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Zhang B, Zhang C, Zhang J, Lu S, Zhao H, Jiang Y, Ma W. Regulatory roles of long non-coding RNAs in short-term heat stress in adult worker bees. BMC Genomics 2024; 25:506. [PMID: 38778290 PMCID: PMC11110378 DOI: 10.1186/s12864-024-10399-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial modulators of post-transcriptional gene expression regulation, cell fate determination, and disease development. However, lncRNA functions during short-term heat stress in adult worker bees are poorly understood. Here, we performed deep sequencing and bioinformatic analyses of honeybee lncRNAs. RNA interference was performed by using siRNA targeting the most highly expressed lncRNA. The silencing effect on lncRNA and the relative expression levels of seven heat shock protein (HSP) genes, were subsequently examined. Overall, 7,842 lncRNAs and 115 differentially expressed lncRNAs (DELs) were identified in adult worker bees following heat stress exposure. Structural analysis revealed that the overall expression abundance, length of transcripts, exon number, and open reading frames of lncRNAs were lower than those of mRNAs. GO analysis revealed that the target genes were mainly involved in "metabolism," "protein folding," "response to stress," and "signal transduction" pathways. KEGG analysis indicated that the "protein processing in endoplasmic reticulum" and "longevity regulating pathway-multiple species" pathways were most enriched. Quantitative real-time polymerase chain reaction (qRT-PCR) detection of the selected DELs confirmed the reliability of the sequencing data. Moreover, the siRNA experiment indicated that feeding siRNA yielded a silencing efficiency of 77.51% for lncRNA MSTRG.9645.5. Upon silencing this lncRNA, the expression levels of three HSP genes were significantly downregulated (p < 0.05), whereas those of three other HSP genes were significantly upregulated (p < 0.05). Our results provide a new perspective for understanding the regulatory mechanisms of lncRNAs in adult worker bees under short-term heat stress.
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Affiliation(s)
- Bing Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Chaoying Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Jiangchao Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Surong Lu
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Huiting Zhao
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Yusuo Jiang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Weihua Ma
- College of Horticulture, Shanxi Agricultural University, Taiyuan, Shanxi, China.
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Shen Y, Ulaangerel T, Ren H, Liu Q, Davshilt T, Yi M, Dugarjaviin M, Bou G. Comprehensive analysis of the whole-transcriptome landscape of the ovarian cortex from Mongolian horses that reproduce seasonally. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101179. [PMID: 38134534 DOI: 10.1016/j.cbd.2023.101179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
The reproductive cycle of equines tends to be seasonal and is influenced by factors such as light and temperature. The process and methods of regulating the mare oestrous cycle in the anestrus period are still immature. The effects of noncoding RNAs and mRNAs on the oestrous cycle have aroused much interest, but corresponding analyses of seasonal mare ovaries have not been reported. Here, we report a whole transcriptome analysis of the Mongolian horse ovarian cortex collected in anestrus and diestrus periods. In total, 1081 mRNAs, 205 lncRNAs, 54 circRNAs, and 13 miRNAs were upregulated in winter anestrus ovarian cortex (WAO), and 1261 mRNAs, 90 lncRNAs, 29 circRNAs, and 40 miRNAs were upregulated in summer diestrus ovarian cortex (SDO). The GO and KEGG enrichment analysis of differentially expressed mRNAs and target genes of differentially expressed lncRNAs, circRNAs, and miRNAs revealed some key functions and pathways that may be related to follicle and oocyte development. We found that estrogen-related pathways were enriched in different RNAs. Our data were used to generate miRNA, circRNA, lncRNA, and mRNA databases from the Mongolian horse ovary and differential expression profiles between WAO and SDO; these results provide clues for exploring methods of estrus regulation in mares during the anestrus period.
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Affiliation(s)
- Yingchao Shen
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Tseweendolmaa Ulaangerel
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Hong Ren
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Qi Liu
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Toli Davshilt
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Minna Yi
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Manglai Dugarjaviin
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China.
| | - Gerelchemg Bou
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China.
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3
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Wang S, Pan C, Sheng H, Yang M, Yang C, Feng X, Hu C, Ma Y. Construction of a molecular regulatory network related to fat deposition by multi-tissue transcriptome sequencing of Jiaxian red cattle. iScience 2023; 26:108346. [PMID: 38026203 PMCID: PMC10665818 DOI: 10.1016/j.isci.2023.108346] [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: 08/02/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Intramuscular fat (IMF) refers to the fat that accumulates between muscle bundles or within muscle cells, whose content significantly impacts the taste, tenderness, and flavor of meat products, making it a crucial economic characteristic in livestock production. However, the intricate mechanisms governing IMF deposition, involving non-coding RNAs (ncRNAs), genes, and complex regulatory networks, remain largely enigmatic. Identifying adipose tissue-specific genes and ncRNAs is paramount to unravel these molecular mysteries. This study, conducted on Jiaxian red cattle, harnessed whole transcriptome sequencing to unearth the nuances of circRNAs and miRNAs across seven distinct tissues. The interplay of these ncRNAs was assessed through differential expression analysis and network analysis. These findings are not only pivotal in unveiling the intricacies of fat deposition mechanisms but also lay a robust foundation for future research, setting the stage for enhancing IMF content in Jiaxian red cattle breeding.
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Affiliation(s)
- Shuzhe Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Hui Sheng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Mengli Yang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chaoyun Yang
- Xichang College, Liangshan Prefecture, Sichuan Province, China
| | - Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chunli Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
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Shi X, Liao S, Bi Z, Liu J, Li H, Feng C. Newly discovered circRNAs encoding proteins: recent progress. Front Genet 2023; 14:1264606. [PMID: 37829278 PMCID: PMC10565661 DOI: 10.3389/fgene.2023.1264606] [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: 07/21/2023] [Accepted: 09/12/2023] [Indexed: 10/14/2023] Open
Abstract
Circular RNA (circRNA) is a special class of noncoding RNA molecules and the latest research hotspot in the field of RNA. CircRNA molecules have a closed loop structure, which is not affected by RNA exonuclease and has the characteristics of more stable expression. Previous studies have shown that circRNA molecules are rich in microRNA (miRNA) binding sites and act as miRNA sponges in cells. By interacting with miRNAs associated with tumors and other diseases, circRNAs play an important regulatory role. However, circRNAs have recently been found to have small open reading frames that enable them to encode peptides/proteins. These proteins have been reported to play an important role in the mechanism of regulation of a variety of diseases and have great potential in the diagnosis and treatment of diseases. In this review, we summarize the mechanism of action of the newly discovered circRNA-coding proteins since 2022 and briefly describe their research process. In addition, we also discuss the prediction model of the functional sites and encoded proteins of circRNAs, which provides a potential idea for future research on circRNAs.
