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Zhou Y, Yu H, Li Q, Kong L, Liu S, Xu C. Characterization of piRNAs in Diploid and Triploid Pacific Oyster Gonads: Exploring Their Potential Roles in Triploid Sterility. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10351-7. [PMID: 39073646 DOI: 10.1007/s10126-024-10351-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024]
Abstract
PIWI-interacting RNAs (piRNAs) are crucial for silencing transposable elements, germ cell development, and gametogenesis. Triploid Pacific oysters (Crassostrea gigas) are vital in the oyster aquaculture industry due to reduced fertility and rapid growth. This study integrates piRNA and mRNA expression analyses to elucidate their potential contributions to the sterility of triploid C. gigas. Bioinformatics analysis reveals a distinct U-bias at the 5' terminal of oyster piRNAs. The abundance of piRNA clusters is reduced in triploid gonads compared to diploid gonads, particularly in sterile gonads, with a significant decrease in piRNA numbers. A specific piRNA cluster is annotated with the PPP4R1 gene, which is downregulated in infertile female triploids and exhibits a negative correlation with three piRNAs within the cluster. Differential expression analysis identified 46 and 88 piRNAs in female and male comparison groups, respectively. In female sterile triploids, the expression of three target genes of differentially expressed piRNAs associated with cell division showed downregulation, suggesting the potential roles of piRNAs in the regulation of cell division-related genes, contributing to the gonad arrest observed in female triploid oysters. In male triploid oysters, piRNAs potentially interact with the target genes associated with spermatogenesis, including TSSK4, SPAG17, and CCDC81. This study provides a concise overview of piRNAs expression in oyster gonads, offering insights into the regulatory role of piRNAs in triploid sterility.
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Affiliation(s)
- Yaru Zhou
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), Qingdao, 266003, China
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2
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Danga AK, Kour S, Kumari A, Rath PC. The long noncoding RNA (LINC-RBE) expression in testicular cells is associated with aging of the rat. Biogerontology 2024:10.1007/s10522-024-10119-5. [PMID: 39017749 DOI: 10.1007/s10522-024-10119-5] [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: 05/09/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024]
Abstract
Long noncoding RNAs (lncRNAs) are important regulatory biomolecules responsible for many cellular processes. The aging of mammals is manifested by a slow and gradual decline of physiological functions after adulthood, progressively resulting in age-related diseases. Testis comprises different cell-types with defined functions for producing haploid gametes and androgens in males, contributing gene-pool to the next generation with genetic variations to species for evolutionary advantage. The LINC-RBE (long intergenic noncoding-rat brain expressed) RNA showed highest expression in the Leydig cells, responsible for steroidogenesis and production of testosterone; higher expression in primary spermatocytes (pachytene cells), responsible for generation of haploid gametes and high expression in Sertoli cells, the nursing cells of the testes. Testes of immature (4-weeks), adult (16- and 44-weeks), and nearly-old (70-weeks) rats showed low, high, and again low levels of expression, respectively. This along with the nuclear-cytoplasmic localization of LINC-RBE RNA showed age-related expression and function. Thus, expression of LINC-RBE is involved in the molecular physiology of testes, especially Leydig cells, primary spermatocytes, and Sertoli cells. The decline in its expression correlates with diminishing reproductive function of the testes during aging of the rat.
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Affiliation(s)
- Ajay Kumar Danga
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sukhleen Kour
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15224, USA
| | - Anita Kumari
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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3
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Ahmadi Asouri S, Aghadavood E, Mirzaei H, Abaspour A, Esmaeil Shahaboddin M. PIWI-interacting RNAs (PiRNAs) as emerging biomarkers and therapeutic targets in biliary tract cancers: A comprehensive review. Heliyon 2024; 10:e33767. [PMID: 39040379 PMCID: PMC11261894 DOI: 10.1016/j.heliyon.2024.e33767] [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: 10/20/2023] [Revised: 06/09/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Cancers affecting the biliary tract, such as gallbladder cancer and cholangiocarcinoma, make up a small percentage of adult gastrointestinal malignancies, but their incidence is on the rise. Due to the lack of dependable molecular biomarkers for diagnosis and prognosis, these cancers are often not detected until later stages and have limited treatment options. Piwi-interacting RNAs (piRNAs) are a type of small noncoding RNA that interacts with Piwi proteins and has been linked to various diseases, especially cancer. Manipulation of piRNA expression has the potential to serve as an important biomarker and target for therapy. This review uncovers the relationship between PIWI-interacting RNA (piRNA) and a variety of gastrointestinal cancers, including biliary tract cancer (BTC). It is evident that piRNAs have the ability to impact gene expression and regulate key genes and pathways related to the advancement of digestive cancers. Abnormal expression of piRNAs plays a significant role in the development and progression of digestive-related malignancies. The potential of piRNAs as potential biomarkers for diagnosis and prognosis, as well as therapeutic targets in BTC, is noteworthy. Nevertheless, there are obstacles and limitations that require further exploration to fully comprehend piRNAs' role in BTC and to devise effective diagnostic and therapeutic approaches using piRNAs. In summary, this review underscores the value of piRNAs as valuable biomarkers and promising targets for treating BTC, as we delve into the association between piRNAs and various gastrointestinal cancers, including BTC, and how piRNAs can impact gene expression and control essential pathways for digestive cancer advancement. The present research consists of a thorough evaluation presented in a storytelling style. The databases utilized to locate original sources were PubMed, MEDLINE, and Google Scholar, and the search was conducted using the designated keywords.
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Affiliation(s)
- Sahar Ahmadi Asouri
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Esmat Aghadavood
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Institute for Basic Sciences, Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Alireza Abaspour
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Esmaeil Shahaboddin
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Institute for Basic Sciences, Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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4
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Kamakura T, Kameda K, Manabe M, Torii K, Sugiura Y, Ito S, Nakayama S, Shimizu T, Nagashima E, Kamiya K, Oka M, Tanaka M, Otsuka M, Ohtsuka M, Kotani A. PTBP1 protects Y RNA from cleavage leading to its apoptosis-specific degradation. Cell Death Discov 2024; 10:322. [PMID: 38997262 PMCID: PMC11245482 DOI: 10.1038/s41420-024-02080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Some RNAs such as 28S rRNA, U1 small nuclear RNA (snRNA), and Y RNAs are known to be cleaved during apoptosis. The underlying mechanism, functions, and biological significance of RNA degradation in apoptosis remain elusive. Y RNAs are non-coding RNAs widely conserved from bacteria to mammals, and are major components of Ro ribonucleoprotein (RNP) complexes which contain the 60 kDa Ro protein (SS-A) and the 50 kDa La protein (SS-B). The autoantigenic Ro and La proteins were identified by autoantibodies present in the sera from patients with Systemic lupus erythematosus (SLE) and Sjögren's syndrome (SjS). We previously identified novel, functional small RNAs named AGO-taxis small RNAs (ASRs) that are specifically bound to Argonaute protein 1 (AGO1), which are processed from Y RNAs. Cell-free analysis combined with fractionation methods revealed that the apoptosis-specific biogenesis of ASRs or cleavage of Y RNA was induced by truncation of polypyrimidine tract-binding protein 1 (PTBP1), which is an endoribonuclease inhibitor of Y RNAs by caspase 3. Caspase 3-resistant PTBP1 mutant protected cleavage of Y RNAs in apoptosis induced by staurosporine. Furthermore, caspase 3-resistant PTBP1 mutant knock-in mice showed elevated cytokines, dysregulation of the germinal center formation compared to the wild-type mice at LPS stimulation, and high positivity of antinuclear antibody. Those results suggest that cleavage of Y RNAs or biogenesis of ASR during apoptosis has critical biological functions and their deregulation result in immune dysregulation and the formation of autoantibody, possibly leading to the development of autoimmune diseases.
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Affiliation(s)
- Takeshi Kamakura
- Department of Regulation of Infectious Cancer, Research Institute of Microbiological Disease, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuaki Kameda
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA
| | - Masahiko Manabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Kan Torii
- Department of Regulation of Infectious Cancer, Research Institute of Microbiological Disease, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuki Sugiura
- Multi-Omics Platform, Center for Cancer Immunotherapy and Immunobiology, Kyoto University, Kyoto, 606-8501, Japan
| | - Seiko Ito
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Shunya Nakayama
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
- Laboratory of Veterinary Physiology, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Takanobu Shimizu
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Etsuko Nagashima
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Kosuke Kamiya
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Masahiro Oka
- Department of Regulation of Infectious Cancer, Research Institute of Microbiological Disease, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masafumi Tanaka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology and Hepatology, Academic Field of Medicine, Density and Pharmaceutical Sciences, Okayama University, Okayama, 700-8558, Japan
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Ai Kotani
- Department of Regulation of Infectious Cancer, Research Institute of Microbiological Disease, Osaka University, Suita, Osaka, 565-0871, Japan.
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Peng Q, Chen Y, Xie T, Pu D, Ho VWS, Sun J, Liu K, Chan RCK, Ding X, Teoh JYC, Wang X, Chiu PKF, Ng CF. PiRNA-4447944 promotes castration-resistant growth and metastasis of prostate cancer by inhibiting NEFH expression through forming the piRNA-4447944-PIWIL2-NEFH complex. Int J Biol Sci 2024; 20:3638-3655. [PMID: 38993562 PMCID: PMC11234203 DOI: 10.7150/ijbs.96173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/11/2024] [Indexed: 07/13/2024] Open
Abstract
Castration-resistant prostate cancer (CRPC) is the leading cause of prostate cancer (PCa)-related death in males, which occurs after the failure of androgen deprivation therapy (ADT). PIWI-interacting RNAs (piRNAs) are crucial regulators in many human cancers, but their expression patterns and roles in CRPC remain unknown. In this study, we performed small RNA sequencing to explore CRPC-associated piRNAs using 10 benign prostate tissues, and 9 paired hormone-sensitive PCa (HSPCa) and CRPC tissues from the same patients. PiRNA-4447944 (piR-4447944) was discovered to be highly expressed in CRPC group compared with HSPCa and benign groups. Functional analyses revealed that piR-4447944 overexpression endowed PCa cells with castration resistance ability in vitro and in vivo, whereas knockdown of piR-4447944 using anti-sense RNA suppressed the proliferation, migration and invasion of CRPC cells. Additionally, enforced piR-4447944 expression promoted in vitro migration and invasion of PCa cells, and reduced cell apoptosis. Mechanistically, piR-4447944 bound to PIWIL2 to form a piR-4447944/PIWIL2 complex and inhibited tumor suppressor NEFH through direct interaction at the post-transcriptional level. Collectively, our study indicates that piR-4447944 is essential for prostate tumor-propagating cells and mediates androgen-independent growth of PCa, which extends current understanding of piRNAs in cancer biology and provides a potential approach for CRPC treatment.
