invasion in shrimp germline cells.
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Affiliation(s)
- Teerapong Ho
- Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand
| | - Norbert Eichner
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany
| | - Ponsit Sathapondecha
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkla, Thailand
| | - Thaneeya Nantapojd
- Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany.
| | - Apinunt Udomkit
- Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand.
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Mehta P, Sethi S, Yadav SK, Gupta G, Singh R. Heat stress induced piRNA alterations in pachytene spermatocytes and round spermatids. Reprod Biol Endocrinol 2024; 22:87. [PMID: 39049033 PMCID: PMC11267754 DOI: 10.1186/s12958-024-01249-z] [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: 06/12/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Spermatogenesis is a temperature-sensitive process, and elevation in temperature hampers this process quickly and significantly. We studied the molecular effects of testicular heating on piRNAs and gene expression in rat testicular germ cells. METHODS We generated a cryptorchid rat model by displacing the testis from the scrotal sac (34 °C) to the abdominal area (37 °C) and sacrificed animals after 1 day, 3 days, and 5 days. Pachytene spermatocytes and round spermatids were purified using elutriation centrifugation and percoll gradient methods. We performed transcriptome sequencing in pachytene spermatocytes and round spermatids to identify differentially expressed piRNAs and their probable targets, i.e., TE transcripts and mRNAs. RESULTS As a result of heat stress, we observed significant upregulation of piRNAs and TE transcripts in testicular germ cells. In addition to this, piRNA biogenesis machinery and heat shock proteins (Hsp70 and Hsp90 family members) were upregulated. mRNAs have also been proposed as targets for piRNAs; therefore, we shortlisted certain piRNA-mRNA pairs with an inverse relationship of expression. We observed that in testicular heat stress, the heat shock proteins go hand-in-hand with the upregulation of piRNA biogenesis machinery. The dysregulation of piRNAs in heat-stressed germ cells, increased ping-pong activity, and disturbed expression of piRNA target transcripts suggest a connection between piRNAs, mRNAs, and TE transcripts. CONCLUSIONS In heat stress, piRNAs, piRNA machinery, and heat shock proteins are activated to deal with low levels of stress, which is followed by a rescue approach in prolonged stressaccompained by high TE activity to allow genetic mutations, perhaps for survival and adaptability.
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Affiliation(s)
- Poonam Mehta
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shruti Sethi
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Santosh Kumar Yadav
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Gopal Gupta
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajender Singh
- Division of Endocrinology, CSIR-Central Drug Research Institute, Lucknow, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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3
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Amiri-Yekta A, Sen S, Hazane-Puch F, Tebbakh C, Roux-Buisson N, Cazin C, Thierry-Mieg N, Bouras A, Mohammad Ali SG, Hosseini SH, Goodarzian M, Gourabi H, Ray PF, Kherraf ZE. Whole genome sequencing identifies a homozygous splicing variant in TDRKH segregating with non-obstructive azoospermia in an Iranian family. Clin Genet 2024. [PMID: 38956960 DOI: 10.1111/cge.14584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
Non-obstructive azoospermia (NOA) resulting from primary spermatogenic failure represents one of the most severe forms of male infertility, largely because therapeutic options are very limited. Beyond their diagnostic value, genetic tests for NOA also hold prognostic potential. Specifically, genetic diagnosis enables the establishment of genotype-testicular phenotype correlations, which, in some cases, provide a negative predictive value for testicular sperm extraction (TESE), thereby preventing unnecessary surgical procedures. In this study, we employed whole-genome sequencing (WGS) to investigate two generations of an Iranian family with NOA and identified a homozygous splicing variant in TDRKH (NM_001083965.2: c.562-2A>T). TDRKH encodes a conserved mitochondrial membrane-anchored factor essential for piRNA biogenesis in germ cells. In Tdrkh knockout mice, de-repression of retrotransposons in germ cells leads to spermatogenic arrest and male infertility. Previously, our team reported TDRKH involvement in human NOA cases through the investigation of a North African cohort. This current study marks the second report of TDRKH's role in NOA and human male infertility, underscoring the significance of the piRNA pathway in spermatogenesis. Furthermore, across both studies, we demonstrated that men carrying TDRKH variants, similar to knockout mice, exhibit complete spermatogenic arrest, correlating with failed testicular sperm retrieval.
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Affiliation(s)
- Amir Amiri-Yekta
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Sharanya Sen
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
- CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | - Florence Hazane-Puch
- CHU Grenoble Alpes, Medical Unit of Molecular Genetics (Hereditary Diseases and Oncology), Grenoble, France
| | - Célia Tebbakh
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
- CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | - Nathalie Roux-Buisson
- CHU Grenoble Alpes, Medical Unit of Molecular Genetics (Hereditary Diseases and Oncology), Grenoble, France
| | - Caroline Cazin
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
- CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | | | - Ahmed Bouras
- Centre Léon Bérard, Laboratory of Constitutional Genetics for Frequent Cancer HCL-CLB, Lyon, France
| | - Sadighi-Gilani Mohammad Ali
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Seyedeh-Hanieh Hosseini
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Maedeh Goodarzian
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Hamid Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Pierre F Ray
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
- CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | - Zine-Eddine Kherraf
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Grenoble, France
- CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
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Guo P, Yu Y, Kang H, Liu Y, Zhu D, Sun C, Xing Z, Tang Z, Chen K, Tan A. GASZ is indispensable for gametogenesis in the silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38728119 DOI: 10.1111/imb.12921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
Abstract
The prominent role of the P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway in animals is to silence transposable elements and maintain genome stability, ensuring proper gametogenesis in gonads. GASZ (Germ cell protein with Ankyrin repeats, Sterile alpha motif, and leucine Zipper) is an evolutionarily conserved protein located on the outer mitochondrial membrane of germ cells and plays vital roles in the piRNA pathway and spermatogenesis in mammals. In the model insect Drosophila melanogaster, GASZ is essential for piRNA biogenesis and oogenesis, whereas its biological functions in non-drosophilid insects are still unknown. Here, we describe a comprehensive investigation of GASZ functions in the silkworm, Bombyx mori, a lepidopteran model insect, by using a binary transgenic CRISPR/Cas9 system. The BmGASZ mutation did not affect growth and development, but led to sterility in both males and females. Eupyrene sperm bundles of mutant males exhibited developmental defects, while the apyrene sperm bundles were normal, which were further confirmed through double copulation experiments with sex-lethal mutants, which males possess functional eupyrene sperm and abnormal apyrene sperm. In female mutant moths, ovarioles were severely degenerated and the eggs in ovarioles were deformed compared with that of wild type (WT). Further RNA-seq and RT-qPCR analysis revealed that amounts of piRNAs and transposon expression were dysregulated in gonads of mutants. In summary, this study has demonstrated vital roles of BmGASZ in gametogenesis through regulating the piRNA pathway in B. mori.
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Affiliation(s)
- Peilin Guo
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ye Yu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Hongxia Kang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Yutong Liu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Dalin Zhu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Chenxin Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Zhiping Xing
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ziyue Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Kai Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Anjiang Tan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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5
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Zhang H, Li Y. Potential roles of PIWI-interacting RNAs in breast cancer, a new therapeutic strategy. Pathol Res Pract 2024; 257:155318. [PMID: 38688203 DOI: 10.1016/j.prp.2024.155318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Breast cancer (BC) has been the focus of numerous studies aimed at identifying novel biological markers for its early detection. PIWI-interacting RNAs (piRNAs), a subset of small non-coding RNAs, have emerged as potential markers due to their aberrant expression in various cancers. PiRNAs have recently gained attention due to their aberrant expression in various cancers, including BC. PiRNAs, exhibit diverse biological activities, such as epigenetic regulation of gene and protein expression and their association with cell proliferation and metastasis has been well-established. As the field of non-coding RNAs rapidly evolves, there is great anticipation that therapies targeting piRNAs will advance swiftly. This review will delve into the various biological functions of piRNAs, such as gene suppression, transposon silencing, and epigenetic regulation of genes. The review will also highlight the role of piRNAs as either progenitors or suppressors in cancers, with a particular focus on BC. Lastly, it will touch upon the potential of piRNAs as biomarkers and therapeutic targets for BC.
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Affiliation(s)
- Hongpeng Zhang
- The Second Clinical College, China Medical University, Shenyang 110122, China
| | - Yanshu Li
- School of Life Sciences, China Medical University, Shenyang 110122, China.
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6
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Ren Y, Dong W, Bu W, Xue H. Identification and expression patterns of somatic piRNAs and PIWI genes in Riptortus pedestris (Hemiptera: Alydidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22107. [PMID: 38591567 DOI: 10.1002/arch.22107] [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: 12/01/2023] [Revised: 02/29/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
RNA interference (RNAi)-based gene silencing is a feasible and sustainable technology for the management of hemipteran pests by double-stranded RNA involvement, including small-interfering RNA, microRNA, and Piwi-interacting RNA (piRNA) pathways, that may help to decrease the usage of chemical insecticides. However, only a few data are available on the somatic piRNAs and their biogenesis genes in Riptortus pedestris, which serves as a significant pest of soybean (Glycine max). In this study, two family members of the PIWI gene were identified and characterized in R. pedestris, containing Argonaute3 (RpAgo3) and Aubergine (RpAub) genes with conserved protein domains, and their clusters were validated by phylogenetic analysis. In addition, they were widely expressed in all developmental stages of the whole body of R. pedestris and had lower expression levels in R. pedestris guts under different rearing conditions based on previous transcriptome sequencing. Furthermore, abundant clean reads were filtered to a total number of 45,998 piRNAs with uridine bias at the first nucleotide (nt) position and 26-32 nt in length by mapping onto the reference genome of R. pedestris according to our previous whole-transcriptome sequencing. Finally, our data revealed that gut bacterial changes were significantly positively or negatively associated with differentially expressed piRNAs among the five comparison groups with Pearson correlation analysis. In conclusion, these findings paved new avenues for the application of RNAi-based biopesticides for broad-spectrum hemipteran pest control.