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Affiliation(s)
- Xiaotong Shi
- Department of Obstetrics and Gynecology, Beijing Chao-yang Hospital of Capital Medical University, Beijing, China
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Shiyu Liao
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Zhiguo Bi
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Jianguo Liu
- Department of Orthopedics, The First Hospital of Jilin University, Changchun, China
| | - Hua Li
- Department of Obstetrics and Gynecology, Beijing Chao-yang Hospital of Capital Medical University, Beijing, China
| | - Chunyang Feng
- Department of Obstetrics and Gynecology, Beijing Chao-yang Hospital of Capital Medical University, Beijing, China
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Zhang S, Wang C, Wang Y, Zhang H, Xu C, Cheng Y, Yuan Y, Sha J, Guo X, Cui Y. A novel protein encoded by circRsrc1 regulates mitochondrial ribosome assembly and translation during spermatogenesis. BMC Biol 2023; 21:94. [PMID: 37095490 PMCID: PMC10127071 DOI: 10.1186/s12915-023-01597-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/13/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are a large class of mammalian RNAs. Several protein products translated by circRNAs have been reported to be involved in the development of various tissues and systems; however, their physiological functions in male reproduction have yet not been explored. RESULTS Here, we report an endogenous circRNA (circRsrc1) that encodes a novel 161-amino-acid protein which we named Rsrc1-161aa through circRNA sequencing coupled with mass spectrometry analysis on mouse testicular tissues. Deletion of Rsrc1-161aa in mice impaired male fertility with a significant decrease in sperm count and motility due to dysfunctions of mitochondrial energy metabolism. A series of in vitro rescue experiments revealed that circRsrc1 regulates mitochondrial functions via its encoded protein Rsrc1-161aa. Mechanistically, Rsrc1-161aa directly interacts with mitochondrial protein C1qbp and enhances its binding activity to mitochondrial mRNAs, thereby regulating the assembly of mitochondrial ribosomes and affecting the translation of oxidative phosphorylation (OXPHOS) proteins and mitochondrial energy metabolism. CONCLUSIONS Our studies reveal that Rsrc1-161aa protein encoded by circRsrc1 regulates mitochondrial ribosome assembly and translation during spermatogenesis, thereby affecting male fertility.
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Affiliation(s)
- Shu Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Chang Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yue Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hao Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Chen Xu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yiwei Cheng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yan Yuan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210029, China.
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Yiqiang Cui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China.
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Abstract
Circular RNAs (circRNAs) are closed-loop RNA transcripts formed by a noncanonical back splicing mechanism. circRNAs are expressed in various tissues and cell types in a temporospatially regulated manner and have diverse molecular functions including their ability to act as miRNA sponges, transcriptional and splicing regulators, protein traps, and even templates for polypeptide synthesis. Emerging evidence suggests that circRNAs are themselves dynamically regulated throughout development in various organisms, with a substantial accumulation during ageing. Their regulatory roles in cellular pathways associated with ageing and senescence, as well as their implications in ageing-related diseases, such as neurological disease, cancer, and cardiovascular disease, suggest that circRNAs are key molecular determinants of the ageing process. Their unique structure, expression specificity, and biological functions highlight a potential capacity for use as novel biomarkers for diagnosis, prognosis, and treatment outcomes in a variety of conditions including pathological ageing. CircRNA may also have potential as target for interventions that manipulate ageing and longevity. In this chapter, we discuss the most recent advances in circRNA changes in ageing and ageing-associated disease.
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Saberiyan M, Karimi E, Safi A, Movahhed P, Dehdehi L, Haririan N, Mirfakhraie R. Circular RNAs: Novel Biomarkers in Spermatogenesis Defects and Male Infertility. Reprod Sci 2023; 30:62-71. [PMID: 35178677 DOI: 10.1007/s43032-022-00885-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/09/2022] [Indexed: 01/06/2023]
Abstract
Circular RNAs (circRNAs) are a new class of endogenous non-coding RNAs involved in several cellular and biological processes, including gene expression regulation, microRNA function, transcription regulation, and translation modification. Therefore, these non-coding RNAs have important roles in the pathogenesis of various diseases. Male infertility is mainly due to abnormal sperm parameters such as motility, morphology, and concentration. Recent studies have confirmed the role of circRNAs in spermatogenesis, and the expression of several circRNAs is confirmed in seminal plasma, spermatozoa, and testicular tissue. It is suggested that deregulation of circRNAs is involved in different types of male infertility, including azoospermia, oligozoospermia, and asthenozoospermia. In the present review, we aimed to discuss the potential roles of circRNAs in spermatogenesis failure, sperm defects, and male infertility. Due to their conserved and special structure and tissue-specific expression pattern, circRNAs can be applied as reliable noninvasive molecular biomarkers, therapeutic and pharmaceutical targets in male infertility.
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Affiliation(s)
- Mohammadreza Saberiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Elham Karimi
- Department of Medical Genetics, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Amir Safi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
- Young Researchers and Elite Club, Islamic Azad University, Najafabad Branch, , Najafabad, Iran
| | - Parvaneh Movahhed
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Dehdehi
- Clinical Research Developmental Unit, Hajar Hospital, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Nazanin Haririan
- Biology Department, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Koodakyar St, Velenjak Ave, Chamran highway, 19395-4719, Tehran, Iran.
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Circ-CREBBP inhibits sperm apoptosis via the PI3K-Akt signaling pathway by sponging miR-10384 and miR-143-3p. Commun Biol 2022; 5:1339. [PMID: 36476986 PMCID: PMC9729231 DOI: 10.1038/s42003-022-04263-2] [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: 07/04/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Male reproductive diseases are becoming increasingly prominent, and sperm quality is an important indicator to reflect these diseases. Seminal plasma extracellular vesicles (SPEVs) are involved in sperm motility. However, their effects on sperm remain unclear. Here, we identified 222 differentially expressed circRNAs in SPEVs between boars with high or low sperm motility. We found that circ-CREBBP promoted sperm motility and inhibited sperm apoptosis by sponging miR-10384 and miR-143-3p. In addition, miR-10384 and miR-143-3p can regulate the expression of MCL1, CREB1 and CREBBP. Furthermore, we demonstrated that MCL1 interacted directly with BAX and that CREBBP interacted with CREB1 in sperm. We showed that inhibition of circ-CREBBP can reduce the expression of MCL1, CREB1 and CREBBP and increase the expression of BAX and CASP3, thus promoting sperm apoptosis. Our results suggest that circ-CREBBP may be a promising biomarker and therapeutic target for male reproductive diseases.
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Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that widely exist in eukaryotes. As a new focus in the field of molecular regulation, circRNAs have attracted much attention in recent years. Previous studies have confirmed that circRNAs are associated with many physiological and pathological processes. CircRNAs also participate in the regulation of stem cells. Stem cells have the properties of self-renewal and differentiation, which make stem cell therapy popular. CircRNAs may serve as new targets in stem cell therapy due to their regulation in stem cells. However, the underlying relationships between circRNAs and stem cells are still being explored. In this review, we briefly summarize the effects of circRNAs on stem cells, in the context of biological activities, aging and apoptosis, and aberrant changes. Moreover, we also examine the biological roles of stem cell-derived exosomal circRNAs. We believe our review will provide insights into the effects of circRNAs on stem cells.