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Affiliation(s)
- Qiang Peng
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
- HitGen Inc., Building 6, No.8 Huigu First East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu, Sichuan, China
| | - Tingting Xie
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Dandan Pu
- Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Vincy Wing-Sze Ho
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Jingkai Sun
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Kang Liu
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Ronald Cheong-Kin Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaofan Ding
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Jeremy Yuen-Chun Teoh
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Peter Ka-Fung Chiu
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi-Fai Ng
- SH Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
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Karpagavalli M, Sivagurunathan S, Panda TS, Srikakulam N, Arora R, Dohadwala L, Tiwary BK, Sadras SR, Arunachalam JP, Pandi G, Chidambaram S. piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress. Mol Omics 2024; 20:248-264. [PMID: 38314503 DOI: 10.1039/d3mo00122a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Long considered active only in the germline, the PIWI/piRNA pathway is now known to play a significant role in somatic cells, especially neurons. In this study, piRNAs were profiled in the human retina and retinal pigment epithelium (RPE). Furthermore, RNA immunoprecipitation with HIWI2 (PIWIL4) in ARPE19 cells yielded 261 piRNAs, and the expression of selective piRNAs in donor eyes was assessed by qRT-PCR. Intriguingly, computational analysis revealed complete and partial seed sequence similarity between piR-hsa-26131 and the sensory organ specific miR-183/96/182 cluster. Furthermore, the expression of retina-enriched piR-hsa-26131 was positively correlated with miR-182 in HIWI2-silenced Y79 cells. In addition, the lnc-ZNF169 sequence matched with two miRNAs of the let-7 family, and piRNAs, piR-hsa-11361 and piR-hsa-11360, which could modulate the regulatory network of retinal differentiation. Interestingly, we annotated four enriched motifs among the piRNAs and found that the piRNAs containing CACAATG and CTCATCAKYG motifs were snoRNA-derived piRNAs, which are significantly associated with developmental functions. However, piRNAs consisting of ACCACTANACCAC and AKCACGYTCSC motifs were mainly tRNA-derived fragments linked to stress response and sensory perception. Additionally, co-expression network analysis revealed cell cycle control, intracellular transport and stress response as the important biological functions regulated by piRNAs in the retina. Moreover, loss of piRNAs in HIWI2 knockdown ARPE19 confirmed altered expression of targets implicated in intracellular transport, circadian clock, and retinal degeneration. Moreover, piRNAs were dysregulated under oxidative stress conditions, indicating their potential role in retinal pathology. Therefore, we postulate that piRNAs, miRNAs, and lncRNAs might have a functional interplay during retinal development and functions to regulate retinal homeostasis.
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Affiliation(s)
| | - Suganya Sivagurunathan
- RS Mehta Jain Department of Biochemistry and Cell Biology, Vision Research Foundation, Chennai, India
| | - T Sayamsmruti Panda
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Nagesh Srikakulam
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Reety Arora
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | | | - Basant K Tiwary
- Department of Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
| | - Jayamuruga Pandian Arunachalam
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry-607402, India
| | - Gopal Pandi
- Laboratory of RNA Biology and Epigenomics, Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Subbulakshmi Chidambaram
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry-605014, India.
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7
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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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8
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Li M, Zhou Y, Cheng J, Wang Y, Lan C, Shen Y. Response of the mosquito immune system and symbiotic bacteria to pathogen infection. Parasit Vectors 2024; 17:69. [PMID: 38368353 PMCID: PMC10874582 DOI: 10.1186/s13071-024-06161-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/24/2024] [Indexed: 02/19/2024] Open
Abstract
Mosquitoes are the deadliest animal in the word, transmitting a variety of insect-borne infectious diseases, such as malaria, dengue fever, yellow fever, and Zika, causing more deaths than any other vector-borne pathogen. Moreover, in the absence of effective drugs and vaccines to prevent and treat insect-borne diseases, mosquito control is particularly important as the primary measure. In recent decades, due to the gradual increase in mosquito resistance, increasing attention has fallen on the mechanisms and effects associated with pathogen infection. This review provides an overview of mosquito innate immune mechanisms in terms of physical and physiological barriers, pattern recognition receptors, signalling pathways, and cellular and humoral immunity, as well as the antipathogenic effects of mosquito symbiotic bacteria. This review contributes to an in-depth understanding of the interaction process between mosquitoes and pathogens and provides a theoretical basis for biological defence strategies against mosquito-borne infectious diseases.
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Affiliation(s)
- Manjin Li
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, 214023, China
| | - Yang Zhou
- Nanjing Medical University, Nanjing, 211166, China
| | - Jin Cheng
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, 214023, China
| | - Yiqing Wang
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, 214023, China
| | - Cejie Lan
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, 214023, China.
| | - Yuan Shen
- The Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi Center for Disease Control and Prevention, Wuxi, 214023, China.
- Nanjing Medical University, Nanjing, 211166, China.
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9
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Siniscalchi C, Di Palo A, Petito G, Senese R, Manfrevola F, Leo ID, Mosca N, Chioccarelli T, Porreca V, Marchese G, Ravo M, Chianese R, Cobellis G, Lanni A, Russo A, Potenza N. A landscape of mouse mitochondrial small non-coding RNAs. PLoS One 2024; 19:e0293644. [PMID: 38165955 PMCID: PMC10760717 DOI: 10.1371/journal.pone.0293644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/17/2023] [Indexed: 01/04/2024] Open
Abstract
Small non-coding RNAs (ncRNAs), particularly miRNAs, play key roles in a plethora of biological processes both in health and disease. Although largely operative in the cytoplasm, emerging data indicate their shuttling in different subcellular compartments. Given the central role of mitochondria in cellular homeostasis, here we systematically profiled their small ncRNAs content across mouse tissues that largely rely on mitochondria functioning. The ubiquitous presence of piRNAs in mitochondria (mitopiRNA) of somatic tissues is reported for the first time, supporting the idea of a strong and general connection between mitochondria biology and piRNA pathways. Then, we found groups of tissue-shared and tissue-specific mitochondrial miRNAs (mitomiRs), potentially related to the "basic" or "cell context dependent" biology of mitochondria. Overall, this large data platform will be useful to deepen the knowledge about small ncRNAs processing and their governed regulatory networks contributing to mitochondria functions.
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Affiliation(s)
- Chiara Siniscalchi
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Armando Di Palo
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Giuseppe Petito
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Rosalba Senese
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Francesco Manfrevola
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Ilenia De Leo
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
- Genomix4Life S.r.l., Baronissi (SA), Italy
| | - Nicola Mosca
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Teresa Chioccarelli
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Veronica Porreca
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Giovanna Marchese
- Genomix4Life S.r.l., Baronissi (SA), Italy
- Genome Research Center for Health, CRGS, Baronissi, Italy
| | - Maria Ravo
- Genomix4Life S.r.l., Baronissi (SA), Italy
- Genome Research Center for Health, CRGS, Baronissi, Italy
| | - Rosanna Chianese
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Gilda Cobellis
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Antonia Lanni
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Aniello Russo
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Nicoletta Potenza
- Department of Environmental, Biological, Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Caserta, Italy
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Santana-da-Silva MN, Sena-dos-Santos C, Cáceres-Durán MÁ, de Souza FG, Gobbo AR, Pinto P, Salgado CG, dos Santos SEB. ncRNAs: an unexplored cellular defense mechanism in leprosy. Front Genet 2023; 14:1295586. [PMID: 38116294 PMCID: PMC10729009 DOI: 10.3389/fgene.2023.1295586] [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: 09/16/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Leprosy is an infectious disease primarily caused by the obligate intracellular parasite Mycobacterium leprae. Although it has been considered eradicated in many countries, leprosy continues to be a health issue in developing nations. Besides the social stigma associated with it, individuals affected by leprosy may experience nerve damage leading to physical disabilities if the disease is not properly treated or early diagnosed. Leprosy is recognized as a complex disease wherein socioenvironmental factors, immune response, and host genetics interact to contribute to its development. Recently, a new field of study called epigenetics has emerged, revealing that the immune response and other mechanisms related to infectious diseases can be influenced by noncoding RNAs. This review aims to summarize the significant advancements concerning non-coding RNAs in leprosy, discussing the key perspectives on this novel approach to comprehending the pathophysiology of the disease and identifying molecular markers. In our view, investigations on non-coding RNAs in leprosy hold promise and warrant increased attention from researches in this field.
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Affiliation(s)
- Mayara Natália Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Imunologia, Seção de Virologia (SAVIR), Instituto Evandro Chagas, Ananindeua, Brazil
| | - Camille Sena-dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Miguel Ángel Cáceres-Durán
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Angelica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Sidney Emanuel Batista dos Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Belém, Brazil
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11
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Srivastava A, Srivastava A, Singh RK. Insight into the Epigenetics of Kaposi's Sarcoma-Associated Herpesvirus. Int J Mol Sci 2023; 24:14955. [PMID: 37834404 PMCID: PMC10573522 DOI: 10.3390/ijms241914955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 10/15/2023] Open
Abstract
Epigenetic reprogramming represents a series of essential events during many cellular processes including oncogenesis. The genome of Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic herpesvirus, is predetermined for a well-orchestrated epigenetic reprogramming once it enters into the host cell. The initial epigenetic reprogramming of the KSHV genome allows restricted expression of encoded genes and helps to hide from host immune recognition. Infection with KSHV is associated with Kaposi's sarcoma, multicentric Castleman's disease, KSHV inflammatory cytokine syndrome, and primary effusion lymphoma. The major epigenetic modifications associated with KSHV can be labeled under three broad categories: DNA methylation, histone modifications, and the role of noncoding RNAs. These epigenetic modifications significantly contribute toward the latent-lytic switch of the KSHV lifecycle. This review gives a brief account of the major epigenetic modifications affiliated with the KSHV genome in infected cells and their impact on pathogenesis.
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Affiliation(s)
- Anusha Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Ankit Srivastava
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Rajnish Kumar Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
- Faculty of Medical Sciences, Charotar University of Science and Technology, Changa 388421, Gujarat, India
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12
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Chakrabarty P, Sen R, Sengupta S. From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution. Funct Integr Genomics 2023; 23:278. [PMID: 37610667 DOI: 10.1007/s10142-023-01206-w] [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: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.
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Affiliation(s)
- Prayas Chakrabarty
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
| | - Raneet Sen
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
- Institute of Bioorganic Chemistry, Department of RNA Metabolism, Polish Academy of Sciences, Poznan, Poland
| | - Sugopa Sengupta
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India.