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Affiliation(s)
- Yipeng Ren
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Wenhao Dong
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, P.R. China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, P.R. China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, P.R. China
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Youness RA, Habashy DA, Khater N, Elsayed K, Dawoud A, Hakim S, Nafea H, Bourquin C, Abdel-Kader RM, Gad MZ. Role of Hydrogen Sulfide in Oncological and Non-Oncological Disorders and Its Regulation by Non-Coding RNAs: A Comprehensive Review. Noncoding RNA 2024; 10:7. [PMID: 38250807 PMCID: PMC10801522 DOI: 10.3390/ncrna10010007] [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: 12/02/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
Recently, myriad studies have defined the versatile abilities of gasotransmitters and their synthesizing enzymes to play a "Maestro" role in orchestrating several oncological and non-oncological circuits and, thus, nominated them as possible therapeutic targets. Although a significant amount of work has been conducted on the role of nitric oxide (NO) and carbon monoxide (CO) and their inter-relationship in the field of oncology, research about hydrogen sulfide (H2S) remains in its infancy. Recently, non-coding RNAs (ncRNAs) have been reported to play a dominating role in the regulation of the endogenous machinery system of H2S in several pathological contexts. A growing list of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are leading the way as upstream regulators for H2S biosynthesis in different mammalian cells during the development and progression of human diseases; therefore, their targeting can be of great therapeutic benefit. In the current review, the authors shed the light onto the biosynthetic pathways of H2S and their regulation by miRNAs and lncRNAs in various oncological and non-oncological disorders.
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Affiliation(s)
- Rana A. Youness
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
- Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), New Administrative Capital, Cairo 11835, Egypt
| | - Danira Ashraf Habashy
- Pharmacology and Toxicology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
- Clinical Pharmacy Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
| | - Nour Khater
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
| | - Kareem Elsayed
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
| | - Alyaa Dawoud
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
| | - Sousanna Hakim
- Pharmacology and Toxicology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
| | - Heba Nafea
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
| | - Carole Bourquin
- School of Pharmaceutical Sciences, Institute of Pharmaceutical Sciences of Western Switzerland, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, University of Geneva, 1211 Geneva, Switzerland;
| | - Reham M. Abdel-Kader
- Pharmacology and Toxicology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
| | - Mohamed Z. Gad
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo (GUC), Cairo 11835, Egypt
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Kloc M, Halasa M, Kubiak JZ, Ghobrial RM. Invertebrate Immunity, Natural Transplantation Immunity, Somatic and Germ Cell Parasitism, and Transposon Defense. Int J Mol Sci 2024; 25:1072. [PMID: 38256145 PMCID: PMC10815962 DOI: 10.3390/ijms25021072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
While the vertebrate immune system consists of innate and adaptive branches, invertebrates only have innate immunity. This feature makes them an ideal model system for studying the cellular and molecular mechanisms of innate immunity sensu stricto without reciprocal interferences from adaptive immunity. Although invertebrate immunity is evolutionarily older and a precursor of vertebrate immunity, it is far from simple. Despite lacking lymphocytes and functional immunoglobulin, the invertebrate immune system has many sophisticated mechanisms and features, such as long-term immune memory, which, for decades, have been exclusively attributed to adaptive immunity. In this review, we describe the cellular and molecular aspects of invertebrate immunity, including the epigenetic foundation of innate memory, the transgenerational inheritance of immunity, genetic immunity against invading transposons, the mechanisms of self-recognition, natural transplantation, and germ/somatic cell parasitism.
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Affiliation(s)
- Malgorzata Kloc
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
| | - Marta Halasa
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Jacek Z. Kubiak
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine-National Research Institute (WIM-PIB), Szaserow 128, 04-141 Warsaw, Poland;
- Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
| | - Rafik M. Ghobrial
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
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Kloc M, Tworzydło W, Szklarzewicz T. Germline and Somatic Cell Syncytia in Insects. Results Probl Cell Differ 2024; 71:47-63. [PMID: 37996672 DOI: 10.1007/978-3-031-37936-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Syncytia are common in the animal and plant kingdoms both under normal and pathological conditions. They form through cell fusion or division of a founder cell without cytokinesis. A particular type of syncytia occurs in invertebrate and vertebrate gametogenesis when the founder cell divides several times with partial cytokinesis producing a cyst (nest) of germ line cells connected by cytoplasmic bridges. The ultimate destiny of the cyst's cells differs between animal groups. Either all cells of the cyst become the gametes or some cells endoreplicate or polyploidize to become the nurse cells (trophocytes). Although many types of syncytia are permanent, the germ cell syncytium is temporary, and eventually, it separates into individual gametes. In this chapter, we give an overview of syncytium types and focus on the germline and somatic cell syncytia in various groups of insects. We also describe the multinuclear giant cells, which form through repetitive nuclear divisions and cytoplasm hypertrophy, but without cell fusion, and the accessory nuclei, which bud off the oocyte nucleus, migrate to its cortex and become included in the early embryonic syncytium.
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Affiliation(s)
- Malgorzata Kloc
- The Houston Methodist Research Institute, Houston, TX, USA.
- The Houston Methodist Hospital, Department of Surgery, Houston, TX, USA.
- Department of Genetics, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA.
| | - Wacław Tworzydło
- Department of Developmental Biology and Invertebrate Morphology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University in Krakow, Krakow, Poland
| | - Teresa Szklarzewicz
- Department of Developmental Biology and Invertebrate Morphology, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University in Krakow, Krakow, Poland
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Huang S, Yoshitake K, Kinoshita S, Asakawa S. Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs. RNA Biol 2024; 21:1-13. [PMID: 38693614 PMCID: PMC11067994 DOI: 10.1080/15476286.2024.2348893] [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] [Accepted: 12/07/2022] [Indexed: 05/03/2024] Open
Abstract
Small non-coding RNAs (sncRNAs) are non-coding RNA molecules that play various roles in metazoans. Among the sncRNAs, microRNAs (miRNAs) guide post-translational gene regulation during cellular development, proliferation, apoptosis, and differentiation, while PIWI-interacting RNAs (piRNAs) suppress transposon activity to safeguard the genome from detrimental insertion mutagenesis. While an increasing number of piRNAs are being identified in the soma and germlines of various organisms, they are scarcely reported in molluscs. To unravel the small RNA (sRNA) expression patterns and genomic function in molluscs, we generated a comprehensive sRNA dataset by sRNA sequencing (sRNA-seq) of eight mollusc species. Abundant miRNAs were identified and characterized in all investigated molluscs, and ubiquitous piRNAs were discovered in both somatic and gonadal tissues in six of the investigated molluscs, which are more closely associated with transposon silencing. Tens of piRNA clusters were also identified based on the genomic mapping results, which varied among different tissues and species. Our dataset serves as important reference data for future genomic and genetic studies on sRNAs in these molluscs and related species, especially in elucidating the ancestral state of piRNAs in bilaterians.
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Affiliation(s)
- Songqian Huang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo, Japan
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11
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Wu Z, Yu X, Zhang S, He Y, Guo W. Novel roles of PIWI proteins and PIWI-interacting RNAs in human health and diseases. Cell Commun Signal 2023; 21:343. [PMID: 38031146 PMCID: PMC10685540 DOI: 10.1186/s12964-023-01368-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Non-coding RNA has aroused great research interest recently, they play a wide range of biological functions, such as regulating cell cycle, cell proliferation, and intracellular substance metabolism. Piwi-interacting RNAs (piRNAs) are emerging small non-coding RNAs that are 24-31 nucleotides in length. Previous studies on piRNAs were mainly limited to evaluating the binding to the PIWI protein family to play the biological role. However, recent studies have shed more lights on piRNA functions; aberrant piRNAs play unique roles in many human diseases, including diverse lethal cancers. Therefore, understanding the mechanism of piRNAs expression and the specific functional roles of piRNAs in human diseases is crucial for developing its clinical applications. Presently, research on piRNAs mainly focuses on their cancer-specific functions but lacks investigation of their expressions and epigenetic modifications. This review discusses piRNA's biogenesis and functional roles and the recent progress of functions of piRNA/PIWI protein complexes in human diseases. Video Abstract.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
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12
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Woodruff GC, Willis JH, Johnson E, Phillips PC. Widespread changes in gene expression accompany body size evolution in nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564729. [PMID: 37961435 PMCID: PMC10635002 DOI: 10.1101/2023.10.30.564729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including C. elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata's divergent ecology and morphology. We also used a model comparison approach to identify orthologs with divergent dynamics across this developmental period between the two species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with TGF-β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans. Widespread transcriptional divergence between these species is unexpected and may be a signature of the ecological and morphological divergence of C. inopinata. Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group.
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Affiliation(s)
- Gavin C Woodruff
- University of Oregon, Eugene, Oregon, USA
- Current institution: University of Oklahoma, Norman, Oklahoma, USA
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13
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Sturm Á, Saskői É, Hotzi B, Tarnóci A, Barna J, Bodnár F, Sharma H, Kovács T, Ari E, Weinhardt N, Kerepesi C, Perczel A, Ivics Z, Vellai T. Downregulation of transposable elements extends lifespan in Caenorhabditis elegans. Nat Commun 2023; 14:5278. [PMID: 37644049 PMCID: PMC10465613 DOI: 10.1038/s41467-023-40957-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Mobility of transposable elements (TEs) frequently leads to insertional mutations in functional DNA regions. In the potentially immortal germline, TEs are effectively suppressed by the Piwi-piRNA pathway. However, in the genomes of ageing somatic cells lacking the effects of the pathway, TEs become increasingly mobile during the adult lifespan, and their activity is associated with genomic instability. Whether the progressively increasing mobilization of TEs is a cause or a consequence of ageing remains a fundamental problem in biology. Here we show that in the nematode Caenorhabditis elegans, the downregulation of active TE families extends lifespan. Ectopic activation of Piwi proteins in the soma also promotes longevity. Furthermore, DNA N6-adenine methylation at TE stretches gradually rises with age, and this epigenetic modification elevates their transcription as the animal ages. These results indicate that TEs represent a novel genetic determinant of ageing, and that N6-adenine methylation plays a pivotal role in ageing control.
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Affiliation(s)
- Ádám Sturm
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - Éva Saskői
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Bernadette Hotzi
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Anna Tarnóci
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - János Barna
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - Ferenc Bodnár
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Himani Sharma
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Tibor Kovács
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Eszter Ari
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
- HCEMM-BRC Metabolic Systems Biology Research Group, 6726, Szeged, Hungary
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári krt. 62, 6726, Szeged, Hungary
| | - Nóra Weinhardt
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI), 1111, Budapest, Hungary
- Brigham and Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - András Perczel
- Laboratory of Structural Chemistry and Biology & Hungarian Academy of Sciences (MTA)-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary.
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary.
- Vellab Biotech Ltd., 6722, Szeged, Hungary.