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Zuo Q, Jing J, Zhou J, Zhang Y, Wei W, Chen G, Li B. Dual regulatory actions of LncBMP4 on BMP4 promote chicken primordial germ cell formation. EMBO Rep 2022; 23:e52491. [PMID: 34747116 PMCID: PMC8728602 DOI: 10.15252/embr.202152491] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
The unique characteristics of chicken primordial germ cells (PGCs) provide potential strategies for transgenic animal generation; however, insufficient PGC availability has limited their application. Regulation of bone morphogenic protein 4 (BMP4), a crucial factor for PGCs formation, may provide new strategies for PGC generation. We here identify a long noncoding RNA (lncRNA) that targets BMP4 (LncBMP4). LncBMP4 has similar functions as BMP4, in that it facilitates the formation and migration of PGCs. LncBMP4 promotes BMP4 expression by adsorbing the miRNA gga-mir-12211, thus reducing its inhibitory effect on BMP4 expression. In addition, the small peptide EPC5 encoded by LncBMP4 promotes the transcription of BMP4. The competing endogenous RNA (ceRNA) effect of LncBMP4 requires N6-methyladenosine (m6A) modification, in a dose-dependent manner, and high levels of m6A modification hinder EPC5 translation. Understanding the molecular mechanisms through which LncBMP4 promotes BMP4 expression during PGC formation may provide new avenues for efficient PGC generation.
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Affiliation(s)
- Qisheng Zuo
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Jin Jing
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Jing Zhou
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Yani Zhang
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Wanhong Wei
- Department of Biological SciencesCollege of Bioscience and BiotechnologyYangzhou UniversityYangzhouChina
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
| | - Bichun Li
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhouChina
- Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu ProvinceCollege of Animal Science and TechnologyYangzhou UniversityYangzhouChina
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Long noncoding RNA Meg3 sponges miR-708 to inhibit intestinal tumorigenesis via SOCS3-repressed cancer stem cells growth. Cell Death Dis 2021; 13:25. [PMID: 34934045 PMCID: PMC8692598 DOI: 10.1038/s41419-021-04470-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/16/2021] [Accepted: 12/10/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) remains the most common gastrointestinal cancer and a leading cause of cancer deaths worldwide, with most showing pathologies indicating the malignant transformation of early stage intestinal stem cells. The long non-coding RNA Meg3, which functions as a tumor suppressor, has been reported to be abnormal in multiple tumorigenesis events; however, the underlying mechanism by which Meg3 contributes to the malignant proliferation of colonic stem cells remains unclear. METHODS We analyzed the expression levels of Meg3, miR-708, and SOCS3 in samples from Apc loss-of-function (Apcmin) mice and patients with CRC, particularly in colonic crypt cells. Apcmin mice and AMO/DSS-induced mice model (in vivo) and organoid culture system (in vitro) were used to explore the effect of the Meg3/miR-708/SOCS3 axis on tumorigenesis in the colon. In vitro, we performed RNApull-down, RNA immunoprecipitation, and luciferase reporter assays using DLD1 and RKO cell lines. FINDINGS The Meg3/miR-708/SOCS3 signaling axis plays a critical role in the early stage of CRC development. Our data showed Meg3 levels negatively correlate with miR-708 levels both in clinical samples and in the Apcmin mouse model, which indicated that Meg3 acts as a competitive endogenous RNA (ceRNA) of miR-708. Then, miR-708 served as an oncogene, inducing neoplasia in both Apcmin mice and cultured colonic organoids. Put together, miR-708 appears to promote malignant proliferation of colonic stem cells by targeting SOCS3/STAT3 signaling. INTERPRETATION These data revealed that Meg3 sponges miR-708 to inhibit CRC development via SOCS3-mediated repression of the malignant proliferation of colonic stem cells. The Meg3/miR-708/SOCS3 signaling axis provides potential targets for the diagnosis and treatment of CRC, particularly early stage CRC.
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Quan J, Bode AM, Luo X. ACSL family: The regulatory mechanisms and therapeutic implications in cancer. Eur J Pharmacol 2021; 909:174397. [PMID: 34332918 DOI: 10.1016/j.ejphar.2021.174397] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 12/29/2022]
Abstract
Accumulating evidence shows that deregulation of fatty acid (FA) metabolism is associated with the development of cancer. Long-chain acyl-coenzyme A synthases (ACSLs) are responsible for activating long-chain FAs and are frequently deregulated in cancers. Among the five mammalian ACSL family members, ACSL1 is involved in the TNFα-mediated pro-inflammatory phenotype and mainly facilitates cancer progression. ACSL3 is an androgen-responsive gene. High ACSL3 expression has been detected in a variety of cancers, including melanoma, triple-negative breast cancer (TNBC) and high-grade non-small cell lung carcinoma (NSCLC), and correlates with worse prognosis of patients with these diseases. ACSL4 can exert opposing roles acting as a tumor suppressor or as an oncogene depending on the specific cancer type and tissue environment. Moreover, ACSL4 behaves as a crucial regulator in ferroptosis that is defined as a cell death process caused by iron-dependent peroxidation of lipids. ACSL5 is nuclear-coded and expressed in the mitochondria and physiologically participates in the pro-apoptotic sensing of cells. ACSL5 mainly acts as a tumor suppressor in cancers. ACSL6 downregulation has been observed in many forms of cancers, except in colorectal cancer (CRC). Here, we address the differential regulatory mechanisms of the ACSL family members as well as their functions in carcinogenesis. Moreover, we enumerate the clinical therapeutic implications of ACSLs, which might serve as valuable biomarkers and therapeutic targets for precision cancer treatment.
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Affiliation(s)
- Jing Quan
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, PR China; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, Hunan, 410078, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, PR China; Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Changsha, Hunan, 410078, China; Molecular Imaging Research Center of Central South University, Changsha, Hunan, 410078, China.
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13
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Xi HM, Ren YJ, Ren F, Li Y, Feng TY, Wang Z, Du YQ, Zhang LK, Hu JH. Recent advances in isolation, identification, and culture of mammalian spermatogonial stem cells. Asian J Androl 2021; 24:5-14. [PMID: 34135169 PMCID: PMC8788607 DOI: 10.4103/aja.aja_41_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Continuous spermatogenesis depends on the self-renewal and differentiation of spermatogonial stem cells (SSCs). SSCs, the only male reproductive stem cells that transmit genetic material to subsequent generations, possess an inherent self-renewal ability, which allows the maintenance of a steady stem cell pool. SSCs eventually differentiate to produce sperm. However, in an in vitro culture system, SSCs can be induced to differentiate into various types of germ cells. Rodent SSCs are well defined, and a culture system has been successfully established for them. In contrast, available information on the biomolecular markers and a culture system for livestock SSCs is limited. This review summarizes the existing knowledge and research progress regarding mammalian SSCs to determine the mammalian spermatogenic process, the biology and niche of SSCs, the isolation and culture systems of SSCs, and the biomolecular markers and identification of SSCs. This information can be used for the effective utilization of SSCs in reproductive technologies for large livestock animals, enhancement of human male fertility, reproductive medicine, and protection of endangered species.