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13
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Otsuka K, Sakashita A, Maezawa S, Schultz RM, Namekawa SH. KRAB-zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.24.546405. [PMID: 37720031 PMCID: PMC10503828 DOI: 10.1101/2023.06.24.546405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
As transposable elements (TEs) coevolved with the host genome, the host genome exploited TEs as functional regulatory elements. What remains largely unknown are how the activity of TEs, namely, endogenous retroviruses (ERVs), are regulated and how TEs evolved in the germline. Here we show that KRAB domain-containing zinc-finger proteins (KZFPs), which are highly expressed in mitotically dividing spermatogonia, bind to suppressed ERVs that function following entry into meiosis as active enhancers. These features are observed for independently evolved KZFPs and ERVs in mice and humans, i.e., are evolutionarily conserved in mammals. Further, we show that meiotic sex chromosome inactivation (MSCI) antagonizes the coevolution of KZFPs and ERVs in mammals. Our study uncovers a mechanism by which KZFPs regulate ERVs to sculpt germline transcriptomes. We propose that epigenetic programming in the mammalian germline during the mitosis-to-meiosis transition facilitates coevolution of KZFPs and TEs on autosomes and is antagonized by MSCI.
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Affiliation(s)
- Kai Otsuka
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, 95616, USA
| | - Akihiko Sakashita
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - So Maezawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - Richard M. Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104 USA
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, California 95616, USA
| | - Satoshi H. Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, 95616, USA
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, 45229, USA
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14
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Tan H, Wang W, Zhou C, Wang Y, Zhang S, Yang P, Guo R, Chen W, Zhang J, Ye L, Cui Y, Ni T, Zheng K. Single-cell RNA-seq uncovers dynamic processes orchestrated by RNA-binding protein DDX43 in chromatin remodeling during spermiogenesis. Nat Commun 2023; 14:2499. [PMID: 37120627 DOI: 10.1038/s41467-023-38199-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 04/20/2023] [Indexed: 05/01/2023] Open
Abstract
Mammalian spermatogenesis shows prominent chromatin and transcriptomic switches in germ cells, but it is unclear how such dynamics are controlled. Here we identify RNA helicase DDX43 as an essential regulator of the chromatin remodeling process during spermiogenesis. Testis-specific Ddx43 knockout mice show male infertility with defective histone-to-protamine replacement and post-meiotic chromatin condensation defects. The loss of its ATP hydrolysis activity by a missense mutation replicates the infertility phenotype in global Ddx43 knockout mice. Single-cell RNA sequencing analyses of germ cells depleted of Ddx43 or expressing the Ddx43 ATPase-dead mutant reveals that DDX43 regulates dynamic RNA regulatory processes that underlie spermatid chromatin remodeling and differentiation. Transcriptomic profiling focusing on early-stage spermatids combined with enhanced crosslinking immunoprecipitation and sequencing further identifies Elfn2 as DDX43-targeted hub gene. These findings illustrate an essential role for DDX43 in spermiogenesis and highlight the single-cell-based strategy to dissect cell-state-specific regulation of male germline development.
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Affiliation(s)
- Huanhuan Tan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
- Reproductive Medicine Center, The First Affiliated Hospital of Chongqing Medical University, No. 1 Youyi Road, 400016, Chongqing, Yuzhong District, China
| | - Weixu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, 200438, Shanghai, China
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Congjin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Yanfeng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Shu Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Pinglan Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Rui Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Wei Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, 200438, Shanghai, China
| | - Jinwen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China.
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences and Huashan Hospital, Fudan University, 200438, Shanghai, China.
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166, Nanjing, China.
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15
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Zhou J, Xie H, Liu J, Huang R, Xiang Y, Tian D, Bian E. PIWI-interacting RNAs: Critical roles and therapeutic targets in cancer. Cancer Lett 2023; 562:216189. [PMID: 37076042 DOI: 10.1016/j.canlet.2023.216189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a novel class of small regulatory RNAs (approximately 24-31 nucleotides in length) that often bind to members of the PIWI protein family. piRNAs regulate transposons in animal germ cells; piRNAs are also specifically expressed in many human tissues and regulate pivotal signaling pathways. Additionally, the abnormal expression of piRNAs and PIWI proteins has been associated with various malignant tumours, and multiple mechanisms of piRNA-mediated target gene dysregulation are involved in tumourigenesis and progression, suggesting that they have the potential to serve as new biomarkers and therapeutic targets for tumours. However, the functions and potential mechanisms of action of piRNAs in cancer have not yet been elucidated. This review summarises the current findings on the biogenesis, function, and mechanisms of piRNAs and PIWI proteins in cancer. We also discuss the clinical significance of piRNAs as diagnostic or prognostic biomarkers and therapeutic tools for cancer. Finally, we present some critical questions regarding piRNA research that need to be addressed to provide insight into the future development of the field.
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Affiliation(s)
- Jialin Zhou
- Department of Clinical Medicine, The Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Ruixiang Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Yufei Xiang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Dasheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
| | - Erbao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
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16
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Wang P, Zhang X, Huo H, Li W, Liu Z, Wang L, Li L, Sun YH, Huo J. Transcriptomic analysis of testis and epididymis tissues from Banna mini-pig inbred line boars with single-molecule long-read sequencing†. Biol Reprod 2023; 108:465-478. [PMID: 36477198 DOI: 10.1093/biolre/ioac216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/04/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
In mammals, testis and epididymis are critical components of the male reproductive system for androgen production, spermatogenesis, sperm transportation, as well as sperm maturation. Here, we report single-molecule real-time sequencing data from the testis and epididymis of the Banna mini-pig inbred line (BMI), a promising laboratory animal for medical research. We obtained high-quality full-length transcriptomes and identified 9879 isoforms and 8761 isoforms in the BMI testis and epididymis, respectively. Most of the isoforms we identified have novel exon structures that will greatly improve the annotation of testis- and epididymis-expressed genes in pigs. We also found that 3055 genes (over 50%) were shared between BMI testis and epididymis, indicating widespread expression profiles of genes related to reproduction. We characterized extensive alternative splicing events in BMI testis and epididymis and showed that 96 testis-expressed genes and 79 epididymis-expressed genes have more than six isoforms, revealing the complexity of alternative splicing. We accurately defined the transcribed isoforms in BMI testis and epididymis by combining Pacific Biotechnology Isoform-sequencing (PacBio Iso-Seq) and Illumina RNA Sequencing (RNA-seq) techniques. The refined annotation of some key genes governing male reproduction will facilitate further understanding of the molecular mechanisms underlying BMI male sterility. In addition, the high-confident identification of 548 and 669 long noncoding RNAs (lncRNAs) in these two tissues has established a candidate gene set for future functional investigations. Overall, our study provides new insights into the role of the testis and epididymis during BMI reproduction, paving the path for further studies on BMI male infertility.
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Affiliation(s)
- Pei Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xia Zhang
- College of Life Science, Lyuliang University, Lvliang, China
| | - Hailong Huo
- Yunnan Vocational and Technical college of Agriculture, Kunming, China
| | - Weizhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Zhipeng Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Lina Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Luogang Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yu H Sun
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- Department of Biology, University of Rochester, Rochester, NY, USA
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Rayford KJ, Cooley A, Strode AW, Osi I, Arun A, Lima MF, Misra S, Pratap S, Nde PN. Trypanosoma cruzi dysregulates expression profile of piRNAs in primary human cardiac fibroblasts during early infection phase. Front Cell Infect Microbiol 2023; 13:1083379. [PMID: 36936778 PMCID: PMC10017870 DOI: 10.3389/fcimb.2023.1083379] [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: 10/28/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas Disease, causes severe morbidity, mortality, and economic burden worldwide. Though originally endemic to Central and South America, globalization has led to increased parasite presence in most industrialized countries. About 40% of infected individuals will develop cardiovascular, neurological, and/or gastrointestinal pathologies. Accumulating evidence suggests that the parasite induces alterations in host gene expression profiles in order to facilitate infection and pathogenesis. The role of regulatory gene expression machinery during T. cruzi infection, particularly small noncoding RNAs, has yet to be elucidated. In this study, we aim to evaluate dysregulation of a class of sncRNAs called piRNAs during early phase of T. cruzi infection in primary human cardiac fibroblasts by RNA-Seq. We subsequently performed in silico analysis to predict piRNA-mRNA interactions. We validated the expression of these selected piRNAs and their targets during early parasite infection phase by stem loop qPCR and qPCR, respectively. We found about 26,496,863 clean reads (92.72%) which mapped to the human reference genome. During parasite challenge, 441 unique piRNAs were differentially expressed. Of these differentially expressed piRNAs, 29 were known and 412 were novel. In silico analysis showed several of these piRNAs were computationally predicted to target and potentially regulate expression of genes including SMAD2, EGR1, ICAM1, CX3CL1, and CXCR2, which have been implicated in parasite infection, pathogenesis, and various cardiomyopathies. Further evaluation of the function of these individual piRNAs in gene regulation and expression will enhance our understanding of early molecular mechanisms contributing to infection and pathogenesis. Our findings here suggest that piRNAs play important roles in infectious disease pathogenesis and can serve as potential biomarkers and therapeutic targets.
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Affiliation(s)
- Kayla J. Rayford
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Ayorinde Cooley
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Anthony W. Strode
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Inmar Osi
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Ashutosh Arun
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Maria F. Lima
- Biomedical Sciences, School of Medicine, City College of New York, New York, NY, United States
| | - Smita Misra
- School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, United States
| | - Siddharth Pratap
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
- Bioinformatics Core, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, United States
| | - Pius N. Nde
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
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18
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Piccinini G, Milani L. Germline-related molecular phenotype in Metazoa: conservation and innovation highlighted by comparative transcriptomics. EvoDevo 2023; 14:2. [PMID: 36717890 PMCID: PMC9885605 DOI: 10.1186/s13227-022-00207-3] [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: 10/20/2022] [Accepted: 12/27/2022] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND In Metazoa, the germline represents the cell lineage devoted to the transmission of genetic heredity across generations. Its functions intuitively evoke the crucial roles that it plays in organism development and species evolution, and its establishment is tightly tied to animal multicellularity itself. The molecular toolkit expressed in germ cells has a high degree of conservation between species, and it also shares many components with the molecular phenotype of some animal totipotent cell lineages, like planarian neoblasts and sponge archaeocytes. The present study stems from these observations and represents a transcriptome-wide comparative analysis between germline-related samples of 9 animal species (7 phyla), comprehending also totipotent lineages classically considered somatic. RESULTS Differential expression analyses were performed for each species between germline-related and control somatic tissues. We then compared the different germline-related transcriptional profiles across the species without the need for an a priori set of genes. Through a phylostratigraphic analysis, we observed that the proportion of phylum- and Metazoa-specific genes among germline-related upregulated transcripts was lower than expected by chance for almost all species. Moreover, homologous genes related to proper DNA replication resulted the most common when comparing the considered species, while the regulation of transcription and post-transcriptional mechanisms appeared more variable, showing shared upregulated functions and domains, but very few homologous whole-length sequences. CONCLUSIONS Our wide-scale comparative analysis mostly confirmed previous molecular characterizations of specific germline-related lineages. Additionally, we observed a consistent signal throughout the whole data set, therefore comprehending both canonically defined germline samples (germ cells), and totipotent cell lineages classically considered somatic (neoblasts and archaeocytes). The phylostratigraphic analysis supported the less probable involvement of novel molecular factors in the germline-related transcriptional phenotype and highlighted the early origin of such cell programming and its conservation throughout evolution. Moreover, the fact that the mostly shared molecular factors were involved in DNA replication and repair suggests how fidelity in genetic material inheritance is a strong and conserved driver of germline-related molecular phenotype, while transcriptional and post-transcriptional regulations appear differently tuned among the lineages.