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14
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Taverna S, Masucci A, Cammarata G. PIWI-RNAs Small Noncoding RNAs with Smart Functions: Potential Theranostic Applications in Cancer. Cancers (Basel) 2023; 15:3912. [PMID: 37568728 PMCID: PMC10417041 DOI: 10.3390/cancers15153912] [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: 06/23/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a new class of small noncoding RNAs (ncRNAs) that bind components of the PIWI protein family. piRNAs are specifically expressed in different human tissues and regulate important signaling pathways. Aberrant expressions of piRNAs and PIWI proteins have been associated with tumorigenesis and cancer progression. Recent studies reported that piRNAs are contained in extracellular vesicles (EVs), nanosized lipid particles, with key roles in cell-cell communication. EVs contain several bioactive molecules, such as proteins, lipids, and nucleic acids, including emerging ncRNAs. EVs are one of the components of liquid biopsy (LB) a non-invasive method for detecting specific molecular biomarkers in liquid samples. LB could become a crucial tool for cancer diagnosis with piRNAs as biomarkers in a precision oncology approach. This review summarizes the current findings on the roles of piRNAs in different cancer types, focusing on potential theranostic applications of piRNAs contained in EVs (EV-piRNAs). Their roles as non-invasive diagnostic and prognostic biomarkers and as new therapeutic options have been also discussed.
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Affiliation(s)
- Simona Taverna
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 90146 Palermo, Italy
| | - Anna Masucci
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Clinical Biochemistry, Clinical Molecular Medicine, Laboratory Medicine, University of Palermo, 90127 Palermo, Italy;
| | - Giuseppe Cammarata
- Institute of Translational Pharmacology (IFT), National Research Council (CNR), 90146 Palermo, Italy
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15
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Zhang K, Li Y, Huang Y, Sun K. PiRNA in Cardiovascular Disease: Focus on Cardiac Remodeling and Cardiac Protection. J Cardiovasc Transl Res 2023; 16:768-777. [PMID: 37407865 DOI: 10.1007/s12265-023-10353-1] [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: 09/23/2022] [Accepted: 01/08/2023] [Indexed: 07/07/2023]
Abstract
Cardiovascular diseases (CVDs) are common causes of death, which take about 18.6 million lives worldwide every year. Currently, exploring strategies that delay ventricular remodeling, reduce cardiomyocyte death, and promote cardiomyocyte regeneration has been the hotspot and difficulty of the ischemic heart disease (IHD) research field. Previous studies indicate that piwi-interacting RNA (piRNA) plays a vital role in the occurrence and development of cardiac remodeling and may offer novel therapeutic strategies for cardiac repair. The best-known biological function of piRNA is to silence transposons in cells. In the cardiovascular system, piRNA is known to participate in cardiac progenitor cell proliferation, AKT pathway regulation, and cardiac remodeling and decompensation. In this review, we systematically discuss the research progress on piRNA in CVDs, especially the mechanism of cardiac remodeling and the potential functions in cardiac protection, which provides new insights for the progress and treatment of cardiovascular diseases. Piwi-interacting RNA (piRNA) is one of the noncoding RNAs, with the best -known biological function to silence transposons in cells. Now piRNA is found to participate in cardiac progenitor cell proliferation, AKT pathway regulation, cardiac remodeling and decompensation, which implies the potential of piRNA in the diagnosis and treatment of cardiovascular diseases. Over expression of piRNA could promote cardiac apoptosis and cardiac hypertrophy, thus targeted therapy which inhibits expression of associated piRNA may reduce cardiac remodeling and reduce inflammation caused by necrotic cardiomyocytes. PiRNA is also speculated to participate in the proliferation of cardiac progenitor cells, implying the potential to induce cardiac regeneration th erapy, which provides new insights for treatment of cardiovascular diseases. At present, the treatment strategy of cardiac remodeling emphasizes the control of risk factors, prevention of disease progression and individualized treatment. With further studies in mechanism of piRNA, potential therapies above may come true and more therapies in cardiovascular diseases may be found.
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Affiliation(s)
- Kaiyu Zhang
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China
| | - Yafei Li
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China
| | - Ying Huang
- Central Laboratory, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Kangyun Sun
- Department of Cardiology, Gusu School, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, 215000, Jiangsu Province, China.
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16
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Carotti E, Carducci F, Barucca M, Canapa A, Biscotti MA. Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin. Int J Mol Sci 2023; 24:11591. [PMID: 37511347 PMCID: PMC10380595 DOI: 10.3390/ijms241411591] [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: 07/04/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for genome instability, and thus silencing mechanisms were evolved to allow the coexistence between TEs and eukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatory elements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs are not sequences merely to silence; rather, they can be domesticated for the regulation of host-coding gene expression, permitting species adaptation and resilience as well as ensuring human health. This review presents the main silencing mechanisms acting in vertebrates and the importance of exploiting these mechanisms for TE control to rewire gene expression networks, challenging the general view of TEs as threatening elements.
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Affiliation(s)
| | - Federica Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (E.C.); (M.B.); (A.C.); (M.A.B.)
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17
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Lloyd AC, Gregory KS, Isaac RE, Acharya KR. A Molecular Analysis of the Aminopeptidase P-Related Domain of PID-5 from Caenorhabditis elegans. Biomolecules 2023; 13:1132. [PMID: 37509168 PMCID: PMC10377022 DOI: 10.3390/biom13071132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, the silencing mechanism has not yet been fully characterised. In this study, bioinformatic tools were used to compare pre-existing aminopeptidase P molecular structures to the AlphaFold2-predicted aminopeptidase P-related domain of PID-5 (PID-5 APP-RD). Structural homology, metal composition, inhibitor-bonding interactions, and the potential for dimerisation were critically assessed through computational techniques, including structural superimposition and protein-ligand docking. Results from this research suggest that the metallopeptidase-like domain shares high structural homology with known aminopeptidase P enzymes and possesses the canonical 'pita-bread fold'. However, the absence of conserved metal-coordinating residues indicates that only a single Zn2+ may be bound at the active site. The PID-5 APP-RD may form transient interactions with a known aminopeptidase P inhibitor and may therefore recognise substrates in a comparable way to the known structures. However, loss of key catalytic residues suggests the domain will be inactive. Further evidence suggests that heterodimerisation with C. elegans aminopeptidase P is feasible and therefore PID-5 is predicted to regulate proteolytic cleavage in the silencing pathway. PID-5 may interact with PID-2 to bring aminopeptidase P activity to the Z-granule, where it could influence WAGO-4 activity to ensure the balanced production of 22G-RNA signals for transgenerational silencing. Targeted experiments into APPs implicated in malaria and cancer are required in order to build upon the biological and therapeutic significance of this research.
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Affiliation(s)
- Anna C. Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
| | - Kyle S. Gregory
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
| | - R. Elwyn Isaac
- School of Biology, University of Leeds, Leeds LS2 9JT, UK;
| | - K. Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
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18
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Mann JM, Wei C, Chen C. How genetic defects in piRNA trimming contribute to male infertility. Andrology 2023; 11:911-917. [PMID: 36263612 PMCID: PMC10115909 DOI: 10.1111/andr.13324] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/25/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022]
Abstract
In germ cells, small non-coding PIWI-interacting RNAs (piRNAs) work to silence harmful transposons to maintain genomic stability and regulate gene expression to ensure fertility. However, these piRNAs must undergo a series of steps during biogenesis to be properly loaded onto PIWI proteins and reach the correct nucleotide length. This review is focused on what we are learning about a crucial step in this process, piRNA trimming, in which pre-piRNAs are shortened to final lengths of 21-35 nucleotides. Recently, the 3'-5' exonuclease trimmer has been identified in various models as PNLDC1/PARN-1. Mutations of the piRNA trimmers in vivo lead to increased transposon expression, elevated levels of untrimmed pre-piRNAs, decreased piRNA stability, and male infertility. Here, we will discuss the role of piRNA trimmers in piRNA biogenesis and function, describe consequences of piRNA trimmer mutations using mammalian models and human patients, and examine future avenues of piRNA trimming-related study for clinical advancements for male infertility.
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Affiliation(s)
- Jeffrey M. Mann
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chao Wei
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, Michigan, USA
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19
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Saquib M, Agnihotri P, Biswas S. Interrelated grid of non-coding RNA: An important aspect in Rheumatoid Arthritis pathogenesis. Mol Biol Rep 2023:10.1007/s11033-023-08543-w. [PMID: 37294467 DOI: 10.1007/s11033-023-08543-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Inflammation and autoimmunity are the root cause of rheumatoid arthritis, a destructive disease of joints. Multiple biomolecules are involved in the pathogenesis of RA and are related to various events of molecular biology. RNA is a versatile biomolecule, playing numerous roles at structural, functional, and regulatory stages to maintain cellular homeostasis. The involvement of RNA (coding/non-coding) in disease development and progression has left a wide whole to fill with newer approaches. Non-coding RNAs belong to the housekeeping and regulatory categories and both have their specific roles, and their alteration causes specific implications in disease pathogenesis. Housekeeping RNAs, rRNA, tRNA and regulatory RNA, micro-RNA, circular RNA, piRNA and long non-coding RNA were found to be important regulators of inflammation. They work at the pre-and post-transcriptional levels and were found to be more intriguing to study their regulatory impact on disease pathogenesis. The review addresses a question on how the non-coding RNA gets involved in early RA pathogenesis and can be utilized to know their targets to understand the disease better and make way towards the unresolved mystery of RA development.
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Affiliation(s)
- Mohd Saquib
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prachi Agnihotri
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sagarika Biswas
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Integrative and Functional Biology Department CSIR- Institute of Genomics & Integrative Biology, Mall Road, Delhi, 110 007, India.
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20
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Chen K, Yang X, Yang D, Huang Y. Spindle-E is essential for gametogenesis in the silkworm, Bombyx mori. INSECT SCIENCE 2023; 30:293-304. [PMID: 35866721 DOI: 10.1111/1744-7917.13096] [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: 02/09/2022] [Revised: 06/06/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
As a defense mechanism against transposable elements, the PIWI-interacting RNA (piRNA) pathway maintains genomic integrity and ensures proper gametogenesis in gonads. Numerous factors are orchestrated to ensure normal operation of the piRNA pathway. Spindle-E (Spn-E) gene was one of the first genes shown to participate in the piRNA pathway. In this study, we performed functional analysis of Spn-E in the model lepidopteran insect, Bombyx mori. Unlike the germline-specific expression pattern observed in Drosophila and mouse, BmSpn-E was ubiquitously expressed in all tissues tested, and it was highly expressed in gonads. Immunofluorescent staining showed that BmSpn-E was localized in both germ cells and somatic cells in ovary and was expressed in spermatocytes in testis. We used a binary transgenic CRISPR/Cas9 system to construct BmSpn-E mutants. Loss of BmSpn-E expression caused derepression of transposons in gonads. We also found that mutant gonads were much smaller than wild-type gonads and that the number of germ cells was considerably lower in mutant gonads. Quantitative real-time PCR analysis and TUNEL staining revealed that apoptosis was greatly enhanced in mutant gonads. Further, we found that the BmSpn-E mutation impacted gonadal development and gametogenesis at the early larval stage. In summary, our data provided the first evidence that BmSpn-E plays vital roles in gonadal development and gametogenesis in B. mori.