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Affiliation(s)
- Hua-Ming Xi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
| | - Yi-Jie Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
| | - Fa Ren
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
| | - Yu Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
| | - Tian-Yu Feng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
| | - Zhi Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
| | - Ye-Qing Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
| | - Li-Kun Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
| | - Jian-Hong Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling 712100, China
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14
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Li X, Tian G, Wu J. Novel circGFRα1 Promotes Self-Renewal of Female Germline Stem Cells Mediated by m 6A Writer METTL14. Front Cell Dev Biol 2021; 9:640402. [PMID: 33928080 PMCID: PMC8076159 DOI: 10.3389/fcell.2021.640402] [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: 12/11/2020] [Accepted: 03/22/2021] [Indexed: 01/15/2023] Open
Abstract
Circular RNAs (circRNAs) play important roles in the self-renewal of stem cells. However, their significance and regulatory mechanisms in female germline stem cells (FGSCs) are largely unknown. Here, we identified an N 6-methyladenosine (m6A)-modified circRNA, circGFRα1, which is highly abundant in mouse ovary and stage-specifically expressed in mouse FGSC development. Knockdown of circGFRα1 in FGSCs significantly reduced their self-renewal. In contrast, overexpression of circGFRα1 enhanced FGSC self-renewal. Mechanistically, circGFRα1 promotes FGSC self-renewal by acting as a competing endogenous RNA (ceRNA) that sponges miR-449, leading to enhanced GFRα1 expression and activation of the glial cell derived neurotrophic factor (GDNF) signaling pathway. Furthermore, circGFRα1 acts as a ceRNA based on METTL14-mediated cytoplasmic export through the GGACU motif. Our study should help to understand the mechanisms regulating germ cell development, add new evidence on the mechanism of action of circRNA, and deepen our understanding of the development of FGSCs.
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Affiliation(s)
- Xiaoyong Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Renji Hospital, School of Medicine, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Geng Tian
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Renji Hospital, School of Medicine, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Renji Hospital, School of Medicine, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China
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15
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Zhou J, Qiu C, Fan Z, Liu T, Liu T. Circular RNAs in stem cell differentiation: a sponge-like role for miRNAs. Int J Med Sci 2021; 18:2438-2448. [PMID: 33967622 PMCID: PMC8100645 DOI: 10.7150/ijms.56457] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are novel endogenous non-coding RNAs that play a critical role during cellular signal transduction, gene transcription and translation. With the rapid advancement of bioinformatics analysis tools and high-throughput RNA sequencing, numerous circRNAs with important biological features have been identified. They function as competing endogenous RNAs (ceRNAs) of microRNAs and as such exhibit the potential to act as biomarkers for stem cell differentiation. In the recent past, several studies have shown the involvement of circRNAs in stem cells differentiation. The present review summarizes the molecular characteristics, biogenesis and mechanisms of newly identified circRNAs in the differentiation of stem cells. In conclusion, circRNAs regulate the stem cells differentiation via their ambient binding efficacy to modulate miRNA expression, as well as related gene translation. We believe that this review will provide reference guidance for future studies on stem cell differentiation.
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Affiliation(s)
- Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, P. R. China
| | - Cheng Qiu
- Department of Orthopaedic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, P. R. China.,Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Zhihua Fan
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, P. R. China.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Tianyi Liu
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, P. R. China
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16
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Chao Chen, Jian YY, Zhao XY, Liu YL, Xie QK. The involvement of hsa_circ_0000417 in the development of hypospadias by regulating AR. Differentiation 2020; 116:9-15. [PMID: 33080410 DOI: 10.1016/j.diff.2020.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 09/06/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Congenital hypospadias is a common congenital malformation of the urinary system in male children. However, the role of circRNA in congenital hypospadias remains unknown. METHODS Differentially expressed circRNAs and mRNAs were identified by RNA sequencing. GO and KEEG analysis were performed to uncover the key function and pathways. The interaction networks were constructed and analyzed by competing endogenous (ce)RNA analysis. Immunohistochemistry (IHC) and qRT-PCR were used to detect the expressions of androgen receptor (AR) and hsa_circ_0000417 in normal and hypospadias tissues. Further, the correlation between hsa_circ_0000417 and other clinical indicators were calculated. RESULTS Compared with normal foreskin tissues, 1329 circRNAs and 978 mRNAs were significantly upregulated, 3176 circRNAs and 614 mRNAs were significantly downregulated in hypospadias tissues, respectively. MAPK and PI3K-Akt signaling pathways play important roles in congenital hypospadias. The expression of AR and hsa_circ_0000417 in 68 hypospadias tissues was significantly lower than that in 68 normal foreskin tissues (P < 0.05). The expression of the AR, as analyzed using IHC, was consistent with the qPCR results. A significant correlation was noted between the expression of AR and hsa_circ_0000417 in 68 clinical samples (P < 0.05). Furthermore, the expression level of hsa_circ_0000417 was associated with the incidence of other diseases and the location of the hypospadias site (P < 0.05). Expression of hsa_circ_0000417 was significantly downregulated in hypospadias patients without other diseases (P < 0.05). CONCLUSION Hsa_circ_0000417 may regulate the expression of AR, and the expression of hsa_circ_0000417 in normal foreskin tissues is associated with the occurrence of hypospadias.
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Affiliation(s)
- Chao Chen
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China.
| | - Yong-Yuan Jian
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Xiang-You Zhao
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Yu-Ling Liu
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
| | - Qi-Ke Xie
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, China
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17
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Xie S, Li M, Chen Y, Liu Y, Ma L, Sun X, Sun Y, Gao R, Huang T. Identification of circular RNAs in the ovarian follicles of Meishan and Duroc sows during the follicular phase. J Ovarian Res 2020; 13:104. [PMID: 32917247 PMCID: PMC7488758 DOI: 10.1186/s13048-020-00709-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/28/2020] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs) are a newly discovered class of endogenous non-coding RNAs that play an important role in growth and development by regulating gene expression and participating in a variety of biological processes. However, the role of circRNAs in porcine follicles remains unclear. Therefore, this study examined middle-sized ovarian follicles obtained from Meishan and Duroc sows at day 4 of the follicular phase. High-throughput RNA sequencing (RNA-seq) was utilized to construct circRNAs, and differential expression was identified. The findings were validated using reverse transcription PCR (RT-PCR) and DNA sequencing, GO and KEGG analyses were performed, and potential miRNA targets were identified. The RNA-seq identified a total of 15,866 circRNAs, with 244 differentially expressed in the Meishan relative to the Duroc (111 up-regulated and 133 down-regulated). The RT-PCR finding confirmed the RNA-seq results, and quantitative real-time PCR (qPCR) analysis examining a subset of the circRNAs showed that they are resistant to RNase R digestion. Bioinformatics analysis (GO and KEGG) showed that the host genes associated with the differentially expressed circRNAs are involved in reproduction and follicular development signaling pathways. Furthermore, many of the circRNAs were found to interact with miRNAs that are associated with follicular development. This study presents a new perspective for studying circRNAs and provides a valuable resource for further examination into the potential roles of circRNAs in porcine follicular development.