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Affiliation(s)
- Giovanni Piccinini
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Liliana Milani
- grid.6292.f0000 0004 1757 1758Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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19
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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20
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Sato K, Takayama KI, Inoue S. Role of piRNA biogenesis and its neuronal function in the development of neurodegenerative diseases. Front Aging Neurosci 2023; 15:1157818. [PMID: 37207075 PMCID: PMC10191213 DOI: 10.3389/fnagi.2023.1157818] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 05/21/2023] Open
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), are caused by neuronal loss and dysfunction. Despite remarkable improvements in our understanding of these pathogeneses, serious worldwide problems with significant public health burdens are remained. Therefore, new efficient diagnostic and therapeutic strategies are urgently required. PIWI-interacting RNAs (piRNAs) are a major class of small non-coding RNAs that silence gene expression through transcriptional and post-transcriptional processes. Recent studies have demonstrated that piRNAs, originally found in the germ line, are also produced in non-gonadal somatic cells, including neurons, and further revealed the emerging roles of piRNAs, including their roles in neurodevelopment, aging, and neurodegenerative diseases. In this review, we aimed to summarize the current knowledge regarding the piRNA roles in the pathophysiology of neurodegenerative diseases. In this context, we first reviewed on recent updates on neuronal piRNA functions, including biogenesis, axon regeneration, behavior, and memory formation, in humans and mice. We also discuss the aberrant expression and dysregulation of neuronal piRNAs in neurodegenerative diseases, such as AD, PD, and ALS. Moreover, we review pioneering preclinical studies on piRNAs as biomarkers and therapeutic targets. Elucidation of the mechanisms underlying piRNA biogenesis and their functions in the brain would provide new perspectives for the clinical diagnosis and treatment of AD and various neurodegenerative diseases.
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Affiliation(s)
- Kaoru Sato
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Tokyo, Japan
- Integrated Research Initiative for Living Well with Dementia (IRIDE), Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Tokyo, Japan
| | - Ken-ichi Takayama
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Tokyo, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology (TMIG), Tokyo, Japan
- *Correspondence: Satoshi Inoue,
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21
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A Novel PiRNA Enhances CA19-9 Sensitivity for Pancreatic Cancer Identification by Liquid Biopsy. J Clin Med 2022; 11:jcm11247310. [PMID: 36555927 PMCID: PMC9784851 DOI: 10.3390/jcm11247310] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer is one of the deadliest tumours worldwide, and its poor prognosis is due to an inability to detect the disease at the early stages, thereby creating an urgent need to develop non-invasive biomarkers. P-element-induced wimpy testis (PIWI) proteins work together with piwi-interacting RNAs (piRNAs) to perform epigenetic regulation and as such hold great potential as biomarkers for pancreatic cancer. PIWIL2 and PIWIL4 are associated with better prognosis, while PIWIL1 and PIWIL3 involvement appears to be associated with carcinogenesis. We aimed to discover PIWIL3- and PIWIL4-modulated piRNAs and determine their potential mechanisms in pancreatic cancer and the clinical implications. PIWIL3 or PIWIL4 was downregulated in pancreatic cancer-derived cell lines or in a non-tumour cell line. Differentially expressed piRNAs were analysed by next generation sequencing of small RNA. Nine fresh-frozen samples from solid human pancreases (three healthy pancreases, three intraductal papillary mucinous neoplasms, and three early-stage pancreatic cancers) were included in the sequencing analysis. Two piRNAs associated with PIWIL3 (piR-168112 and piR-162725) were identified in the neoplastic cells; in untransformed samples, we identified one piRNA associated with PIWIL4 (pir-366845). After validation in pancreatic cancer-derived cell lines and one untransformed pancreatic cell line, these piRNAs were evaluated in plasma samples from healthy donors (n = 27) or patients with pancreatic cancer (n = 45). Interestingly, piR-162725 expression identified pancreatic cancer patients versus healthy donors in liquid biopsies. Moreover, the potential of the serum carbohydrate antigen 19-9 (CA19-9) biomarker to identify pancreatic cancer patients was greatly enhanced when combined with piR-162725 detection. The enhanced diagnostic potential for the early detection of pancreatic cancer in liquid biopsies of these new small non-coding RNAs will likely improve the prognosis and management of this deadly cancer.
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22
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AmeliMojarad M, Amelimojarad M. piRNAs and PIWI proteins as potential biomarkers in Breast cancer. Mol Biol Rep 2022; 49:9855-9862. [PMID: 35612777 DOI: 10.1007/s11033-022-07506-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/22/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND PIWI interacting RNAs (piRNAs) are another subgroup of small non-coding RNAs, that can play different biological activity further to their capabilities in the germline such as regulating the gene and protein expression, epigenetic silencing of transposable elements, and regulating the spermatogenesis by interacting with PIWI proteins. METHODS We search online academic data bases including (Google Scholar, Web of Science and Pub Med), the relevant literature was extracted from the databases by using search terms of piRNAs and breast cancer as free-text words and also with the combination with OR /AND by may 2022. RESULTS Recently, with the help of next-generation sequencing abnormal piRNA expression has been observed to associate with the occurrence and development of human cancers, such as breast cancer (BC). Recent investigation proposing piRNA as a prognostic and diagnostic biomarker based on their cancer-related interaction in the treatment of BC. CONCLUSION This review aims to focus on the role of piRNAs in the initiation, progression, and the occurrence of breast cancer in order to understand its function and provide a better therapeutic strategy.
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23
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Goh TX, Tan SL, Roebuck MM, Teo SH, Kamarul T. A systematic review of EV-piRNA in human body fluid and its role in disease progression. Tissue Eng Part C Methods 2022; 28:511-528. [PMID: 35959742 DOI: 10.1089/ten.tec.2022.0092] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The state of host cells is reflected in the cargo carried by their extracellular vesicles (EVs). This makes EV a potential source of biomarkers for human diseases. Piwi-interacting RNA (piRNA) regulates gene expression through epigenetic regulation and post-transcriptional gene silencing. Thus, piRNA profiles in EVs derived from human clinical samples could identify markers that characterize disease stages, and unveil their roles in disease pathology. This review aimed to report the expression profiles of EV-derived piRNA (EV-piRNA) in various human samples, as well as their role in each pathology. A systematic review was conducted to collate the findings of human EV-piRNA from original research articles published in indexed scientific journals up to 16th Feb 2022. Article searches were performed in PubMed, Web of Science, and Scopus databases, using a combination of keywords including 'EV' and 'piRNA'. A total of 775 non-redundant original articles were identified. After subjecting articles to inclusion and exclusion criteria, 34 articles were accepted for this review. The piRNA expression levels among the small RNA profiles of human-derived EVs range from 0.09% to 43.84%, with the lowest expression level reported in urine-derived EVs and the highest percentage in plasma-derived EVs. Differentially expressed EV-piRNAs have been identified in patients with specific disease conditions compared to their counterparts (healthy control), suggesting an association between piRNA and progression in various diseases. Seven articles identified piRNA putative target genes and/or the pathway enrichment of piRNA target genes, and one study demonstrated a direct tole of piRNA candidates in disease pathology. In conclusion, EV-piRNA has been isolated successfully from various human body fluids. EV-piRNA is a new research niche in human disease pathology. The expression profiles of EV-piRNA in various tissue types and disease conditions remain largely unexplored. Furthermore, there is currently a lack of guidelines on piRNA bioinformatics analysis, which could lead to inconsistent results and thus hinder the progression of piRNA discoveries. Lastly, the lack of published scientific evidence on the role of EV-piRNA supports the need for future research to focus on the functional analysis of EV-piRNA as part of the route in piRNA discoveries.
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Affiliation(s)
- Tuan Xin Goh
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Malaysia;
| | - Sik Loo Tan
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Malaysia;
| | - Margaret M Roebuck
- University of Liverpool Faculty of Health and Life Sciences, Department of Musculoskeletal & Ageing Science Institute of Life Course & Medical Sciences (ILCaMS) Faculty of Health & Life Sciences William Henry Duncan Building University of Liverpool, Liverpool, 6 West Derby Street Liverpool L7 8TX, United Kingdom of Great Britain and Northern Ireland;
| | - Seow-Hui Teo
- Division of Sports Injuries and Arthroscopic Surgery, National Orthopaedic Center of Excellence for Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, MALAYSIA., Division of Sports Injuries and Arthroscopic Surgery, National Orthopaedic Center of Excellence for Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Federal Territory, Kuala Lumpur, Malaysia;
| | - Tunku Kamarul
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Wilayah Persekutuan, Malaysia;
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24
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Lim LX, Isshiki W, Iki T, Kawaguchi S, Kai T. The Tudor Domain-Containing Protein, Kotsubu (CG9925), Localizes to the Nuage and Functions in piRNA Biogenesis in D. melanogaster. Front Mol Biosci 2022; 9:818302. [PMID: 35425810 PMCID: PMC9002060 DOI: 10.3389/fmolb.2022.818302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/11/2022] [Indexed: 11/30/2022] Open
Abstract
Silencing of transposable elements (TEs) by Piwi-interacting RNAs (piRNAs) is crucial for maintaining germline genome integrity and fertility in animals. To repress TEs, PIWI clade Argonaute proteins cooperate with several Tudor domain-containing (Tdrd) proteins at membraneless perinuclear organelles, called nuage, to produce piRNAs to repress transposons. Here, we identify and characterize Kotsubu (Kots), one of the Drosophila Tudor domain-containing protein-1 (Tdrd1) orthologs, encoded by the CG9925 gene, that localizes to the nuage in gonads. We further show the dynamic localization of Kots in the male germline, where it shows perinuclear signals in spermatogonia but forms large cytoplasmic condensates in the spermatocytes that overlap with components of piNG-body, a nuage-associated organelle. The loss of kots results in a notable upregulation of stellate and a corresponding reduction in the suppressor of stellate piRNAs in the mutants. Furthermore, a moderate yet significant reduction of other piRNAs was observed in kots mutant testes. Taken together, we propose that Kots functions in the piRNA pathway, predominantly in the male germline by forming discrete cytoplasmic granules.