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Affiliation(s)
- Kai Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu Province, China
| | - Xu Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Dehong Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
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21
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Hoguin A, Yang F, Groisillier A, Bowler C, Genovesio A, Ait-Mohamed O, Vieira FRJ, Tirichine L. The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases. Commun Biol 2023; 6:253. [PMID: 36894681 PMCID: PMC9998398 DOI: 10.1038/s42003-023-04629-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.
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Affiliation(s)
- Antoine Hoguin
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Feng Yang
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | | | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Auguste Genovesio
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Ouardia Ait-Mohamed
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
- Laboratory of Computational and Quantitative Biology-LCQB - UMR 7238 CNRS-Sorbonne Université. Institut de Biologie Paris Seine, 75005, Paris, France.
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France.
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22
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Eugénio AT, Marialva MSP, Beldade P. Effects of Wolbachia on Transposable Element Expression Vary Between Drosophila melanogaster Host Genotypes. Genome Biol Evol 2023; 15:7059559. [PMID: 36929176 PMCID: PMC10025071 DOI: 10.1093/gbe/evad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 02/13/2023] [Accepted: 02/19/2023] [Indexed: 03/18/2023] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences capable of changing position in host genomes, thereby causing mutations. TE insertions typically have deleterious effects but they can also be beneficial. Increasing evidence of the contribution of TEs to adaptive evolution further raises interest in understanding what factors impact TE activity. Based on previous studies associating the bacterial endosymbiont Wolbachia with changes in the abundance of piRNAs, a mechanism for TE repression, and to transposition of specific TEs, we hypothesized that Wolbachia infection would interfere with TE activity. We tested this hypothesis by studying the expression of 14 TEs in a panel of 25 Drosophila melanogaster host genotypes, naturally infected with Wolbachia and annotated for TE insertions. The host genotypes differed significantly in Wolbachia titers inside individual flies, with broad-sense heritability around 20%, and in the number of TE insertions, which depended greatly on TE identity. By removing Wolbachia from the target host genotypes, we generated a panel of 25 pairs of Wolbachia-positive and Wolbachia-negative lines in which we quantified transcription levels for our target TEs. We found variation in TE expression that was dependent on Wolbachia status, TE identity, and host genotype. Comparing between pairs of Wolbachia-positive and Wolbachia-negative flies, we found that Wolbachia removal affected TE expression in 21.1% of the TE-genotype combinations tested, with up to 2.3 times differences in the median level of transcript. Our data show that Wolbachia can impact TE activity in host genomes, underscoring the importance this endosymbiont can have in the generation of genetic novelty in hosts.
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Affiliation(s)
| | | | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- cE3c (Center for Ecology, Evolution and Environmental Changes) and CHANGE (Global Change and Sustainability Institute), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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23
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Feng X, Pan S, Tu H, Huang J, Xiao C, Shen X, You L, Zhao X, Chen Y, Xu D, Qu X, Hu H. IQ67 DOMAIN protein 21 is critical for indentation formation in pavement cell morphogenesis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:721-738. [PMID: 36263896 DOI: 10.1111/jipb.13393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/15/2022] [Indexed: 05/26/2023]
Abstract
In plants, cortical microtubules anchor to the plasma membrane in arrays and play important roles in cell shape. However, the molecular mechanism of microtubule binding proteins, which connect the plasma membrane and cortical microtubules in cell morphology remains largely unknown. Here, we report that a plasma membrane and microtubule dual-localized IQ67 domain protein, IQD21, is critical for cotyledon pavement cell (PC) morphogenesis in Arabidopsis. iqd21 mutation caused increased indentation width, decreased lobe length, and similar lobe number of PCs, whereas IQD21 overexpression had a different effect on cotyledon PC shape. Weak overexpression led to increased lobe number, decreased indentation width, and similar lobe length, while moderate or great overexpression resulted in decreased lobe number, indentation width, and lobe length of PCs. Live-cell observations revealed that IQD21 accumulation at indentation regions correlates with lobe initiation and outgrowth during PC development. Cell biological and genetic approaches revealed that IQD21 promotes transfacial microtubules anchoring to the plasma membrane via its polybasic sites and bundling at the indentation regions in both periclinal and anticlinal walls. IQD21 controls cortical microtubule organization mainly through promoting Katanin 1-mediated microtubule severing during PC interdigitation. These findings provide the genetic evidence that transfacial microtubule arrays play a determinant role in lobe formation, and the insight into the molecular mechanism of IQD21 in transfacial microtubule organization at indentations and puzzle-shaped PC development.
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Affiliation(s)
- Xinhua Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shujuan Pan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junjie Huang
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430070, China
| | - Chuanlei Xiao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinyan Zhao
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Yongqiang Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Danyun Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaolu Qu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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24
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Measuring Transposable Element Activity in Adult Drosophila Ovaries. Methods Mol Biol 2023; 2626:309-321. [PMID: 36715912 DOI: 10.1007/978-1-0716-2970-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Transposons are genetic elements that use various mechanisms of transposition to move around the genome, thus posing a risk to genomic integrity. Repression of transposable elements (TEs) involves the complex PIWI pathway and several proteins associated with heterochromatinization. All players of TE repression are indispensable for proper reproductive fitness, as loss-of-function mutations in these genes result primarily in sterility and impaired reproductive development. When investigating the function of novel genes with similar phenotypes, elevated transposon expression in reproductive tissues can be a marker for involvement in the aforementioned processes. Here, we present a protocol for investigating TE levels in adult Drosophila ovaries, from dissection to data analysis.
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25
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Sohn EJ, Oh SO. P-Element-Induced Wimpy Testis Proteins and P-Element-Induced Wimpy Testis-Interacting RNAs Expression in Ovarian Cancer Stem Cells. Genet Test Mol Biomarkers 2023; 27:56-64. [PMID: 36853842 DOI: 10.1089/gtmb.2022.0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Background: P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a type of noncoding RNA and are predominantly expressed in germline cells. piRNAs function as gene regulators and potential biomarkers for the development of a number of malignancies. The biological importance of piRNAs in ovarian cancer is still unknown. In this study, we investigated the expression of piRNAs in ovarian cancer stem cells and compared it with that in adherent cells. Methods: To assess changes in the expression levels of PIWIL1/HIWI, PIWIL2/HILI, PIWIL3, and PIWIL4/HIWI2, we used quantitative reverse-transcription polymerase chain reaction (RT-qPCR) analysis. Changes in piRNA expression levels in ovarian cancer stem cells were analyzed using Arraystar piRNA microarray screening. Gene Ontology (GO) enrichment analysis was conducted to determine the potential functions of piRNAs. Results: Using microarray analysis, we identified a cohort of differentially expressed piRNAs. Fifteen piRNAs, including DQ570763 and DQ597396, were downregulated, and 58 piRNAs were upregulated when compared with those in adherent A2780 and SKOV3 cells (p > 0.05, >2.0, respectively). GO functions of the downregulated piRNAs (DQ570763 and DQ570797) suggest that their roles are commonly associated with the Golgi apparatus. In addition, A2780-SP and SKOV3-SP cells had higher PIWIL3 and PIWIL4 mRNA levels than adherent cells (A2780 and SKOV3). Moreover, we determined, using receiver operating characteristic plot, that the expression level of PIWIL4 was lower in responders than in nonresponders after treatment with platins in patients with ovarian cancer. Finally, in ovarian cancer, PIWIL4 expression was associated with somatic mutations of dynein axonemal heavy chain 2, signal induced proliferation associated 1 like 2, YTH N6-methyladenosine RNA-binding protein 1, TBC1 domain family member 8, and LPS responsive Beige-like anchor protein. Conclusion: Our study showed that PIWI proteins and piRNAs are potential diagnostic and prognostic biomarkers for ovarian cancer.
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Affiliation(s)
- Eun Jung Sohn
- College of Medicine, Pusan National University, Yangsan, Korea
| | - Sae-Ock Oh
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Korea
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26
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The Role of microRNAs in Inflammation. Int J Mol Sci 2022; 23:ijms232415479. [PMID: 36555120 PMCID: PMC9779565 DOI: 10.3390/ijms232415479] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Inflammation is a biological response of the immune system to various insults, such as pathogens, toxic compounds, damaged cells, and radiation. The complex network of pro- and anti-inflammatory factors and their direction towards inflammation often leads to the development and progression of various inflammation-associated diseases. The role of small non-coding RNAs (small ncRNAs) in inflammation has gained much attention in the past two decades for their regulation of inflammatory gene expression at multiple levels and their potential to serve as biomarkers and therapeutic targets in various diseases. One group of small ncRNAs, microRNAs (miRNAs), has become a key regulator in various inflammatory disease conditions. Their fine-tuning of target gene regulation often turns out to be an important factor in controlling aberrant inflammatory reactions in the system. This review summarizes the biogenesis of miRNA and the mechanisms of miRNA-mediated gene regulation. The review also briefly discusses various pro- and anti-inflammatory miRNAs, their targets and functions, and provides a detailed discussion on the role of miR-10a in inflammation.
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27
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Di R, Zhang R, Mwacharo JM, Wang X, He X, Liu Y, Zhang J, Gong Y, Zhang X, Chu M. Characteristics of piRNAs and their comparative profiling in testes of sheep with different fertility. Front Genet 2022; 13:1078049. [PMID: 36568364 PMCID: PMC9768229 DOI: 10.3389/fgene.2022.1078049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
As a novel class of small RNAs, piRNAs are highly expressed in the animal gonads and their main known role is to inhibit transposon activity for ensuring the correctness and integrity of genome. In order to explore the characteristics of piRNAs in sheep testis and their possible regulatory roles on male reproduction, deep sequencing technology was used to sequence small RNAs and identify piRNAs in testes of sheep. The length of piRNAs in sheep testes showed a unimodal distribution between 26 and 31 nt, with a peak at 29 nt. These piRNAs exhibited obvious ping-pong signature and strand specificity. In the genome, they were mainly aligned to CDS, intron, repetitive sequence regions and unannotated regions. Furthermore, in transposon analysis, piRNAs were aligned predominantly to LINE, SINE, and LTR types of retrotransposon in sheep testes, and the piRNAs derived from each type showed obvious ping-pong signature. The piRNA clusters identified in sheep testes were mainly distributed on chromosomes 3, 7, 15, 17, 18 and 20. The results combining semen determination with pathway enrichment analysis implied that differentially expressed piRNAs between the testes of rams with different fertility might participate in spermatogenesis by regulating multiple pathways closely related to stabilization of blood-testis barrier and renewal and differentiation of spermatogonial stem cell. Taken together, the study provided new insights into the characteristics, origin and expression patterns of piRNAs in sheep testes tissue, which would help us better understand the role of piRNAs in sheep reproduction.