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Affiliation(s)
- Su Xie
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi, 832000, China
| | - Mengxun Li
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi, 832000, China.,Key Laboratory of Animal Breeding and Reproduction of Minstry of Education,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yansen Chen
- University of Liège, Gembloux Agro-Bio Tech (ULiège-GxABT), Gembloux, Belgium
| | - Yi Liu
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi, 832000, China
| | - Lipeng Ma
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi, 832000, China
| | - Xiaomei Sun
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi, 832000, China
| | - Yishan Sun
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi, 832000, China
| | - Ruonan Gao
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi, 832000, China
| | - Tao Huang
- College of Animal Science and Technology, Shihezi University, 221 North Fourth Road, Shihezi, 832000, China.
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18
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Xu X, Gong C, Wang Y, Hu Y, Liu H, Fang Z. Multi-omics analysis to identify driving factors in colorectal cancer. Epigenomics 2020; 12:1633-1650. [PMID: 32573269 DOI: 10.2217/epi-2020-0073] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: We aim to identify driving genes of colorectal cancer (CRC) through multi-omics analysis. Materials & methods: We downloaded multi-omics data of CRC from The Cancer Genome Atlas dataset. Integrative analysis of single-nucleotide variants, copy number variations, DNA methylation and differentially expressed genes identified candidate genes that carry CRC risk. Kernal genes were extracted from the weighted gene co-expression network analysis. A competing endogenous RNA network composed of CRC-related genes was constructed. Biological roles of genes were further investigated in vitro. Results: We identified LRRC26 and REP15 as novel prognosis-related driving genes for CRC. LRRC26 hindered tumorigenesis of CRC in vitro. Conclusion: Our study identified novel driving genes and may provide new insights into the molecular mechanisms of CRC.
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Affiliation(s)
- Xi Xu
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Chaoju Gong
- Central Laboratory, The Municipal Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221106, PR China
| | - Yunfeng Wang
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS, Commissariat à l'Energie Atomique et aux Énergies Alternatives (CEA), Université Paris-Sud, 91198 Gif-sur-Yvette, Palaiseau, 91120, France
| | - Yanyan Hu
- Central Laboratory, Sanmen People's Hospital of Zhejiang Province, Sanmen, 317100, PR China
| | - Hong Liu
- Zhejiang Normal University - Jinhua People's Hospital Joint Center for Biomedical Research, Jinhua, 321004, PR China.,The Affiliated Hospital of Jinhua Polytechnic College, Jinhua, 321000, PR China
| | - Zejun Fang
- Central Laboratory, Sanmen People's Hospital of Zhejiang Province, Sanmen, 317100, PR China.,Central Laboratory, Sanmenwan Branch, The First Affiliated Hospital, College of Medicine, Zhejiang University, Sanmen, 317100, PR China
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19
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Zhang S, Shen S, Yang Z, Kong X, Liu F, Zhen Z. Coding and Non-coding RNAs: Molecular Basis of Forest-Insect Outbreaks. Front Cell Dev Biol 2020; 8:369. [PMID: 32596236 PMCID: PMC7300193 DOI: 10.3389/fcell.2020.00369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Insect population dynamics are closely related to 'human' ecological and economic environments, and a central focus of research is outbreaks. However, the lack of molecular-based investigations restricts our understanding of the intrinsic mechanisms responsible for insect outbreaks. In this context, the moth Dendrolimus punctatus Walker can serve as an ideal model species for insect population dynamics research because it undergoes periodic outbreaks. Here, high-throughput whole-transcriptome sequencing was performed using D. punctatus, sampled during latent and outbreak periods, to systemically explore the molecular basis of insect outbreaks and to identify the involved non-coding RNA (ncRNA) regulators, namely microRNAs, long non-coding RNAs, and circular RNAs. Differentially expressed mRNAs of D. punctatus from different outbreak periods were involved in developmental, reproductive, immune, and chemosensory processes; results that were consistent with the physiological differences in D. punctatus during differing outbreak periods. Targets analysis of the non-coding RNAs indicated that long non-coding RNAs could be the primary ncRNA regulators of D. punctatus outbreaks, while circular RNAs mainly regulated synapses and cell junctions. The target genes of differentially expressed microRNAs mainly regulated the metabolic and reproductive pathways during the D. punctatus outbreaks. Developmental, multi-organismal, and reproductive processes, as well as biological adhesion, characterized the competing endogenous RNA network. Chemosensory and immune genes closely related to the outbreak of D. punctatus were further analyzed in detail: from their ncRNA regulators' analysis, we deduce that both lncRNA and miRNA may play significant roles. This is the first report to examine the molecular basis of coding and non-coding RNAs' roles in insect outbreaks. The results provide potential biomarkers for control targets in forest insect management, as well as fresh insights into underlying outbreak-related mechanisms, which could be used for improving insect control strategies in the future.
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Affiliation(s)
- Sufang Zhang
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Sifan Shen
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhongwu Yang
- Forestry Comprehensive Development Center of Guilin, Guilin, China
| | - Xiangbo Kong
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Fu Liu
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhang Zhen
- Key Laboratory of Forest Protection of State Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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20
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Di Agostino S, Riccioli A, De Cesaris P, Fontemaggi G, Blandino G, Filippini A, Fazi F. Circular RNAs in Embryogenesis and Cell Differentiation With a Focus on Cancer Development. Front Cell Dev Biol 2020; 8:389. [PMID: 32528957 PMCID: PMC7266935 DOI: 10.3389/fcell.2020.00389] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
In the recent years thousands of non-coding RNAs have been identified, also thanks to highthroughput sequencing technologies. Among them, circular RNAs (circRNAs) are a well-represented class characterized by the high sequence conservation and cell type specific expression in eukaryotes. They are covalently closed loops formed through back-splicing. Recently, circRNAs were shown to regulate a variety of cellular processes functioning as miRNA sponges, RBP binding molecules, transcriptional regulators, scaffold for protein translation, as well as immune regulators. A growing number of studies are showing that deregulated expression of circRNAs plays important and decisive actions during the development of several human diseases, including cancer. The research on their biogenesis and on the various molecular mechanisms in which they are involved is going very fast, however, there are still few studies that address their involvement in embryogenesis and eukaryotic development. This review has the intent to describe the most recent progress in the study of the biogenesis and molecular activities of circRNAs providing insightful information in the field of embryogenesis and cell differentiation. In addition, we describe the latest research on circRNAs as novel promising biomarkers in diverse types of tumors.