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25
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Raza A, Khan AQ, Inchakalody VP, Mestiri S, Yoosuf ZSKM, Bedhiafi T, El-Ella DMA, Taib N, Hydrose S, Akbar S, Fernandes Q, Al-Zaidan L, Krishnankutty R, Merhi M, Uddin S, Dermime S. Dynamic liquid biopsy components as predictive and prognostic biomarkers in colorectal cancer. J Exp Clin Cancer Res 2022; 41:99. [PMID: 35292091 PMCID: PMC8922757 DOI: 10.1186/s13046-022-02318-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/07/2022] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. The diagnosis, prognosis and therapeutic monitoring of CRC depends largely on tissue biopsy. However, due to tumor heterogeneity and limitations such as invasiveness, high cost and limited applicability in longitudinal monitoring, liquid biopsy has gathered immense attention in CRC. Liquid biopsy has several advantages over tissue biopsy including ease of sampling, effective monitoring, and longitudinal assessment of treatment dynamics. Furthermore, the importance of liquid biopsy is signified by approval of several liquid biopsy assays by regulatory bodies indicating the powerful approach of liquid biopsy for comprehensive CRC screening, diagnostic and prognostics. Several liquid biopsy biomarkers such as novel components of the microbiome, non-coding RNAs, extracellular vesicles and circulating tumor DNA are extensively being researched for their role in CRC management. Majority of these components have shown promising results on their clinical application in CRC including early detection, observe tumor heterogeneity for treatment and response, prediction of metastases and relapse and detection of minimal residual disease. Therefore, in this review, we aim to provide updated information on various novel liquid biopsy markers such as a) oral microbiota related bacterial network b) gut microbiome-associated serum metabolites c) PIWI-interacting RNAs (piRNAs), microRNA(miRNAs), Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and d) circulating tumor DNAs (ctDNA) and circulating tumor cells (CTC) for their role in disease diagnosis, prognosis, treatment monitoring and their applicability for personalized management of CRC.
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Affiliation(s)
- Afsheen Raza
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Philipose Inchakalody
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | | | - Takwa Bedhiafi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Dina Moustafa Abo El-Ella
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shereena Hydrose
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shayista Akbar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Queenie Fernandes
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,College of Medicine, Qatar University, Doha, Qatar
| | - Lobna Al-Zaidan
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Roopesh Krishnankutty
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.
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PIWI-Interacting RNA Pathway Genes: Potential Biomarkers for Clear Cell Renal Cell Carcinoma. DISEASE MARKERS 2022; 2022:3480377. [PMID: 35273654 PMCID: PMC8904100 DOI: 10.1155/2022/3480377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/16/2021] [Indexed: 11/17/2022]
Abstract
Background. Clear cell renal cell carcinoma (ccRCC) is one of the most lethal malignancies in the urinary system, yet effective diagnostic and prognostic markers are lacking. Recently, several of piRNA pathway genes have been reported to be associated with cancer diagnosis and prognosis, but their role in ccRCC is still unclear. Methods. We analysed the expression of 27 piRNA pathway genes in 539 kidney renal clear cell carcinoma (KIRC) and 72 nontumor tissue samples (data from TCGA), and 12 mRNAs were significantly different. The aim was to sift the piRNA pathway genes that are correlated with ccRCC patient survival and to construct a piRNA pathway gene risk prognostic model using Kaplan-Meier survival curve and ROC curve, respectively. Results. 5 piRNA pathway genes (TDRD7, GPAT2, PLD6, SUV39H1, and DOM3Z) were picked out and used to construct the piRNA pathway gene risk model. Kaplan-Meier survival curve analysis showed that compared with that of the low-risk group of ccRCC patients, the OS of the high-risk group of ccRCC patients was significantly reduced. The predictive performance of the prognostic risk model was measured using a ROC curve, which individually showed AUC values for 1 year of 0.707, for 3 years of 0.713, and for 5 years of 0.701. Moreover, the mRNA and protein expression levels of TDRD7 were overexpressed in the ccRCC datasets (data from our cohort, TCGA, GEO, and CPTAC) and ccRCC cell lines, and the expression levels correlated with the clinicopathological characteristics in ccRCC. The Tumor Immune Estimation Resource (TIMER) showed that the mRNA expression level of TDRD7 was positively related to tumor immune infiltrating cells (TICs) in ccRCC. Mechanistically, gene set enrichment analysis (GSEA) was performed to uncover the mechanism of TDRD7 in ccRCC. In summary, the piRNA pathway genes,especially TDRD7, may be potential cancer diagnostic and prognostic biomarkers of ccRCC.
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27
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AmeliMojarad M, AmeliMojarad M, Wang J. The function of novel small non-coding RNAs (piRNAs, tRFs) and PIWI protein in colorectal cancer. Cancer Treat Res Commun 2022; 31:100542. [PMID: 35248886 DOI: 10.1016/j.ctarc.2022.100542] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Although great research has been done to clarify the pathogenesis of colorectal cancer (CRC), it is still the third common cancer worldwide. Pathogenesis of CRC as a heterogeneous disease is correlated with mutations and epigenetic alterations that result in the inactivation of tumor-suppressive and activation of an oncogene. Small non-coding RNAs (sncRNAs), emerging as a key player in regulating the genes and protein expression, with a length less than 200 nucleotide (nt). In this review, we aimed to focus on the role and the biogenesis of PIWI-interacting RNA (piRNAs), and tRNA-derived small RNA (tRFs) and PIWI proteins in the initiation, progression, and metastasis of CRC and their molecular mechanisms to understand their function in cancers and to provide better therapeutic strategies for CRC.
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Affiliation(s)
| | | | - Jian Wang
- Department Genetic, Medical University of Tehran, Tehran, Iran; Department Molecular Medicine, University of Leeds, England, United Kingdom.
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28
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Arkov AL. Looking at the Pretty "Phase" of Membraneless Organelles: A View From Drosophila Glia. Front Cell Dev Biol 2022; 10:801953. [PMID: 35198559 PMCID: PMC8859445 DOI: 10.3389/fcell.2022.801953] [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: 10/26/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Membraneless granules assemble in different cell types and cellular loci and are the focus of intense research due to their fundamental importance for cellular organization. These dynamic organelles are commonly assembled from RNA and protein components and exhibit soft matter characteristics of molecular condensates currently characterized with biophysical approaches and super-resolution microscopy imaging. In addition, research on the molecular mechanisms of the RNA-protein granules assembly provided insights into the formation of abnormal granules and molecular aggregates, which takes place during many neurodegenerative disorders including Parkinson's diseases (PD), Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and frontotemporal dementia (FTD). While these disorders are associated with formation of abnormal granules, membraneless organelles are normally assembled in neurons and contribute to translational control and affect stability of neuronal RNAs. More recently, a new subtype of membraneless granules was identified in Drosophila glia (glial granules). Interestingly, glial granules were found to contain proteins which are the principal components of the membraneless granules in germ cells (germ granules), indicating some similarity in the functional assembly of these structures in glia and germline. This mini review highlights recent research on glial granules in the context of other membraneless organelles, including their assembly mechanisms and potential functions in the nervous system.
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Affiliation(s)
- Alexey L Arkov
- Department of Biological Sciences, Murray State University, Murray, KY, United States
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29
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Zhang J, Chen S, Liu K. Structural insights into piRNA biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194799. [PMID: 35182819 DOI: 10.1016/j.bbagrm.2022.194799] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 01/24/2023]
Abstract
Discovered two decades ago, Piwi-interacting RNAs (piRNAs) play critical roles in gene regulation, transposon element repression, and antiviral defense. Dysregulation of piRNAs has been noted in diverse human diseases including cancers. Recently, extensive studies have revealed that many more proteins are involved in piRNA biogenesis. This review will summarize the recent progress in piRNA biogenesis and functions, especially the molecular mechanisms by which piRNA biogenesis-related proteins contribute to piRNA processing.
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Affiliation(s)
- Jin Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Sizhuo Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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30
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A universal catalytic hairpin assembly system for direct plasma biopsy of exosomal PIWI-interacting RNAs and microRNAs. Anal Chim Acta 2022; 1192:339382. [DOI: 10.1016/j.aca.2021.339382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 12/22/2022]
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31
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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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32
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Ben Youssef M, Christelle Ouédraogo B, Bastarache P, Dumas P, Moffat CE, Vickruck JL, Morin PJ. Exposure to Temperature and Insecticides Modulates the Expression of Small Noncoding RNA-Associated Transcripts in the Colorado Potato Beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2022; 22:23. [PMID: 35172010 PMCID: PMC8849280 DOI: 10.1093/jisesa/ieac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 06/14/2023]
Abstract
The Colorado potato beetle (Leptinotarsa decemlineata (Say)) is an insect that can adapt to various challenges, including temperature fluctuations or select insecticide treatments. This pest is also an ongoing threat to the potato industry. Small noncoding RNAs such as miRNAs, which can control posttranscriptionally the expression of various genes, and piRNAs, which can notably impact mRNA turnover, are modulated in insects under different conditions. Unfortunately, information regarding the expression status of key players involved in their synthesis and function is for the most part lacking. The current study thus aims at assessing the levels of such targets in L. decemlineata exposed to hot and cold temperatures as well as treated to the insecticides chlorantraniliprole, clothianidin, imidacloprid, and spinosad. Transcript expression levels of Ago1, Ago2, Ago3, Dcr2a, Dcr2b, Expo-5, Siwi-1, and Siwi-2, components of pathways associated with small noncoding RNA production or function, were measured by qRT-PCR and revealed modulation of select transcripts in response to temperature challenges and to select insecticides. RNAi-mediated reduction of Ago2 transcript levels in L. decemlineata injected with Ago2-targeting dsRNA and exposed to cold and warm temperatures was also conducted. Changes in survival rates were observed for the latter condition in dsRNA- versus saline-injected insects. These results showcase the differential expression of select targets involved in small noncoding RNA homeostasis and provide leads for the subsequent assessment of their involvement during stress response in L. decemlineata using RNAi-based approaches.