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Affiliation(s)
- Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rensen Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China,School of Advanced Agricultural Sciences, Yiyang Vocational & Technical College, Yiyang, China
| | - Joram Mwashigadi Mwacharo
- Small Ruminant Genomics International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia,Institute of Animal and Veterinary Sciences, SRUC and Center for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinlong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yiming Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaosheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China,*Correspondence: Xiaosheng Zhang, ; Mingxing Chu,
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Xiaosheng Zhang, ; Mingxing Chu,
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28
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He S, Feng X. DNA methylation dynamics during germline development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2240-2251. [PMID: 36478632 PMCID: PMC10108260 DOI: 10.1111/jipb.13422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
DNA methylation plays essential homeostatic functions in eukaryotic genomes. In animals, DNA methylation is also developmentally regulated and, in turn, regulates development. In the past two decades, huge research effort has endorsed the understanding that DNA methylation plays a similar role in plant development, especially during sexual reproduction. The power of whole-genome sequencing and cell isolation techniques, as well as bioinformatics tools, have enabled recent studies to reveal dynamic changes in DNA methylation during germline development. Furthermore, the combination of these technological advances with genetics, developmental biology and cell biology tools has revealed functional methylation reprogramming events that control gene and transposon activities in flowering plant germlines. In this review, we discuss the major advances in our knowledge of DNA methylation dynamics during male and female germline development in flowering plants.
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Affiliation(s)
- Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, College of AgricultureSouth China Agricultural UniversityGuangzhou510642China
| | - Xiaoqi Feng
- John Innes Centre, Colney LaneNorwichNR4 7UHUK
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29
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Ye X, Yang Y, Zhao C, Xiao S, Sun YH, He C, Xiong S, Zhao X, Zhang B, Lin H, Shi J, Mei Y, Xu H, Fang Q, Wu F, Li D, Ye G. Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps. Nat Commun 2022; 13:6417. [PMID: 36302851 PMCID: PMC9613689 DOI: 10.1038/s41467-022-34202-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 10/13/2022] [Indexed: 12/25/2022] Open
Abstract
Parasitoid wasps are rapidly developing as a model for evolutionary biology. Here we present chromosomal genomes of two Anastatus wasps, A. japonicus and A. fulloi, and leverage these genomes to study two fundamental questions-genome size evolution and venom evolution. Anastatus shows a much larger genome than is known among other wasps, with unexpectedly recent bursts of LTR retrotransposons. Importantly, several genomic innovations, including Piwi gene family expansion, ubiquitous Piwi expression profiles, as well as transposable element-piRNA coevolution, have likely emerged for transposable element silencing to maintain genomic stability. Additionally, we show that the co-option evolution arose by expression shifts in the venom gland plays a dominant role in venom turnover. We also highlight the potential importance of non-venom genes that are coexpressed with venom genes during venom evolution. Our findings greatly advance the current understanding of genome size evolution and venom evolution, and these genomic resources will facilitate comparative genomics studies of insects in the future.
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Affiliation(s)
- Xinhai Ye
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XShanghai Institute for Advanced Study, Zhejiang University, Shanghai, China ,grid.13402.340000 0004 1759 700XCollege of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Yi Yang
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Can Zhao
- grid.484195.5Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Shan Xiao
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yu H. Sun
- grid.16416.340000 0004 1936 9174Department of Biology, University of Rochester, Rochester, NY USA
| | - Chun He
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shijiao Xiong
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xianxin Zhao
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Bo Zhang
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Haiwei Lin
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jiamin Shi
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongxing Xu
- grid.410744.20000 0000 9883 3553State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qi Fang
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wu
- grid.13402.340000 0004 1759 700XShanghai Institute for Advanced Study, Zhejiang University, Shanghai, China ,grid.13402.340000 0004 1759 700XCollege of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Dunsong Li
- grid.484195.5Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Gongyin Ye
- grid.13402.340000 0004 1759 700XState Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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30
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Romero MA, Mumford PW, Roberson PA, Osburn SC, Young KC, Sedivy JM, Roberts MD. Translational Significance of the LINE-1 Jumping Gene in Skeletal Muscle. Exerc Sport Sci Rev 2022; 50:185-193. [PMID: 35749745 PMCID: PMC9651911 DOI: 10.1249/jes.0000000000000301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Retrotransposons are gene segments that proliferate in the genome, and the Long INterspersed Element 1 (LINE-1 or L1) retrotransposon is active in humans. Although older mammals show enhanced skeletal muscle L1 expression, exercise generally reverses this trend. We hypothesize skeletal muscle L1 expression influences muscle physiology, and additional innovative investigations are needed to confirm this hypothesis.
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Affiliation(s)
- Matthew A. Romero
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California USA
| | - Petey W. Mumford
- Department of Exercise Science, Lindenwood University, St. Charles, Missouri USA
| | - Paul A. Roberson
- Department of Cellular and Molecular Physiology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania USA
| | | | - Kaelin C. Young
- School of Kinesiology, Auburn University, Auburn, Alabama USA
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn, Auburn, Alabama, USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center on the Biology of Aging, Brown University, Providence, Rhode Island, USA
| | - Michael D. Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama USA
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn, Auburn, Alabama, USA
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31
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Chattopadhyay T, Gupta P, Nayak R, Mallick B. Genome-wide profiling of dysregulated piRNAs and their target genes implicated in oncogenicity of Tongue Squamous Cell Carcinoma. Gene 2022; 849:146919. [PMID: 36179965 DOI: 10.1016/j.gene.2022.146919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are single-stranded, 23-36 nucleotide long RNAs that regulate gene expression in the germline but are also detected in some cancers. However, there are no reports yet on piRNA expression in tongue squamous cell carcinoma (TSCC), the most common oral cancer (80-90% percent of all oral cancers). We performed small RNA and whole transcriptome sequencing in H357 tongue cancer and HOK cells (GEO database accession numbers: GSE196674 and GSE196688). We also examined nine published sets of gene expression array data of TSCC tissues from the GEO database to decode piRNAs and their putative targets that may be involved in tumorigenesis. We identified a pool of 16058 and 25677 piRNAs in H357 and HOK, respectively, among which 406 are differentially expressed. We also found that 2094 protein-coding genes are differentially expressed in either TSCC tissues or cell lines. We performed target predictions for these piRNA, pathway and disease function (DF) analyses, as well as qRT-PCR validation of piRNA-target pairs. These experiments revealed one up-regulated (FDFT1) and four down-regulated (OGA, BDH1, TAT, HYAL4) target genes that are enriched in 11 canonical pathways (CPs), with postulated roles in the initiation and progression of TSCC. Downregulation of piR-33422 is predicted to upregulate the FDFT1 gene, which encodes a mevalonate/cholesterol-pathway related farnesyl-diphosphate farnesyltransferase. The FDFT1 appears to be involved in the largest number of oncogenesis-related processes and is interacting with statins, which is a classical cancer drug. This study provides the first evidence of the piRNome of TSCC, which could be investigated further to decode piRNA-mediated gene regulations in malignancy and potential drug targets, such as FDFT1.
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Affiliation(s)
- Trisha Chattopadhyay
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Pooja Gupta
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Rojalin Nayak
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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32
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He X, Wu H, Ye Y, Gong X, Bao B. Transcriptome analysis revealed gene expression feminization of testis after exogenous tetrodotoxin administration in pufferfish Takifugu flavidus. BMC Genomics 2022; 23:553. [PMID: 35922761 PMCID: PMC9347094 DOI: 10.1186/s12864-022-08787-z] [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: 09/30/2021] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
Tetrodotoxin (TTX) is a deadly neurotoxin and usually accumulates in large amounts in the ovaries but is non-toxic or low toxic in the testis of pufferfish. The molecular mechanism underlying sexual dimorphism accumulation of TTX in ovary and testis, and the relationship between TTX accumulation with sex related genes expression remain largely unknown. The present study investigated the effects of exogenous TTX treatment on Takifugu flavidus. The results demonstrated that exogenous TTX administration significantly incresed level of TTX concentration in kidney, cholecyst, skin, liver, heart, muscle, ovary and testis of the treatment group (TG) than that of the control group (CG). Transcriptome sequencing and analysis were performed to study differential expression profiles of mRNA and piRNA after TTX administration of the ovary and testis. The results showed that compared with female control group (FCG) and male control group (MCG), TTX administration resulted in 80 and 23 piRNAs, 126 and 223 genes up and down regulated expression in female TTX-treated group (FTG), meanwhile, 286 and 223 piRNAs, 2 and 443 genes up and down regulated expression in male TTX-treated group (MTG). The female dominant genes cyp19a1, gdf9 and foxl2 were found to be up-regulated in MTG. The cyp19a1, whose corresponding target piRNA uniq_554482 was identified as down-regulated in the MTG, indicating the gene expression feminization in testis after exogenous TTX administration. The KEGG enrichment analysis revealed that differentially expressed genes (DEGs) and piRNAs (DEpiRNAs) in MTG vs MCG group were more enriched in metabolism pathways, indicating that the testis produced more metabolic pathways in response to exogenous TTX, which might be a reason for the sexual dimorphism of TTX distribution in gonads. In addition, TdT-mediated dUTP-biotin nick end labeling staining showed that significant apoptosis was detected in the MTG testis, and the role of the cell apoptotic pathways was further confirmed. Overall, our research revealed that the response of the ovary and testis to TTX administration was largely different, the ovary is more tolerant whereas the testis is more sensitive to TTX. These data will deepen our understanding on the accumulation of TTX sexual dimorphism in Takifugu.