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Affiliation(s)
- Silvia Di Agostino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Anna Riccioli
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Paola De Cesaris
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, Department of Diagnostic Research and Technological Innovation, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Antonio Filippini
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy.,Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
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21
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La Y, He X, Zhang L, Di R, Wang X, Gan S, Zhang X, Zhang J, Hu W, Chu M. Comprehensive Analysis of Differentially Expressed Profiles of mRNA, lncRNA, and circRNA in the Uterus of Seasonal Reproduction Sheep. Genes (Basel) 2020; 11:genes11030301. [PMID: 32178360 PMCID: PMC7140836 DOI: 10.3390/genes11030301] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/23/2022] Open
Abstract
Photoperiod is one of the important factors leading to seasonal reproduction of sheep. However, the molecular mechanisms underlying the photoperiod regulation of seasonal reproduction remain poorly understood. In this study, we compared the expression profiles of mRNAs, lncRNAs, and circRNAs in uterine tissues from Sunite sheep during three different photoperiods, namely, the short photoperiod (SP), short transfer to long photoperiod (SLP), and long photoperiod (LP). The results showed that 298, 403, and 378 differentially expressed (DE) mRNAs, 171, 491, and 499 DE lncRNAs, and 124, 270, and 400 DE circRNAs were identified between SP and LP, between SP and SLP, and between LP and SLP, respectively. Furthermore, functional enrichment analysis showed that the differentially expressed RNAs were mainly involved in the GnRH signaling pathway, thyroid hormone synthesis, and thyroid hormone signaling pathway. In addition, co-expression networks of lncRNA–mRNA were constructed based on the correlation analysis between the differentially expressed RNAs. Our study provides new insights into the expression changes of RNAs in different photoperiods, which might contribute to understanding the molecular mechanisms of seasonal reproduction in sheep.
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Affiliation(s)
- Yongfu La
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (X.H.); (R.D.); (X.W.)
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (X.H.); (R.D.); (X.W.)
| | - Liping Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (X.H.); (R.D.); (X.W.)
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (X.H.); (R.D.); (X.W.)
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China;
| | - Xiaosheng Zhang
- Tianjin Institute of Animal Sciences, Tianjin 300381, China; (X.Z.); (J.Z.)
| | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin 300381, China; (X.Z.); (J.Z.)
| | - Wenping Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (X.H.); (R.D.); (X.W.)
- Correspondence: (W.H.); (M.C.); Tel.: +86-15901106848 (W.H.); +86-010-62819850 (M.C.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.L.); (X.H.); (R.D.); (X.W.)
- Correspondence: (W.H.); (M.C.); Tel.: +86-15901106848 (W.H.); +86-010-62819850 (M.C.)
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22
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Han R, Han L, Wang S, Li H. Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development. Front Genet 2020; 10:1403. [PMID: 32133026 PMCID: PMC7040488 DOI: 10.3389/fgene.2019.01403] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 12/23/2019] [Indexed: 01/04/2023] Open
Abstract
Deer antler is the only completely regenerable organ in mammals. During the rapid growth period, the antler proliferates even faster than cancerous tissue growth. However, the proliferation and development of antler have been in a stable and controllable growth cycle. In this study, we analyzed the time series expression data of nine samples from mesenchyme layer in three male sika deer in the early period of the antler with a saddle-like appearance (30 days), the rapid growth period of the antler with two branches (60 days), and the final period of the antler with three branches (90 days). Whole Transcriptome sequencing results show that in the 30 d versus 60 d group, 1,464 genes, 85 long noncoding RNAs (lncRNAs), and 61 miRNAs were identified as differentially expressed; 1,748 genes, 138 lncRNAs, and 78 miRNAs were identified as differentially expressed in 30d versus 90d group; and 816 differentially expressed genes (DEGs), 49 differentially expressed lncRNAs (DE lncRNAs), and 24 differentially expressed miRNA (DE miRNAs) were identified in 60d versus 90d group. A total of 182 miRNA-mRNA interaction pairs and 89 miRNA-lncRNA interaction pairs were screened from DEGs, DE miRNAs, and DE lncRNAs to construct the ceRNA regulatory network (ceRNET). In summary, we identified candidate mRNAs, miRNAs and lncRNAs that regulate the development of antler tip. It may lay the foundation for further investigating the molecular mechanism of antler rapid growth and development.
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Affiliation(s)
- Ruobing Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shengnan Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Heping Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
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23
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Microarray Analysis For Expression Profiles of lncRNAs and circRNAs in Rat Liver after Brain-Dead Donor Liver Transplantation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5604843. [PMID: 31828106 PMCID: PMC6881575 DOI: 10.1155/2019/5604843] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/01/2019] [Accepted: 07/18/2019] [Indexed: 12/18/2022]
Abstract
The mechanisms underlying severe liver injury after brain-dead (BD) donor liver transplantation (BDDLT) remain unclear. In this study, we aimed to explore the roles of lncRNAs and circRNAs in liver injury after BDDLT. Rat liver injury was detected in the sham, BD, control, and BDDLT groups. We examined the expression profiles of lncRNAs and circRNAs in the livers of the BDDLT and control group using microarray analysis. The main functions of the differentially expressed genes were analyzed by gene ontology (GO) and KEGG pathway enrichment analysis. In addition, we used bioinformatic analyses to construct related expression networks. Liver injury was aggravated in the BD and BDDLT groups. We found various mRNAs, lncRNAs, and circRNAs that were differentially expressed in the BDDLT group compared with those in the control group. Coding-noncoding gene co-expression (CNC) network analysis showed that expression of the lncRNA LOC102553657 was associated with that of the apoptosis-related genes including HMOX1 and ATF3. Furthermore, competing endogenous RNAs (ceRNAs) network analysis revealed that the lncRNA LOC103692832 and rno_circRNA_007609 were ceRNAs of rno-miR-135a-5p targeting Atf3, Per2, and Mras. These results suggest that lncRNAs and circRNAs play important roles in the pathogenesis and development of liver injury during BDDLT.
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24
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Cao Z, Gao D, Xu T, Zhang L, Tong X, Zhang D, Wang Y, Ning W, Qi X, Ma Y, Ji K, Yu T, Li Y, Zhang Y. Circular RNA profiling in the oocyte and cumulus cells reveals that circARMC4 is essential for porcine oocyte maturation. Aging (Albany NY) 2019; 11:8015-8034. [PMID: 31562810 PMCID: PMC6781969 DOI: 10.18632/aging.102315] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 09/21/2019] [Indexed: 12/13/2022]
Abstract
Thousands of circular RNAs (circRNAs) have been recently discovered in cumulus cells and oocytes from several species. However, the expression and function of circRNA during porcine oocyte meiotic maturation have been never examined. Here, we separately identified 7,067 and 637 circRNAs in both cumulus cells and oocytes via deep sequencing and bioinformatic analysis. Further analysis revealed that a faction of circRNAs is differentially expressed (DE) in a developmental stage-specific manner. The host genes of DE circRNAs are markedly enriched to multiple signaling pathways associated with cumulus cell function and oocyte maturation. Additionally, most DE circRNAs harbor several miRNA targets, suggesting that these DE circRNAs potentially act as miRNA sponge. Importantly, we found that maternal circARMC4 knockdown by siRNA microinjection caused a severely impaired chromosome alignment, and significantly inhibited first polar body extrusion and early embryo development. Taken together, these results demonstrate for the first time that circRNAs are abundantly and dynamically expressed in a developmental stage-specific manner in cumulus cells and oocytes, and maternally expressed circARMC4 is essential for porcine oocyte meiotic maturation and early embryo development.