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Affiliation(s)
- Mariem Ben Youssef
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Brigitte Christelle Ouédraogo
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Pierre Bastarache
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Pascal Dumas
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Chandra E Moffat
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Jessica L Vickruck
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Pier Jr Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
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Shome S, Jernigan RL, Beitz DC, Clark S, Testroet ED. Non-coding RNA in raw and commercially processed milk and putative targets related to growth and immune-response. BMC Genomics 2021; 22:749. [PMID: 34657595 PMCID: PMC8520644 DOI: 10.1186/s12864-021-07964-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/27/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Bovine milk contains extracellular vesicles (EVs) that play a role in cellular communication, acting in either an autocrine, paracrine, or an exocrine manner. The unique properties of the EVs protect the cargo against degradation. We profiled the ncRNAs (non-coding RNA) present in the EVs from seven dairy products - raw whole milk, heat-treated skim milk, homogenized heat-treated skim milk, pasteurized homogenized skim milk, pasteurized heavy whipping cream, sweet cream buttermilk and cultured buttermilk with four replicates each, obtained at different processing steps from a commercial dairy plant. EVs and their cargo were extracted by using a validated commercial kit that has been shown to be efficient and specific for EVs. Further, to find the annotation of ncRNAs, we probed bovine and other organism repositories(such as miRBase, miRTarBase, Ensemble) to find homolog ncRNA annotation in case the annotations of ncRNA are not available in Bos Taurus database. RESULTS Specifically, 30 microRNAs (miRNAs), were isolated throughout all the seven milk samples, which later when annotated with their corresponding 1546 putative gene targets have functions associated with immune response and growth and development. This indicates the potential for these ncRNAs to beneficially support mammary health and growth for the cow as well as neonatal gut maturation. The most abundant miRNAs were bta-miR-125a and human homolog miR-718 based on the abundance values of read count obtained from the milk samples.bta-miR-125a is involved in host bacterial and viral immune response, and human homolog miR-718 is involved in the regulation of p53, VEGF, and IGF signaling pathways, respectively. Sixty-two miRNAs were up-regulated and 121 miRNAs were down-regulated throughout all the milk samples when compared to raw whole milk. In addition, our study explored the putative roles of other ncRNAs which included 88 piRNAs (piwi-interacting RNA), 64 antisense RNAs, and 105 lincRNAs (long-intergenic ncRNAs) contained in the bovine exosomes. CONCLUSION Together, the results indicate that bovine milk contains significant numbers of ncRNAs with putative regulatory targets associated with immune- and developmental-functions important for neonatal bovine health, and that processing significantly affects the ncRNA expression values; but statistical testing of overall abundance(read counts) of all miRNA samples suggests abundance values aren't much affected. This can be attributed to the breakage of exosomal vesicles during the processing stages. It is worth noting, however, that these gene regulatory targets are putative, and further evidence could be generated through experimental validation.
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Affiliation(s)
- S Shome
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - R L Jernigan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - D C Beitz
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - S Clark
- Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, USA
| | - E D Testroet
- Department of Animal and Veterinary Sciences, The University of Vermont, 509 Main Street, Burlington, VT, 05402, USA.
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Peng Q, Chiu PKF, Wong CYP, Cheng CKL, Teoh JYC, Ng CF. Identification of piRNA Targets in Urinary Extracellular Vesicles for the Diagnosis of Prostate Cancer. Diagnostics (Basel) 2021; 11:diagnostics11101828. [PMID: 34679526 PMCID: PMC8534571 DOI: 10.3390/diagnostics11101828] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
Emerging studies demonstrate that PIWI-interacting RNAs (piRNAs) are associated with various human cancers. This study aimed to evaluate the urinary extracellular vesicles (EVs) piRNAs as non-invasive biomarkers for prostate cancer (PCa) diagnosis. RNA was extracted from urinary EVs from five PCa patients and five healthy controls (HC), and the piRNAs were analyzed by small RNA sequencing. Dysregulated piRNAs were identified and then validated in another 30 PCa patients and 10 HC by reverse-transcription polymerase chain reaction (RT-qPCR). The expressions of novel_pir349843, novel_pir382289, novel_pir158533, and hsa_piR_002468 in urinary EVs were significantly increased in the PCa group compared with the HC group. The area under the curve (AUC) of novel_pir158533, novel_pir349843, novel_pir382289, hsa_piR_002468, and the combination of the four piRNA in PCa diagnosis was 0.723, 0.757, 0.777, 0.783, and 0.853, respectively. After the RNAhybrid program analysis, all four piRNAs had multiple potential binding sites with key mRNAs in PTEN/PI3K/Akt, Wnt/beta-catenin, or androgen receptor pathway, which are critical in PCa development and progression. In conclusion, our findings indicate that specific piRNAs in urinary EVs may serve as non-invasive diagnostic biomarkers for PCa.
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Karimpour M, Ravanbakhsh R, Maydanchi M, Rajabi A, Azizi F, Saber A. Cancer driver gene and non-coding RNA alterations as biomarkers of brain metastasis in lung cancer: A review of the literature. Biomed Pharmacother 2021; 143:112190. [PMID: 34560543 DOI: 10.1016/j.biopha.2021.112190] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 02/07/2023] Open
Abstract
Brain metastasis (BM) is the most common event in patients with lung cancer. Despite multimodal treatments and advances in systemic therapies, development of BM remains one of the main factors associated with poor prognosis and mortality in patients with lung cancer. Therefore, better understanding of mechanisms involved in lung cancer brain metastasis (LCBM) is of great importance to suppress cancer cells and to improve the overall survival of patients. Several cancer-related genes such as EGFR and KRAS have been proposed as potential predictors of LCBM. In addition, there is ample evidence supporting crucial roles of non-coding RNAs (ncRNAs) in mediating LCBM. In this review, we provide comprehensive information on risk assessment, predictive, and prognostic panels for early detection of BM in patients with lung cancer. Moreover, we present an overview of LCBM molecular mechanisms, cancer driver genes, and ncRNAs which may predict the risk of BM in lung cancer patients. Recent clinical studies have focused on determining mechanisms involved in LCBM and their association with diagnosis, prognosis, and treatment outcomes. These studies have shown that alterations in EGFR, KRAS, BRAF, and ALK, as the most frequent coding gene alterations, and dysregulation of ncRNAs such as miR-423, miR-330-3p, miR-145, piR-651, and MALAT1 can be considered as potential biomarkers of LCBM.
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Affiliation(s)
- Mina Karimpour
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reyhaneh Ravanbakhsh
- Department of Aquatic Biotechnology, Artemia and Aquaculture Research Institute, Urmia University, Urmia, Iran
| | - Melika Maydanchi
- Zimagene Medical Genetics Laboratory, Avicenna St., Hamedan, Iran
| | - Ali Rajabi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Faezeh Azizi
- Genetics Office, Non-Communicable Disease Control Department, Public Health Department, Ministry of Health and Medical Education, Tehran, Iran
| | - Ali Saber
- Zimagene Medical Genetics Laboratory, Avicenna St., Hamedan, Iran.
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Chu C, Yu L, Henry-Berger J, Ru YF, Kocer A, Champroux A, Li ZT, He M, Xie SS, Ma WB, Ni MJ, Ni ZM, Guo YL, Fei ZL, Gou LT, Liu Q, Sharma S, Zhou Y, Liu MF, Chen CD, Eamens AL, Nixon B, Zhou YC, Drevet JR, Zhang YL. Knockout of glutathione peroxidase 5 down-regulates the piRNAs in the caput epididymidis of aged mice. Asian J Androl 2021; 22:590-601. [PMID: 32270769 PMCID: PMC7705982 DOI: 10.4103/aja.aja_3_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mammalian epididymis not only plays a fundamental role in the maturation of spermatozoa, but also provides protection against various stressors. The foremost among these is the threat posed by oxidative stress, which arises from an imbalance in reactive oxygen species and can elicit damage to cellular lipids, proteins, and nucleic acids. In mice, the risk of oxidative damage to spermatozoa is mitigated through the expression and secretion of glutathione peroxidase 5 (GPX5) as a major luminal scavenger in the proximal caput epididymidal segment. Accordingly, the loss of GPX5-mediated protection leads to impaired DNA integrity in the spermatozoa of aged Gpx5-/- mice. To explore the underlying mechanism, we have conducted transcriptomic analysis of caput epididymidal epithelial cells from aged (13 months old) Gpx5-/- mice. This analysis revealed the dysregulation of several thousand epididymal mRNA transcripts, including the downregulation of a subgroup of piRNA pathway genes, in aged Gpx5-/- mice. In agreement with these findings, we also observed the loss of piRNAs, which potentially bind to the P-element-induced wimpy testis (PIWI)-like proteins PIWIL1 and PIWIL2. The absence of these piRNAs was correlated with the elevated mRNA levels of their putative gene targets in the caput epididymidis of Gpx5-/- mice. Importantly, the oxidative stress response genes tend to have more targeting piRNAs, and many of them were among the top increased genes upon the loss of GPX5. Taken together, our findings suggest the existence of a previously uncharacterized somatic piRNA pathway in the mammalian epididymis and its possible involvement in the aging and oxidative stress-mediated responses.
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Affiliation(s)
- Chen Chu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lu Yu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Joelle Henry-Berger
- Genetics Reproduction and Development Laboratory, CNRS UMR 6293 - INSERM U1103 - Universitι Clermont Auvergne, Clermont-Ferrand 63001, France
| | - Yan-Fei Ru
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ayhan Kocer
- Genetics Reproduction and Development Laboratory, CNRS UMR 6293 - INSERM U1103 - Universitι Clermont Auvergne, Clermont-Ferrand 63001, France
| | - Alexandre Champroux
- Genetics Reproduction and Development Laboratory, CNRS UMR 6293 - INSERM U1103 - Universitι Clermont Auvergne, Clermont-Ferrand 63001, France
| | - Zhi-Tong Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Miao He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Sheng-Song Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Wu-Bin Ma
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Min-Jie Ni
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zi-Mei Ni
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun-Li Guo
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhao-Liang Fei
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lan-Tao Gou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Qiang Liu
- Department of Anatomy, Histology and Embryology, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| | - Samanta Sharma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yu Zhou
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Andrew L Eamens
- Priority Research Centre for Reproductive Sciences, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Sciences, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Yu-Chuan Zhou
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Joël R Drevet
- Genetics Reproduction and Development Laboratory, CNRS UMR 6293 - INSERM U1103 - Universitι Clermont Auvergne, Clermont-Ferrand 63001, France
| | - Yong-Lian Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
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Ben Maamar M, Nilsson EE, Skinner MK. Epigenetic transgenerational inheritance, gametogenesis and germline development†. Biol Reprod 2021; 105:570-592. [PMID: 33929020 PMCID: PMC8444706 DOI: 10.1093/biolre/ioab085] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
One of the most important developing cell types in any biological system is the gamete (sperm and egg). The transmission of phenotypes and optimally adapted physiology to subsequent generations is in large part controlled by gametogenesis. In contrast to genetics, the environment actively regulates epigenetics to impact the physiology and phenotype of cellular and biological systems. The integration of epigenetics and genetics is critical for all developmental biology systems at the cellular and organism level. The current review is focused on the role of epigenetics during gametogenesis for both the spermatogenesis system in the male and oogenesis system in the female. The developmental stages from the initial primordial germ cell through gametogenesis to the mature sperm and egg are presented. How environmental factors can influence the epigenetics of gametogenesis to impact the epigenetic transgenerational inheritance of phenotypic and physiological change in subsequent generations is reviewed.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
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38
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Hsu PS, Yu SH, Tsai YT, Chang JY, Tsai LK, Ye CH, Song NY, Yau LC, Lin SP. More than causing (epi)genomic instability: emerging physiological implications of transposable element modulation. J Biomed Sci 2021; 28:58. [PMID: 34364371 PMCID: PMC8349491 DOI: 10.1186/s12929-021-00754-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022] Open
Abstract
Transposable elements (TEs) initially attracted attention because they comprise a major portion of the genomic sequences in plants and animals. TEs may jump around the genome and disrupt both coding genes as well as regulatory sequences to cause disease. Host cells have therefore evolved various epigenetic and functional RNA-mediated mechanisms to mitigate the disruption of genomic integrity by TEs. TE associated sequences therefore acquire the tendencies of attracting various epigenetic modifiers to induce epigenetic alterations that may spread to the neighboring genes. In addition to posting threats for (epi)genome integrity, emerging evidence suggested the physiological importance of endogenous TEs either as cis-acting control elements for controlling gene regulation or as TE-containing functional transcripts that modulate the transcriptome of the host cells. Recent advances in long-reads sequence analysis technologies, bioinformatics and genetic editing tools have enabled the profiling, precise annotation and functional characterization of TEs despite their challenging repetitive nature. The importance of specific TEs in preimplantation embryonic development, germ cell differentiation and meiosis, cell fate determination and in driving species specific differences in mammals will be discussed.