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Affiliation(s)
- Xue He
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hexing Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yaping Ye
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaolin Gong
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education; International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Chattopadhyay T, Biswal P, Lalruatfela A, Mallick B. Emerging roles of PIWI-interacting RNAs (piRNAs) and PIWI proteins in head and neck cancer and their potential clinical implications. Biochim Biophys Acta Rev Cancer 2022; 1877:188772. [PMID: 35931391 DOI: 10.1016/j.bbcan.2022.188772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 02/08/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) are among the well-known neoplasms originating in the oral cavity, pharynx, and larynx. Despite advancements in chemotherapy, radiotherapy, and surgery, the survival rates of the patients are low, which has posed a major therapeutic challenge. A growing number of non-coding RNAs (ncRNAs), for instance, microRNAs, have been identified whose abnormal expression patterns have been implicated in HNSCC. However, more recently, several seminal research has shown that piwi-interacting RNAs (piRNAs), a promising and young class of small ncRNA, are linked to the emergence and progression of cancer. They can regulate transposable elements (TE) and gene expression through multiple mechanisms, making them potentially more powerful regulators than miRNAs. Hence, they can be more promising ncRNAs candidates for cancer therapeutic intervention. Here, we surveyed the roles and clinical implications of piRNAs and their PIWI proteins partners in tumorigenesis and associated molecular processes of cancer, with a particular focus on HNSCC, to offer a new avenue for diagnosis, prognosis, and therapeutic interventions for the malignancy, improving patient's outcomes.
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Affiliation(s)
- Trisha Chattopadhyay
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Priyajit Biswal
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Anthony Lalruatfela
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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Jin L, Zhang Z, Wang Z, Tan X, Wang Z, Shen L, Long C, Wei G, He D. Novel piRNA MW557525 regulates the growth of Piwil2-iCSCs and maintains their stem cell pluripotency. Mol Biol Rep 2022; 49:6957-6969. [PMID: 35411481 DOI: 10.1007/s11033-022-07443-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 04/01/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND CSCs play an important role in tumor development. Some studies have demonstrated that piRNAs participate in the progression of various cancers. However, the detailed function of piRNAs in CSCs requires further investigation. This study aimed to investigate the significance of novel piRNA MW557525, one of the top five up-regulated piRNAs screened by gene chip and it has been verified by RT-q-PCR that it is indeed the most obvious up-regulated expression in Piwil2-iCSCs. METHODS AND RESULTS Differentially expressed piRNAs in Piwil2-iCSCs were screened by gene chip. Target genes were predicted by the miRanda algorithm and subjected to GO and KEGG analysis. One of the differential piRNAs, novel piRNA MW557525, was transfected and its target gene NOP56 was silenced in Piwil2-iCSCs, respectively. RT-qPCR, western blot (WB) and dual luciferase reporter assay were used to investigate the interaction of piRNA MW557525 and NOP56. We identified the effect of piRNA MW557525 and NOP56 knockdown on cell proliferation, migration, invasion, and apoptosis via CCK-8, transwell assay, and flow cytometry. The expressions of CD24, CD133, KLF4, and SOX2 were detected via WB. The results showed that piRNA MW557525 was negatively correlated with NOP56, and it promoted the proliferation, migration, invasion, and inhibited apoptosis in Piwil2-iCSCs, and it also promoted the expressions of CD24, CD133, KLF4, and SOX2, while NOP56 showed the opposite effect. CONCLUSIONS These findings suggested that novel piRNA MW557525 might be a novel therapeutic target in Piwil2-iCSCs.
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Affiliation(s)
- Liming Jin
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China
| | - Zhaoxia Zhang
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China
| | - Zhang Wang
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China
| | - Xiaojun Tan
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China
| | - Zhaoying Wang
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China
| | - Lianju Shen
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China
| | - Chunlan Long
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China
| | - Guanghui Wei
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China
| | - Dawei He
- Department of Urology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.
- Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering, Chongqing, 400014, China.
- China International Science and Technology Cooperation Base of Child Development and Critical, Ministry of Education Key Laboratory of Child Development and Disorders; Chongqing Key Laboratory of Pediatrics, National Clinical Research Center for Child Health and Disorders, ChongqingChongqing, 400014, China.
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Santos D, Verdonckt TW, Mingels L, Van den Brande S, Geens B, Van Nieuwerburgh F, Kolliopoulou A, Swevers L, Wynant N, Vanden Broeck J. PIWI Proteins Play an Antiviral Role in Lepidopteran Cell Lines. Viruses 2022; 14:v14071442. [PMID: 35891422 PMCID: PMC9321812 DOI: 10.3390/v14071442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 01/27/2023] Open
Abstract
Insect antiviral immunity primarily relies on RNAi mechanisms. While a key role of small interfering (si)RNAs and AGO proteins has been well established in this regard, the situation for PIWI proteins and PIWI-interacting (pi)RNAs is not as clear. In the present study, we investigate whether PIWI proteins and viral piRNAs are involved in the immunity against single-stranded RNA viruses in lepidopteran cells, where two PIWIs are identified (Siwi and Ago3). Via loss- and gain-of-function studies in Bombyx mori BmN4 cells and in Trichoplusia ni High Five cells, we demonstrated an antiviral role of Siwi and Ago3. However, small RNA analysis suggests that viral piRNAs can be absent in these lepidopteran cells. Together with the current literature, our results support a functional diversification of PIWI proteins in insects.
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Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (T.-W.V.); (L.M.); (S.V.d.B.); (B.G.); (N.W.); (J.V.B.)
- Correspondence:
| | - Thomas-Wolf Verdonckt
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (T.-W.V.); (L.M.); (S.V.d.B.); (B.G.); (N.W.); (J.V.B.)
| | - Lina Mingels
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (T.-W.V.); (L.M.); (S.V.d.B.); (B.G.); (N.W.); (J.V.B.)
| | - Stijn Van den Brande
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (T.-W.V.); (L.M.); (S.V.d.B.); (B.G.); (N.W.); (J.V.B.)
| | - Bart Geens
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (T.-W.V.); (L.M.); (S.V.d.B.); (B.G.); (N.W.); (J.V.B.)
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Gent University, Ottergemsesteenweg 460, 9000 Gent, Belgium;
| | - Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, 153 10 Athens, Greece; (A.K.); (L.S.)
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, 153 10 Athens, Greece; (A.K.); (L.S.)
| | - Niels Wynant
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (T.-W.V.); (L.M.); (S.V.d.B.); (B.G.); (N.W.); (J.V.B.)
| | - Jozef Vanden Broeck
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (T.-W.V.); (L.M.); (S.V.d.B.); (B.G.); (N.W.); (J.V.B.)
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Suleiman M, Kounosu A, Murcott B, Dayi M, Pawluk R, Yoshida A, Viney M, Kikuchi T, Hunt VL. piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode. Sci Rep 2022; 12:10156. [PMID: 35710810 PMCID: PMC9203780 DOI: 10.1038/s41598-022-14247-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21-22 nt long sRNAs with a 5' uridine (21-22Us) and a 5' monophosphate, and (ii) 27 nt long sRNAs with a 5' guanine/adenine (27GAs) and a 5' modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V.
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Affiliation(s)
- Mona Suleiman
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Asuka Kounosu
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Ben Murcott
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Mehmet Dayi
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
- Forestry Vocational School, Duzce University, 81620, Duzce, Turkey
| | - Rebecca Pawluk
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Akemi Yoshida
- Laboratory of Genomics, Frontier Science Research Center, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Mark Viney
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Taisei Kikuchi
- Parasitology, Department of Infectious Dieses, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.
| | - Vicky L Hunt
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
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Lee S, Kuramochi-Miyagawa S, Nagamori I, Nakano T. Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs. RNA (NEW YORK, N.Y.) 2022; 28:683-696. [PMID: 35145000 PMCID: PMC9014882 DOI: 10.1261/rna.078905.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
PIWI-interacting RNAs (piRNAs), which are germ cell-specific small RNAs, are essential for spermatogenesis. In fetal mouse germ cells, piRNAs are synthesized from sense and antisense RNAs of transposable element sequences for retrotransposon silencing. In a previous study, we reported that transgenic mice expressing antisense-Dnmt3L under the control of the Miwi2 promoter (Tg-Miwi2P-asDnmt3L) exhibited piRNA-mediated DNMT3L down-regulation. In this study, two transgene integration loci (B3 and E1) were identified on chromosome 18 of the Tg-Miwi2P-asDnmt3L mice; these loci were weak piRNA clusters. Crossbreeding was performed to obtain mice with the transgene cassette inserted into a single locus. DNMT3L was silenced and spermatogenesis was severely impaired in mice with the transgene cassette inserted at the B3 locus (Tg-B mice). In contrast, spermatogenesis in mice bearing the transgene at the E1 locus (Tg-E mice) was normal. The number of piRNAs for Dnmt3L in Tg-B mice was eightfold higher than that in Tg-E mice. Therefore, both gene silencing and impaired spermatogenesis depended on the transgene copy number rather than on the insertion loci. Additionally, the endogenous Dnmt3L promoter was not methylated in Tg mice, suggesting that Dnmt3L silencing was caused by post-transcriptional gene silencing. Based on these data, we discuss a piRNA-dependent gene silencing mechanism against novel gene insertions.
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Affiliation(s)
- SePil Lee
- Graduate School of Frontier Biosciences, Osaka University, Yamada-oka 2-2 Suita, Osaka 565-0871, Japan
| | - Satomi Kuramochi-Miyagawa
- Graduate School of Frontier Biosciences, Osaka University, Yamada-oka 2-2 Suita, Osaka 565-0871, Japan
- Medical School, Department of Pathology, Osaka University, Yamada-oka 2-2 Suita, Osaka 565-0871, Japan
| | - Ippei Nagamori
- Medical School, Department of Pathology, Osaka University, Yamada-oka 2-2 Suita, Osaka 565-0871, Japan
| | - Toru Nakano
- Graduate School of Frontier Biosciences, Osaka University, Yamada-oka 2-2 Suita, Osaka 565-0871, Japan
- Medical School, Department of Pathology, Osaka University, Yamada-oka 2-2 Suita, Osaka 565-0871, Japan
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Huang S, Nishiumi S, Asaduzzaman M, Pan Y, Liu G, Yoshitake K, Maeyama K, Kinoshita S, Nagai K, Watabe S, Yoshida T, Asakawa S. Exosome-derived small non-coding RNAs reveal immune response upon grafting transplantation in Pinctada fucata (Mollusca). Open Biol 2022; 12:210317. [PMID: 35506205 PMCID: PMC9065966 DOI: 10.1098/rsob.210317] [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] [Indexed: 01/04/2023] Open
Abstract
Exosomes, a subset of small extracellular vesicles, carry various nucleic acids, proteins, lipids, amino acids and metabolites. They function as a mode of intercellular communication and molecular transfer. Exosome cargo molecules, including small non-coding RNAs (sncRNAs), are involved in the immune response in various organisms. However, the role of exosome-derived sncRNAs in immune responses in molluscs remains unclear. Here, we aimed to reveal the sncRNAs involved in the immune response during grafting transplantation by the pearl oyster Pinctada fucata. Exosomes were successfully extracted from the P. fucata haemolymph during graft transplantation. Abundant microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) were simultaneously discovered in P. fucata exosomes by small RNA sequencing. The expression patterns of the miRNAs and piRNAs at the grafting and initial stages were not substantially different, but varied significantly between the initial and later stages. Target prediction and functional analysis indicate that these miRNAs and piRNAs are related to immune response upon grafting transplantation, whereas piRNAs may also be associated with transposon silencing by targeting with genome transposon elements. This work provides the basis for a functional understanding of exosome-derived sncRNAs and helps to gain further insight into the PIWI/piRNA pathway function outside of germline cells in molluscs.