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Affiliation(s)
- Zubing Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Di Gao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Tengteng Xu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Ling Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xu Tong
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Dandan Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yiqing Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Wei Ning
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xin Qi
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yangyang Ma
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Kaiyuan Ji
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Tong Yu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yunsheng Li
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yunhai Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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Chen K, Xie S, Jin W. Crucial lncRNAs associated with adipocyte differentiation from human adipose-derived stem cells based on co-expression and ceRNA network analyses. PeerJ 2019; 7:e7544. [PMID: 31534842 PMCID: PMC6733242 DOI: 10.7717/peerj.7544] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/24/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Injection of adipose-derived stem cells (ASCs) is a promising treatment for facial contour deformities. However, its treatment mechanisms remain largely unknown. The study aimed to explain the molecular mechanisms of adipogenic differentiation from ASCs based on the roles of long noncoding RNAs (lncRNAs). METHODS Datasets of mRNA-lncRNA (GSE113253) and miRNA (GSE72429) expression profiling were collected from Gene Expression Omnibus database. The differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs) between undifferentiated and adipocyte differentiated human ASCs were identified using the Linear Models for Microarray Data method. DELs related co-expression and competing endogenous RNA (ceRNA) networks were constructed. Protein-protein interaction (PPI) analysis was performed to screen crucial target genes. RESULTS A total of 748 DEGs, 17 DELs and 51 DEMs were identified. A total of 13 DELs and 279 DEGs with Pearson correlation coefficients > 0.9 and p-value < 0.01 were selected to construct the co-expression network. A total of 151 interaction pairs among 112 nodes (10 DEMs; eight DELs; 94 DEGs) were obtained to construct the ceRNA network. By comparing the lncRNAs and mRNAs in two networks, five lncRNAs (SNHG9, LINC02202, UBAC2-AS1, PTCSC3 and myocardial infarction associated transcript (MIAT)) and 32 genes (i.e., such as phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), protein tyrosine phosphatase receptor type B (PTPRB)) were found to be shared. PPI analysis demonstrated PIK3R1 , forkhead box O1 (FOXO1; a transcription factor) and estrogen receptor 1 (ESR1) were hub genes, which could be regulated by the miRNAs that interacted with the above five lncRNAs, such as LINC02202-miR-136-5p-PIK3R1, LINC02202-miR-381-3p-FOXO1 and MIAT-miR-18a-5p-ESR1. LINC02202 also could directly co-express with PIK3R1. Furthermore, PTPRB was predicted to be modulated by co-expression with LINC01119. CONCLUSION MIAT, LINC02202 and LINC01119 may be potentially important, new lncRNAs associated with adipogenic differentiation of ASCs. They may be involved in adipogenesis by acting as a ceRNA or co-expressing with their targets.
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Affiliation(s)
- Kana Chen
- Department of Plastic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Shujie Xie
- Department of Hepatobiliary Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Wujun Jin
- Department of Plastic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
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Fallah H, Azari I, Neishabouri SM, Oskooei VK, Taheri M, Ghafouri-Fard S. Sex-specific up-regulation of lncRNAs in peripheral blood of patients with schizophrenia. Sci Rep 2019; 9:12737. [PMID: 31484957 PMCID: PMC6726592 DOI: 10.1038/s41598-019-49265-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023] Open
Abstract
Schizophrenia as a common disabling psychiatric disorder has been associated with dysregulation of several genes and pathways among them are those being regulated by long non-coding RNAs (lncRNAs). Based on the acknowledged roles of lncRNAs in neurodevelopment, in the current study, we assessed expression of six lncRNAs namely HOXA-AS2, Linc-ROR, MALAT1, MEG3, SPRY4-IT1 and UCA1 in peripheral blood of 60 patients with schizophrenia and 60 healthy subjects. HOXA-AS2, Linc-ROR, MEG3, SPRY4-IT1 and UCA1 levels were significantly higher in total patients compared with total controls. However, when evaluating expression of genes in sex-based subgroups, the differences in the expression of these lncRNAs were significant only among females. Assessment of partial correlation between expression of lncRNAs and age of study participants after controlling the effect of sex, revealed significant correlations for HOXA-AS2, MALAT1 and UCA1 in both patients and controls. Besides, expressions of Linc-ROR and SPRY4-IT1 were correlated with age only in patients. Significant pairwise correlations were recognized between expression levels of lncRNAs in both patients with schizophrenia and controls. Based on the area under curve (AUC) values, SPRY4-IT1 had the best performance in differentiation of female patients with schizophrenia from female controls (AUC = 0.85, P < 0.0001). Combination of Linc-ROR, MEG3, SPRY4-IT1 and UCA1 expression levels could differentiate female patients with 95.2% sensitivity, 76.9% specificity and diagnostic power of 0.88 (P < 0.0001). The current study suggests the presence of a sex-based dysregulation of lncRNAs in patients with schizophrenia and their possible application as diagnostic biomarkers.
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Affiliation(s)
- Hamid Fallah
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Iman Azari
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Vahid Kholghi Oskooei
- Department of Laboratory Sciences, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Neuroscience Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Molecular programs underlying differences in the expression of mood disorders in males and females. Brain Res 2019; 1719:89-103. [DOI: 10.1016/j.brainres.2019.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 04/20/2019] [Accepted: 05/13/2019] [Indexed: 01/13/2023]
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Zhang Z, Tang J, He X, Zhu M, Gan S, Guo X, Zhang X, Zhang J, Hu W, Chu M. Comparative Transcriptomics Identify Key Hypothalamic Circular RNAs that Participate in Sheep ( Ovis aries) Reproduction. Animals (Basel) 2019; 9:ani9080557. [PMID: 31416269 PMCID: PMC6721059 DOI: 10.3390/ani9080557] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The hypothalamus plays crucial roles in sheep reproduction. However, the expression profiles of sheep hypothalamic circular RNA (circRNA), which has been proved to exert important functions in many physiological processes, remain largely unknown. In this study, we used RNA sequencing to explore the expression of circRNAs in the hypothalamus of sheep with the FecB ++ genotype. The results suggested that several key hypothalamic circRNAs may participate in sheep reproduction by influencing gonadotropin-releasing hormone (GnRH) activities or affecting key gene expression indirectly or directly. This study provides a further reference for understanding the differences of sheep fecundity. Abstract Circular RNA (circRNA), as an emerging class of noncoding RNA, has been found to play key roles in many biological processes. However, its expression profile in the hypothalamus, a powerful organ initiating the reproductive process, has not yet been explored. Therefore, we used RNA sequencing to explore the expression of circRNAs in the hypothalamus of sheep with the FecB ++ genotype. We totally identified 41,863 circRNAs from sheep hypothalamus, in which 333 (162 were upregulated, while 171 were downregulated) were differentially expressed in polytocous sheep in the follicular phase versus monotocous sheep in the follicular phase (PF vs. MF), moreover, 340 circRNAs (163 were upregulated, while 177 were downregulated) were differentially expressed in polytocous sheep in the luteal phase versus monotocous sheep in the luteal sheep (PL vs. ML). We also identified several key circRNAs including oar_circ_0018794, oar_circ_0008291, oar_circ_0015119, oar_circ_0012801, oar_circ_0010234, and oar_circ_0013788 through functional enrichment analysis and oar_circ_0012110 through a competing endogenous RNA network, most of which may participate in reproduction by influencing gonadotropin-releasing hormone (GnRH) activities or affecting key gene expression, indirectly or directly. Our study explored the overall expression profile of circRNAs in sheep hypothalamus, which potentially provides an alternative insight into the mechanism of sheep prolificacy without the effects of FecB mutation.