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Affiliation(s)
- Pu-Sheng Hsu
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Shu-Han Yu
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Yi-Tzang Tsai
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Jen-Yun Chang
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Li-Kuang Tsai
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Chih-Hung Ye
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Ning-Yu Song
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.,Department of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
| | - Lih-Chiao Yau
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
| | - Shau-Ping Lin
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan. .,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan. .,Center of Systems Biology, National Taiwan University, Taipei, Taiwan. .,The Research Center of Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan.
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He J, Chen M, Xu J, Fang J, Liu Z, Qi H. Identification and characterization of Piwi-interacting RNAs in human placentas of preeclampsia. Sci Rep 2021; 11:15766. [PMID: 34344990 PMCID: PMC8333249 DOI: 10.1038/s41598-021-95307-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022] Open
Abstract
Preeclampsia is a common disease of pregnancy that poses a serious threat to the safety of pregnant women and the fetus; however, the etiology of preeclampsia is inconclusive. Piwi-interacting RNAs (piRNAs) are novel non-coding RNAs that are present at high levels in germ cells and are associated with spermatogenesis. Emerging evidence demonstrated that piRNA is expressed in a variety of human tissues and is closely associated with tumorigenesis. However, changes in the piRNA expression profile in the placenta have not been investigated. In this study, we used small RNA sequencing to evaluate the differences in piRNA expression profiles between preeclampsia and control patients and potential functions. Differential expression analysis found 41 up-regulated and 36 down-regulated piRNAs in preeclamptic samples. In addition, the functional enrichment analysis of piRNAs target genes indicated that they were related to the extracellular matrix (ECM) formation and tissue-specific. Finally, we examined the expression pattern of the PIWL family proteins in the placenta, and PIWL3 and PIWIL4 were the primary subtypes in the human placenta. In summary, this study first summarized the changes in the expression pattern of piRNA in preeclampsia and provided new clues for the regulatory role of piRNA in the human placenta.
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Affiliation(s)
- Jie He
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, 400016, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Miaomiao Chen
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, 400016, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China.,Maternal and Child Health Hospital of Hubei Province, No. 745 Wuluo Road, Hongshan District, Wuhan City, 430070, Hubei Province, China
| | - Jiacheng Xu
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, 400016, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Jie Fang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, 400016, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Zheng Liu
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, 400016, China.,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Hongbo Qi
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China. .,Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, Chongqing, 400016, China. .,China-Canada-New Zealand Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China.
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Yang Y, Ye X, Dang C, Cao Y, Hong R, Sun YH, Xiao S, Mei Y, Xu L, Fang Q, Xiao H, Li F, Ye G. Genome of the pincer wasp Gonatopus flavifemur reveals unique venom evolution and a dual adaptation to parasitism and predation. BMC Biol 2021; 19:145. [PMID: 34315471 PMCID: PMC8314478 DOI: 10.1186/s12915-021-01081-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Background Hymenoptera comprise extremely diverse insect species with extensive variation in their life histories. The Dryinidae, a family of solitary wasps of Hymenoptera, have evolved innovations that allow them to hunt using venom and a pair of chelae developed from the fore legs that can grasp prey. Dryinidae larvae are also parasitoids of Auchenorrhyncha, a group including common pests such as planthoppers and leafhoppers. Both of these traits make them effective and valuable for pest control, but little is yet known about the genetic basis of its dual adaptation to parasitism and predation. Results We sequenced and assembled a high-quality genome of the dryinid wasp Gonatopus flavifemur, which at 636.5 Mb is larger than most hymenopterans. The expansion of transposable elements, especially DNA transposons, is a major contributor to the genome size enlargement. Our genome-wide screens reveal a number of positively selected genes and rapidly evolving proteins involved in energy production and motor activity, which may contribute to the predatory adaptation of dryinid wasp. We further show that three female-biased, reproductive-associated yellow genes, in response to the prey feeding behavior, are significantly elevated in adult females, which may facilitate the egg production. Venom is a powerful weapon for dryinid wasp during parasitism and predation. We therefore analyze the transcriptomes of venom glands and describe specific expansions in venom Idgf-like genes and neprilysin-like genes. Furthermore, we find the LWS2-opsin gene is exclusively expressed in male G. flavifemur, which may contribute to partner searching and mating. Conclusions Our results provide new insights into the genome evolution, predatory adaptation, venom evolution, and sex-biased genes in G. flavifemur, and present genomic resources for future in-depth comparative analyses of hymenopterans that may benefit pest control. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01081-6.
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Affiliation(s)
- Yi Yang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Cong Dang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yunshen Cao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Rui Hong
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yu H Sun
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Shan Xiao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Le Xu
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Huamei Xiao
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.,Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, College of Life Sciences and Resource Environment, Yichun University, Yichun, China
| | - Fei Li
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
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de Sá Pereira BM, Montalvão de Azevedo R, da Silva Guerra JV, Faria PA, Soares-Lima SC, De Camargo B, Maschietto M. Non-coding RNAs in Wilms' tumor: biological function, mechanism, and clinical implications. J Mol Med (Berl) 2021; 99:1043-1055. [PMID: 33950291 DOI: 10.1007/s00109-021-02075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Non-coding RNAs are involved with maintenance and regulation of physiological mechanisms and are involved in pathological processes, such as cancer. Among the small ncRNAs, miRNAs are the most explored in tumorigenesis, metastasis development, and resistance to chemotherapy. These small molecules of ~ 22 nucleotides are modulated during early renal development, involved in the regulation of gene expression and Wilms' tumor progression. Wilms' tumors are embryonic tumors with few mutations and complex epigenetic dysregulation. In recent years, the small ncRNAs have been explored as potentially related both in physiological development and in the tumorigenesis of several types of cancer. Besides, genes regulated by miRNAs are related to biological pathways as PI3K, Wnt, TGF-β, and Hippo signaling pathways, among others, which may be involved with the underlying mechanisms of resistance to chemotherapy, and in this way, it has emerged as potential targets for cancer therapies, including for Wilms' tumors.
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Affiliation(s)
| | - Rafaela Montalvão de Azevedo
- Brazilian National Cancer Institute (INCa), Rio de Janeiro, RJ, Brazil.,Current institution: Molecular Bases of Genetic Risk and Genetic Testing Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - João Victor da Silva Guerra
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.,Postgraduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutic Sciences, University of Campinas, Campinas, SP, Brazil
| | - Paulo A Faria
- Brazilian National Cancer Institute (INCa), Rio de Janeiro, RJ, Brazil
| | | | | | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil. .,Current: Research Institute, Boldrini Children's Hospital, Rua Dr. Gabriel Porto, 1270 - Cidade Universitária, Campinas, SP, 13083-210, Brazil.
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He J, Wu F, Han Z, Hu M, Lin W, Li Y, Cao M. Biomarkers (mRNAs and Non-Coding RNAs) for the Diagnosis and Prognosis of Colorectal Cancer - From the Body Fluid to Tissue Level. Front Oncol 2021; 11:632834. [PMID: 33996548 PMCID: PMC8118670 DOI: 10.3389/fonc.2021.632834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/09/2021] [Indexed: 12/24/2022] Open
Abstract
In recent years, the diagnosis and treatment of colorectal cancer (CRC) have been continuously improved, but the mortality rate continues to be high, especially in advanced patients. CRC patients usually have no obvious symptoms in the early stage and are already in the advanced stage when they are diagnosed. The 5-year survival rate is only 10%. The blood markers currently used to screen for CRC, such as carcinoembryonic antigen and carbohydrate antigen 19-9, have low sensitivity and specificity, whereas other methods are invasive or too expensive. As a result, recent research has shifted to the development of minimally invasive or noninvasive biomarkers in the form of body fluid biopsies. Non-coding RNA molecules are composed of microRNAs, long non-coding RNAs, small nucleolar RNAs, and circular RNAs, which have important roles in the occurrence and development of diseases and can be utilized for the early diagnosis and prognosis of tumors. In this review, we focus on the latest findings of mRNA-ncRNA as biomarkers for the diagnosis and prognosis of CRC, from fluid to tissue level.
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Affiliation(s)
- Jinhua He
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Feifeng Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zeping Han
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Min Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weida Lin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuguang Li
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Mingrong Cao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
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Noncoding RNAs in Glioblastoma: Emerging Biological Concepts and Potential Therapeutic Implications. Cancers (Basel) 2021; 13:cancers13071555. [PMID: 33800703 PMCID: PMC8037102 DOI: 10.3390/cancers13071555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/28/2021] [Accepted: 03/19/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Since the completion of the Human Genome Project, noncoding RNAs (ncRNAs) have emerged as an important class of genetic regulators. Several classes of ncRNAs, which include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and piwi-interacting RNAs (piRNAs), have been shown to play important roles in controlling developmental and disease processes. In this article, we discuss the potential roles of ncRNAs in regulating glioblastoma (GBM) formation and progression as well as potential strategies to exploit the diagnostic and therapeutic potential of ncRNAs in GBM. Abstract Noncoding RNAs (ncRNAs) have emerged as a novel class of genomic regulators, ushering in a new era in molecular biology. With the advent of advanced genetic sequencing technology, several different classes of ncRNAs have been uncovered, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and piwi-interacting RNAs (piRNAs), which have been linked to many important developmental and disease processes and are being pursued as clinical and therapeutic targets. Molecular phenotyping studies of glioblastoma (GBM), the most common and lethal cancer of the adult brain, revealed that several ncRNAs are frequently dysregulated in its pathogenesis. Additionally, ncRNAs regulate many important aspects of glioma biology including tumour cell proliferation, migration, invasion, apoptosis, angiogenesis, and self-renewal. Here, we present an overview of the biogenesis of the different classes of ncRNAs, discuss their biological roles, as well as their relevance to gliomagenesis. We conclude by discussing potential approaches to therapeutically target the ncRNAs in clinic.