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Affiliation(s)
- Songqian Huang
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shinya Nishiumi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Md Asaduzzaman
- Department of Marine Bioresources Science, Faculty of Fisheries, Chittagong Veterinary and Animal Sciences University, Khulshi 4225, Chittagong, Bangladesh
| | - Yida Pan
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Guanting Liu
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutoshi Yoshitake
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kaoru Maeyama
- Mikimoto Pharmaceutical Co., Ltd., Kurose 1425, Ise, Mie 516-8581, Japan
| | - Shigeharu Kinoshita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyohito Nagai
- Pearl Research Laboratory, K. Mikimoto & Co., Ltd., Osaki Hazako 923, Hamajima, Shima, Mie 517-0403, Japan
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0313, Japan
| | - Tetsuhiko Yoshida
- Institute for Advanced Sciences, Toagosei Co., Ltd., Tsukuba, Ibaraki 300-2611, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan
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Accurate quantification of 3'-terminal 2'-O-methylated small RNAs by utilizing oxidative deep sequencing and stem-loop RT-qPCR. Front Med 2022; 16:240-250. [PMID: 35416629 DOI: 10.1007/s11684-021-0909-7] [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: 05/12/2021] [Accepted: 11/25/2021] [Indexed: 11/04/2022]
Abstract
The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive, convenient, and reliable methods for quantifying RNA modifications. In particular, a subset of small RNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), are modified at their 3'-terminal nucleotides via 2'-O-methylation. However, quantifying the levels of these small RNAs is difficult because 2'-O-methylation at the RNA 3'-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase. These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays. In this study, we profiled 3'-terminal 2'-O-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment. We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach. Likewise, stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3'-terminal 2'-O-methyl piRNAs in human seminal plasma. In summary, this study established a standard procedure for quantifying the levels of 3'-terminal 2'-O-methyl miRNAs in plants and piRNAs. Accurate measurement of the 3'-terminal 2'-O-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.
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Cai A, Hu Y, Zhou Z, Qi Q, Wu Y, Dong P, Chen L, Wang F. PIWI-Interacting RNAs (piRNAs): Promising Applications as Emerging Biomarkers for Digestive System Cancer. Front Mol Biosci 2022; 9:848105. [PMID: 35155584 PMCID: PMC8829394 DOI: 10.3389/fmolb.2022.848105] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a novel type of small non-coding RNAs (sncRNAs), which are 26–31 nucleotides in length and bind to PIWI proteins. Although piRNAs were originally discovered in germline cells and are thought to be essential regulators for germline preservation, they can also influence gene expression in somatic cells. An increasing amount of data has shown that the dysregulation of piRNAs can both promote and repress the emergence and progression of human cancers through DNA methylation, transcriptional silencing, mRNA turnover, and translational control. Digestive cancers are currently a major cause of cancer deaths worldwide. piRNAs control the expression of essential genes and pathways associated with digestive cancer progression and have been reported as possible biomarkers for the diagnosis and treatment of digestive cancer. Here, we highlight recent advances in understanding the involvement of piRNAs, as well as potential diagnostic and therapeutic applications of piRNAs in various digestive cancers.
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Affiliation(s)
- Aiting Cai
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuhao Hu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhou Zhou
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Qianyi Qi
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yixuan Wu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Peixin Dong
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
| | - Lin Chen
- Department of Gastroenterology and Laboratory Medicine, Nantong Third Hospital Affiliated to Nantong University, Nantong, China
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
| | - Feng Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
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41
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Cammarata G, de Miguel-Perez D, Russo A, Peleg A, Dolo V, Rolfo C, Taverna S. Emerging noncoding RNAs contained in extracellular vesicles: rising stars as biomarkers in lung cancer liquid biopsy. Ther Adv Med Oncol 2022; 14:17588359221131229. [PMID: 36353504 PMCID: PMC9638531 DOI: 10.1177/17588359221131229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022] Open
Abstract
Lung cancer has a high morbidity and mortality rate, and affected patients have a
poor prognosis and low survival. The therapeutic approaches for lung cancer
treatment, including surgery, radiotherapy, and chemotherapy, are not completely
effective, due to late diagnosis. Although the identification of genetic drivers
has contributed to the improvement of lung cancer clinical management, the
discovery of new diagnostic and prognostic tools remains a critical issue.
Liquid biopsy (LB) represents a minimally invasive approach and practical
alternative source to investigate tumor-derived alterations and to facilitate
the selection of targeted therapies. LB allows for the testing of different
analytes such as circulating tumor cells, extracellular vesicles (EVs),
tumor-educated platelets, and cell-free nucleic acids including DNAs, RNAs, and
noncoding RNAs (ncRNAs). Several regulatory factors control the key cellular
oncogenic pathways involved in cancers. ncRNAs have a wide range of regulatory
effects in lung cancers. This review focuses on emerging regulatory ncRNAs,
freely circulating in body fluids or shuttled by EVs, such as circular-RNAs,
small nucleolar-RNAs, small nuclear-RNAs, and piwi-RNAs, as new biomarkers for
early detection, prognosis, and monitoring of therapeutic strategy of lung
cancer treatment.
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Affiliation(s)
- Giuseppe Cammarata
- Institute of Translational Pharmacology (IFT), National Research Council (CNR) of Italy, Palermo, Italy
| | - Diego de Miguel-Perez
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alessandro Russo
- Medical Oncology Unit, A.O. Papardo & Department of Human Pathology, University of Messina, Messina, Italy
| | - Ariel Peleg
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vincenza Dolo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, Box 1079, New York, NY 10029-6574, USA
| | - Simona Taverna
- Institute of Translational Pharmacology (IFT), National Research Council (CNR) of Italy, Via Ugo La Malfa, 153, Palermo 90146, Italy
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Riquelme I, Pérez-Moreno P, Letelier P, Brebi P, Roa JC. The Emerging Role of PIWI-Interacting RNAs (piRNAs) in Gastrointestinal Cancers: An Updated Perspective. Cancers (Basel) 2021; 14:202. [PMID: 35008366 PMCID: PMC8750603 DOI: 10.3390/cancers14010202] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) cancers produce ~3.4 million related deaths worldwide, comprising 35% of all cancer-related deaths. The high mortality among GI cancers is due to late diagnosis, the presence of metastasis and drug resistance development. Additionally, current clinical markers do not adequately guide patient management, thereby new and more reliable biomarkers and therapeutic targets are still needed for these diseases. RNA-seq technology has allowed the discovery of new types of RNA transcripts including PIWI-interacting RNAs (piRNAs), which have particular characteristics that enable these molecules to act via diverse molecular mechanisms for regulating gene expression. Cumulative evidence has described the potential role of piRNAs in the development of several tumor types as a likely explanation for certain genomic abnormalities and signaling pathways' deregulations observed in cancer. In addition, these piRNAs might be also proposed as promising diagnostic or prognostic biomarkers or as potential therapeutic targets in malignancies. This review describes important topics about piRNAs including their molecular characteristics, biosynthesis processes, gene expression silencing mechanisms, and the manner in which these transcripts have been studied in samples and cell lines of GI cancers to elucidate their implications in these diseases. Moreover, this article discusses the potential clinical usefulness of piRNAs as biomarkers and therapeutic targets in GI cancers.
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Affiliation(s)
- Ismael Riquelme
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco 4810101, Chile;
| | - Pablo Pérez-Moreno
- Millennium Institute on Immunology and Immunotherapy, Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8380000, Chile;
| | - Pablo Letelier
- Precision Health Research Laboratory, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Manuel Montt 56, Temuco 4813302, Chile;
| | - Priscilla Brebi
- Millennium Institute on Immunology and Immunotherapy, Laboratory of Integrative Biology (LIBi), Center for Excellence in Translational Medicine—Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile;
| | - Juan Carlos Roa
- Millennium Institute on Immunology and Immunotherapy, Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8380000, Chile;
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Degree of piRNA sharing and Piwi gene expression in the skeletal muscle of Piaractus mesopotamicus (pacu), Colossoma macropomum (tambaqui), and the hybrid tambacu. Comp Biochem Physiol A Mol Integr Physiol 2021; 264:111120. [PMID: 34822974 DOI: 10.1016/j.cbpa.2021.111120] [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: 09/16/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 11/24/2022]
Abstract
PiRNAs are a class of small noncoding RNAs that, in their mature form, bind to Piwi proteins to repress transposable element activity. Besides their role in gametogenesis and genome integrity, recent evidence indicates their action in non-germinative tissues. We performed a global analysis of piRNA and Piwi gene expression in the skeletal muscle of juveniles pacu (Piaractus mesopotamicus), tambaqui (Colossoma macropomum), and the hybrid tambacu to evaluate the degree of piRNA sharing among these three genotypes. Total RNA was sequenced and analyzed using specific parameters of piRNAs by bioinformatics tools. piRNA and Piwi gene expression was analyzed by RT-qPCR. We detected 24 piRNA clusters common to the three genotypes, with eight shared between pacu and tambacu, three between pacu and tambaqui, and five between tambaqui and tambacu; seven, five, and four clusters were unique to pacu, tambacu, and tambaqui, respectively. Genomic localization and fold change values showed two clusters and 100 piRNAs shared among the three genotypes. The gene expression of four piRNAs was evaluated to validate our bioinformatics results. piRNAs from cluster 17 were higher in tambacu than pacu and piRNAs from cluster 18 were more highly expressed in tambacu than tambaqui and pacu. In addition, the expression of Piwis 1 and 2 was higher in tambacu and tambaqui than pacu. Our results open an important window to investigate whether these small noncoding RNAs benefit the hybrid in terms of faster growth and offer a new perspective on the function of piRNAs and Piwis in fish skeletal muscle.