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Li Q, Dong A, Zhu Z, Zhang J, Li Y, Xu C. Structural basis for RNA 3'-end recognition by the PIWIL2 PAZ domain. Biochem Biophys Res Commun 2021; 553:187-190. [PMID: 33774220 DOI: 10.1016/j.bbrc.2021.03.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
PIWI family proteins are important members of Argonaute family that play an essential role in spermatogenesis and development when loaded with piRNAs. Here we solved the crystal structure of the human PIWIL2 PAZ domain and found its PAZ domain adopts a canonical PAZ fold. We furhter built a homology model of PIWIL2 bound to 2 nt 3' overhangs. We found that PIWIL2 utilizes a deep hydrophobic concave to accommodate the 2 nt at 3'-end of RNAs. The recognition of 2 nt 3' overhangs by PIWIL2 is conserved in other human PIWIL proteins, implicating the evolutionarily conserved role of PAZ domain in binding to target RNAs.
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Affiliation(s)
- Qianqian Li
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, M5G 1L7, Canada
| | - Zhongliang Zhu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Jiahai Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, Ontario, M5G 1L7, Canada
| | - Chao Xu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
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Huang X, Wong G. An old weapon with a new function: PIWI-interacting RNAs in neurodegenerative diseases. Transl Neurodegener 2021; 10:9. [PMID: 33685517 PMCID: PMC7938595 DOI: 10.1186/s40035-021-00233-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding transcripts that are highly conserved across species and regulate gene expression through pre- and post-transcriptional processes. piRNAs were originally discovered in germline cells and protect against transposable element expression to promote and maintain genome stability. In the recent decade, emerging roles of piRNAs have been revealed, including the roles in sterility, tumorigenesis, metabolic homeostasis, neurodevelopment, and neurodegenerative diseases. In this review, we summarize piRNA biogenesis in C. elegans, Drosophila, and mice, and further elaborate upon how piRNAs mitigate the harmful effects of transposons. Lastly, the most recent findings on piRNA participation in neurological diseases are highlighted. We speculate on the mechanisms of piRNA action in the development and progression of neurodegenerative diseases. Understanding the roles of piRNAs in neurological diseases may facilitate their applications in diagnostic and therapeutic practice.
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Affiliation(s)
- Xiaobing Huang
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, 999078, S.A.R., China
| | - Garry Wong
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, 999078, S.A.R., China.
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HRV16 Infection Induces Changes in the Expression of Multiple piRNAs. Virol Sin 2021; 36:736-745. [PMID: 33616891 DOI: 10.1007/s12250-021-00344-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/30/2020] [Indexed: 10/22/2022] Open
Abstract
Human rhinovirus (HRV) is one of the most important cold-causing pathogens in humans. Piwi-interacting RNAs (piRNAs) are a recently discovered class of small non-coding RNAs whose best-understood function is to repress mobile element (ME) activity in animal germline. However, the profile of human/host piRNA during HRV infection is largely unknown. Here we performed high-throughput sequencing of piRNAs from H1-HeLa cells infected with HRV16 at 12 h, 24 h, and 36 h. The results showed that 22,151,664, 24,362,486 and 22,726,546 piRNAs displayed differential expression after HRV16 infection for three time points. A significant differential expression of 21 piRNAs was found in all time points and further verified by RT-qPCR, including 7 known piRNAs and 14 newly found piRNAs. In addition, piRNA prediction was performed on Piano using the SVM algorithm and transposon information. It found that novel_pir78110, novel_pir78107, novel_pir78097, novel_pir78094 and novel_pir76584 are associated with the DNA/hobo of Drosophila, Ac of maize and Tam3 of snapdragon (hAT)-Charlie transposon. The novel_pir97924, novel_pir105705 and novel_pir105700 recognize long interspersed nuclear elements 1 (LINE-1). The novel_pir33182 and novel_pir46604 are related to the long terminal repeat (LTR)/(Endogenous Retrovirus1) ERV1 repetitive element. The novel_pir73855 is related to the LTR/ERVK repetitive element. Both novel_pir70108 and novel_pir70106 are associated with the LTR/ERVL-MaLR repetitive element. The novel_pir15900 is associated with the DNA/hAT-Tip100 repetitive element. Overall, our results indicated that rhinovirus infection could reduce the expression of some piRNAs to facilitate upregulation of LINE-1 transcription or retrotransposons' expression, which is helpful to further explore the mechanism of rhinovirus infection.
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Ho T, Panyim S, Udomkit A. Assessment of the function of gonad-specific PmAgo4 in viral replication and spermatogenesis in Penaeus monodon. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103824. [PMID: 32791174 DOI: 10.1016/j.dci.2020.103824] [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: 06/26/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Argonaute family is phylogenetically subdivided into Ago and Piwi subfamilies that operate either transcriptional or post-transcriptional regulation in association with particular types of small RNAs. Among the four members of Ago subfamily (PmAgo1-4) found in black tiger shrimp Penaeus monodon, PmAgo4 exhibits gonad-restricted expression and takes part in transposon repression as the Piwi subfamily. While PmAgo1-3 participate in RNA interference (RNAi)-based mechanism, the role of PmAgo4 in RNAi is still mysterious, and was therefore investigated in this study. The results showed that knockdown of PmAgo4 in shrimp testis did not have a significant effect on the potency of PmRab7 silencing by dsPmRab7. In addition, replication of YHV as well as YHV-induced cumulative mortality in PmAgo4-knockdown shrimp are comparable to the control shrimp, suggesting the irrelevant association of PmAgo4 with RNAi-mediated gene silencing and antiviral immunity. Since PmAgo4 did not function in common with the Ago subfamily, its potential function in gametogenesis of male shrimp was further investigated. The reduction of PmAgo4 transcript levels in male shrimp revealed significant defect in testicular maturity as measured by Testicular Index (TI). Moreover, the numbers of mature sperm in spermatophore of PmAgo4-knockdown shrimp were significantly decreased comparing with the control shrimp. Our studies thus suggest a distinctive role of PmAgo4 that is not consistent with a dsRNA-mediate gene regulation and virus replication, but has a key function in controlling spermatogenesis in P. monodon.
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Affiliation(s)
- Teerapong Ho
- Institute of Molecular Biosciences, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Sakol Panyim
- Institute of Molecular Biosciences, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Apinunt Udomkit
- Institute of Molecular Biosciences, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand.
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Kumar S, Gonzalez EA, Rameshwar P, Etchegaray JP. Non-Coding RNAs as Mediators of Epigenetic Changes in Malignancies. Cancers (Basel) 2020; 12:E3657. [PMID: 33291485 PMCID: PMC7762117 DOI: 10.3390/cancers12123657] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are untranslated RNA molecules that regulate gene expressions. NcRNAs include small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), circular RNAs (cRNAs) and piwi-interacting RNAs (piRNAs). This review focuses on two types of ncRNAs: microRNAs (miRNAs) or short interfering RNAs (siRNAs) and long non-coding RNAs (lncRNAs). We highlight the mechanisms by which miRNAs and lncRNAs impact the epigenome in the context of cancer. Both miRNAs and lncRNAs have the ability to interact with numerous epigenetic modifiers and transcription factors to influence gene expression. The aberrant expression of these ncRNAs is associated with the development and progression of tumors. The primary reason for their deregulated expression can be attributed to epigenetic alterations. Epigenetic alterations can cause the misregulation of ncRNAs. The experimental evidence indicated that most abnormally expressed ncRNAs impact cellular proliferation and apoptotic pathways, and such changes are cancer-dependent. In vitro and in vivo experiments show that, depending on the cancer type, either the upregulation or downregulation of ncRNAs can prevent the proliferation and progression of cancer. Therefore, a better understanding on how ncRNAs impact tumorigenesis could serve to develop new therapeutic treatments. Here, we review the involvement of ncRNAs in cancer epigenetics and highlight their use in clinical therapy.
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Affiliation(s)
- Subhasree Kumar
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Edward A. Gonzalez
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Pranela Rameshwar
- Department of Medicine, Hematology/Oncology, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
| | - Jean-Pierre Etchegaray
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
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50
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Vinasco-Sandoval T, Moreira FC, F. Vidal A, Pinto P, Ribeiro-dos-Santos AM, Cruz RLS, Fonseca Cabral G, Anaissi AKM, Lopes KDP, Ribeiro-dos-Santos A, Demachki S, de Assumpção PP, Ribeiro-dos-Santos Â, Santos S. Global Analyses of Expressed Piwi-Interacting RNAs in Gastric Cancer. Int J Mol Sci 2020; 21:E7656. [PMID: 33081152 PMCID: PMC7593925 DOI: 10.3390/ijms21207656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer (GC) represents a notable amount of morbidity and mortality worldwide. Understanding the molecular basis of CG will offer insight into its pathogenesis in an attempt to identify new molecular biomarkers to early diagnose this disease. Therefore, studies involving small non-coding RNAs have been widely explored. Among these, PIWI-interacting RNAs (piRNAs) are an emergent class that can play important roles in carcinogenesis. In this study, small-RNA sequencing was used to identify the global piRNAs expression profile (piRNome) of gastric cancer patients. We found 698 piRNAs in gastric tissues, 14 of which were differentially expressed (DE) between gastric cancer (GC), adjacent to gastric cancer (ADJ), and non-cancer tissues (NC). Moreover, three of these DE piRNAs (piR-48966*, piR-49145, piR-31335*) were differently expressed in both GC and ADJ samples in comparison to NC samples, indicating that the tumor-adjacent tissue was molecularly altered and should not be considered as a normal control. These three piRNAs are potential risk biomarkers for GC, especially piR-48966* and piR-31335*. Furthermore, an in-silico search for mRNAs targeted by the differentially expressed piRNAs revealed that these piRNAs may regulate genes that participate in cancer-related pathways, suggesting that these small non-coding RNAs may be directly and indirectly involved in gastric carcinogenesis.
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Affiliation(s)
- Tatiana Vinasco-Sandoval
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Fabiano Cordeiro Moreira
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Amanda F. Vidal
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Pablo Pinto
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - André M. Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Rebecca L. S. Cruz
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Gleyce Fonseca Cabral
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Ana K. M. Anaissi
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Katia de Paiva Lopes
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Arthur Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Samia Demachki
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Paulo Pimentel de Assumpção
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Ândrea Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Sidney Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
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