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Williams AE, Shrivastava G, Gittis AG, Ganesan S, Martin-Martin I, Valenzuela Leon PC, Olson KE, Calvo E. Aedes aegypti Piwi4 Structural Features Are Necessary for RNA Binding and Nuclear Localization. Int J Mol Sci 2021; 22:ijms222312733. [PMID: 34884537 PMCID: PMC8657434 DOI: 10.3390/ijms222312733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/21/2022] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway provides an RNA interference (RNAi) mechanism known from Drosophila studies to maintain the integrity of the germline genome by silencing transposable elements (TE). Aedes aegypti mosquitoes, which are the key vectors of several arthropod-borne viruses, exhibit an expanded repertoire of Piwi proteins involved in the piRNA pathway, suggesting functional divergence. Here, we investigate RNA-binding dynamics and subcellular localization of A. aegypti Piwi4 (AePiwi4), a Piwi protein involved in antiviral immunity and embryonic development, to better understand its function. We found that AePiwi4 PAZ (Piwi/Argonaute/Zwille), the domain that binds the 3′ ends of piRNAs, bound to mature (3′ 2′ O-methylated) and unmethylated RNAs with similar micromolar affinities (KD = 1.7 ± 0.8 μM and KD of 5.0 ± 2.2 μM, respectively; p = 0.05) in a sequence independent manner. Through site-directed mutagenesis studies, we identified highly conserved residues involved in RNA binding and found that subtle changes in the amino acids flanking the binding pocket across PAZ proteins have significant impacts on binding behaviors, likely by impacting the protein secondary structure. We also analyzed AePiwi4 subcellular localization in mosquito tissues. We found that the protein is both cytoplasmic and nuclear, and we identified an AePiwi4 nuclear localization signal (NLS) in the N-terminal region of the protein. Taken together, these studies provide insights on the dynamic role of AePiwi4 in RNAi and pave the way for future studies aimed at understanding Piwi interactions with diverse RNA populations.
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Affiliation(s)
- Adeline E. Williams
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Gaurav Shrivastava
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Apostolos G. Gittis
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Sundar Ganesan
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Ines Martin-Martin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Paola Carolina Valenzuela Leon
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
| | - Ken E. Olson
- Center for Vector-Borne Infectious Diseases, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Correspondence: (K.E.O.); (E.C.)
| | - Eric Calvo
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; (A.E.W.); (G.S.); (A.G.G.); (S.G.); (I.M.-M.); (P.C.V.L.)
- Correspondence: (K.E.O.); (E.C.)
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45
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Merkerova MD, Krejcik Z. Transposable elements and Piwi‑interacting RNAs in hemato‑oncology with a focus on myelodysplastic syndrome (Review). Int J Oncol 2021; 59:105. [PMID: 34779490 DOI: 10.3892/ijo.2021.5285] [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: 06/21/2021] [Accepted: 10/12/2021] [Indexed: 11/06/2022] Open
Abstract
Our current understanding of hematopoietic stem cell differentiation and the abnormalities that lead to leukemogenesis originates from the accumulation of knowledge regarding protein‑coding genes. However, the possible impact of transposable element (TE) mobilization and the expression of P‑element‑induced WImpy testis‑interacting RNAs (piRNAs) on leukemogenesis has been beyond the scope of scientific interest to date. The expression profiles of these molecules and their importance for human health have only been characterized recently due to the rapid progress of high‑throughput sequencing technology development. In the present review, current knowledge on the expression profile and function of TEs and piRNAs was summarized, with specific focus on their reported involvement in leukemogenesis and pathogenesis of myelodysplastic syndrome.
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Affiliation(s)
| | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, 128 20 Prague, Czech Republic
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46
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Huang S, Yoshitake K, Asakawa S. A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans. Int J Mol Sci 2021; 22:ijms222011166. [PMID: 34681826 PMCID: PMC8538981 DOI: 10.3390/ijms222011166] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.
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Affiliation(s)
- Songqian Huang
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
| | | | - Shuichi Asakawa
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
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47
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Zhou Y, Fang Y, Dai C, Wang Y. PiRNA pathway in the cardiovascular system: a novel regulator of cardiac differentiation, repair and regeneration. J Mol Med (Berl) 2021; 99:1681-1690. [PMID: 34533602 DOI: 10.1007/s00109-021-02132-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 07/18/2021] [Accepted: 08/20/2021] [Indexed: 11/25/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a novel group of small non-coding RNA molecules with lengths of 21-35 nucleotides, first identified from the germline. PiRNAs and their associated PIWI clade Argonaute proteins constitute a key part of the piRNA pathway, with the best-known biological function to silence transposable elements in germ cells. The piRNA pathway, in fact, is not exclusive to the germline. Somatic functions of piRNAs have been recorded since their first discovery. To date, involvement of the piRNA pathway has been identified within the biological functions of genome rearrangement, epigenetic regulation, protein regulation in the germline and/or the soma transcriptionally or post-transcriptionally. Emerging evidence has shown that the piRNA pathway is essential for the normal function of the cardiovascular system and that its abnormal expression is correlated with cardiovascular dysfunction, although comprehensive roles of the piRNA pathway in the cardiovascular system and underlying mechanisms remain unclear. In this review, we discuss current findings of piRNA pathway expression in cardiac cell types and their potential functions in cardiac differentiation, repair and regeneration, thus providing new insights into cardiovascular disease development associated with the piRNA pathway.
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Affiliation(s)
- Yuling Zhou
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen Cardiovascular Hospital Xiamen University, Xiamen, China
- The School of Economics, Xiamen University, Xiamen, China
| | - Ya Fang
- School of Public Health, Key Laboratory of Health Technology Assessment of Fujian Province University, Xiamen University, Xiang'an South Road, Xiang'an District, Xiamen, 361102, Fujian, China
| | - Cuilian Dai
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen Cardiovascular Hospital Xiamen University, Xiamen, China
| | - Yan Wang
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen Cardiovascular Hospital Xiamen University, Xiamen, China.
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48
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Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science 2021; 373:373/6550/eabh0556. [PMID: 34210850 DOI: 10.1126/science.abh0556] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/10/2021] [Indexed: 11/02/2022]
Abstract
The plant male germline undergoes DNA methylation reprogramming, which methylates genes de novo and thereby alters gene expression and regulates meiosis. Here, we reveal the molecular mechanism underlying this reprogramming. We demonstrate that genic methylation in the male germline, from meiocytes to sperm, is established by 24-nucleotide small interfering RNAs (siRNAs) transcribed from transposons with imperfect sequence homology. These siRNAs are synthesized by meiocyte nurse cells (tapetum) through activity of CLSY3, a chromatin remodeler absent in other anther cells. Tapetal siRNAs govern germline methylation throughout the genome, including the inherited methylation patterns in sperm. Tapetum-derived siRNAs also silence germline transposons, safeguarding genome integrity. Our results reveal that tapetal siRNAs are sufficient to reconstitute germline methylation patterns and drive functional methylation reprogramming throughout the male germline.
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Affiliation(s)
- Jincheng Long
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - James Walker
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Wenjing She
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Billy Aldridge
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Hongbo Gao
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Samuel Deans
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK.
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Liu N, Neuenkirchen N, Zhong M, Lin H. Genome-wide mapping of Piwi association with specific loci in Drosophila ovaries. G3-GENES GENOMES GENETICS 2021; 11:6066211. [PMID: 33609367 PMCID: PMC8022938 DOI: 10.1093/g3journal/jkaa059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022]
Abstract
Small noncoding RNA pathways have been implicated in diverse mechanisms of gene regulation. In Drosophila ovaries, Piwi binds to Piwi-interacting RNAs (piRNAs) of mostly 24–28 nucleotides (nt) and plays an important role in germline stem cell maintenance, transposon repression, and epigenetic regulation. To understand the mechanism underlying these functions, we report the application of the DamID-seq method to identify genome-wide binding sites of Piwi in Drosophila ovaries. Piwi localizes to at least 4535 euchromatic regions that are enriched with piRNA target sites. Surprisingly, the density of Piwi binding to euchromatin is much higher than in heterochromatin. Disrupting the piRNA binding of Piwi results in an overall change of the genomic binding profile, which indicates the role of piRNAs in directing Piwi to specific genomic sites. Most Piwi binding sites were either within or in the vicinity of protein-coding genes, particularly enriched near the transcriptional start and termination sites. The methylation signal near the transcriptional termination sites is significantly reduced when Piwi was mutated to become defective in piRNA binding. These observations indicate that Piwi might directly regulate the expression of many protein-coding genes, especially through regulating the 3' ends of targeted transcripts.
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Affiliation(s)
- Na Liu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520-8073, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520-8073, USA
| | - Nils Neuenkirchen
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520-8073, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520-8073, USA
| | - Mei Zhong
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520-8073, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520-8073, USA
| | - Haifan Lin
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520-8073, USA.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520-8073, USA
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50
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Chen S, Ben S, Xin J, Li S, Zheng R, Wang H, Fan L, Du M, Zhang Z, Wang M. The biogenesis and biological function of PIWI-interacting RNA in cancer. J Hematol Oncol 2021; 14:93. [PMID: 34118972 PMCID: PMC8199808 DOI: 10.1186/s13045-021-01104-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Small non-coding RNAs (ncRNAs) are vital regulators of biological activities, and aberrant levels of small ncRNAs are commonly found in precancerous lesions and cancer. PIWI-interacting RNAs (piRNAs) are a novel type of small ncRNA initially discovered in germ cells that have a specific length (24-31 nucleotides), bind to PIWI proteins, and show 2'-O-methyl modification at the 3'-end. Numerous studies have revealed that piRNAs can play important roles in tumorigenesis via multiple biological regulatory mechanisms, including silencing transcriptional and posttranscriptional gene processes and accelerating multiprotein interactions. piRNAs are emerging players in the malignant transformation of normal cells and participate in the regulation of cancer hallmarks. Most of the specific cancer hallmarks regulated by piRNAs are involved in sustaining proliferative signaling, resistance to cell death or apoptosis, and activation of invasion and metastasis. Additionally, piRNAs have been used as biomarkers for cancer diagnosis and prognosis and have great potential for clinical utility. However, research on the underlying mechanisms of piRNAs in cancer is limited. Here, we systematically reviewed recent advances in the biogenesis and biological functions of piRNAs and relevant bioinformatics databases with the aim of providing insights into cancer diagnosis and clinical applications. We also focused on some cancer hallmarks rarely reported to be related to piRNAs, which can promote in-depth research of piRNAs in molecular biology and facilitate their clinical translation into cancer treatment.
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Affiliation(s)
- Silu Chen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, People's Republic of China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rui Zheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hao Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lulu Fan
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, People's Republic of China. .,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China. .,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China. .,Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China.
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