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Affiliation(s)
- Zhuangbiao Zhang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jishun Tang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mingxia Zhu
- Agricultural College, Liaocheng University, Liaocheng 252059, China
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Xiaofei Guo
- Tianjin Institute of Animal Sciences, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Xiaosheng Zhang
- Tianjin Institute of Animal Sciences, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Wenping Hu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Zhou F, Chen W, Jiang Y, He Z. Regulation of long non-coding RNAs and circular RNAs in spermatogonial stem cells. Reproduction 2019; 158:R15-R25. [DOI: 10.1530/rep-18-0517] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 04/02/2019] [Indexed: 12/18/2022]
Abstract
Spermatogonial stem cells (SSCs) are one of the most significant stem cells with the potentials of self-renewal, differentiation, transdifferentiation and dedifferentiation, and thus, they have important applications in reproductive and regenerative medicine. They can transmit the genetic and epigenetic information across generations, which highlights the importance of the correct establishment and maintenance of epigenetic marks. Accurate transcriptional and post-transcriptional regulation is required to support the highly coordinated expression of specific genes for each step of spermatogenesis. Increasing evidence indicates that non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), play essential roles in controlling gene expression and fate determination of male germ cells. These ncRNA molecules have distinct characteristics and biological functions, and they independently or cooperatively modulate the proliferation, apoptosis and differentiation of SSCs. In this review, we summarized the features, biological function and fate of mouse and human SSCs, and we compared the characteristics of lncRNAs and circRNAs. We also addressed the roles and mechanisms of lncRNAs and circRNAs in regulating mouse and human SSCs, which would add novel insights into the epigenetic mechanisms underlying mammalian spermatogenesis and provide new approaches to treat male infertility.
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Li X, Hu X, Tian GG, Cheng P, Li Z, Zhu M, Zhou H, Wu J. C89 Induces Autophagy of Female Germline Stem Cells via Inhibition of the PI3K-Akt Pathway In Vitro. Cells 2019; 8:cells8060606. [PMID: 31216656 PMCID: PMC6627605 DOI: 10.3390/cells8060606] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/22/2019] [Accepted: 06/13/2019] [Indexed: 12/17/2022] Open
Abstract
Postnatal female germline stem cells (FGSCs) are a type of germline stem cell with self-renewal ability and the capacity of differentiation toward oocyte. The proliferation, differentiation, and apoptosis of FGSCs have been researched in recent years, but autophagy in FGSCs has not been explored. This study investigated the effects of the small-molecule compound 89 (C89) on FGSCs and the underlying molecular mechanism in vitro. Cytometry, Cell Counting Kit-8 (CCK8), and 5-ethynyl-2'-deoxyuridine (EdU) assay showed that the number, viability, and proliferation of FGSCs were significantly reduced in C89-treated groups (0.5, 1, and 2 µM) compared with controls. C89 had no impact on FGSC apoptosis or differentiation. However, C89 treatment induced the expression of light chain 3 beta II (LC3BII) and reduced the expression of sequestosome-1 (SQSTM1) in FGSCs, indicating that C89 induced FGSC autophagy. To investigate the mechanism of C89-induced FGSC autophagy, RNA-seq technology was used to compare the transcriptome differences between C89-treated FGSCs and controls. Bioinformatics analysis of the sequencing data indicated a potential involvement of the phosphatidylinositol 3 kinase and kinase Akt (PI3K-Akt) pathway in the effects of C89's induction of autophagy in FGSCs. Western blot confirmed that levels of p-PI3K and p-Akt were significantly reduced in the C89- or LY294002 (PI3K inhibitor)-treated groups compared with controls. Moreover, we found cooperative functions of C89 and LY294002 in inducing FGSC autophagy through suppressing the PI3K-Akt pathway. Taken together, this research demonstrates that C89 can reduce the number, viability, and proliferation of FGSCs by inducing autophagy. Furthermore, C89 induced FGSC autophagy by inhibiting the activity of PI3K and Akt. The PI3K-Akt pathway may be a target to regulate FGSC proliferation and death.
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Affiliation(s)
- Xinyue Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Xiaopeng Hu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Geng G Tian
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ping Cheng
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China.
| | - Zezhong Li
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Mingyan Zhu
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Huchen Zhou
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China.
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Jiang L, Hong L, Yang W, Zhao Y, Tan A, Li Y. Co-expression network analysis of the lncRNAs and mRNAs associated with cervical cancer progression. Arch Med Sci 2019; 15:754-764. [PMID: 31110543 PMCID: PMC6524193 DOI: 10.5114/aoms.2019.84740] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/07/2018] [Indexed: 01/16/2023] Open
Abstract
INTRODUCTION Cervical cancer is the second most common type of cancer and the third leading cause of cancer deaths in females in developing countries. Recent studies showed that long non-coding RNAs play a key role in human cancers. However, the molecular mechanisms underlying the initiation and progression of cervical cancer remained to be further explored. MATERIAL AND METHODS In this study, we explored the differential expression of lncRNAs and mRNAs in cervical cancer progression by analyzing the public dataset GSE63514. Next, PPI and co-expression networks were constructed to reveal the potential roles of cervical cancer related mRNAs and lncRNAs. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed to explore functions of differentially expressed genes (DEGs) in cervical cancer. RESULTS In the present study, we observed that 3021 mRNAs were up-regulated and 1605 mRNAs were down-regulated in cervical cancer progression. Meanwhile, we for the first time found that 172 lncRNAs were up-regulated and 106 lncRNAs were down-regulated in cervical cancer progression. Co-expression network analysis showed that lncRNAs were widely co-expressed with cell cycle related genes in cervical cancer, implicating the important roles of these lncRNAs in cell proliferation regulation. Of note, we identified two hub lncRNA-mRNA networks involved in regulating various biological processes in cervical cancer progression. CONCLUSIONS Our results identified key mRNAs and lncRNAs in cervical cancer progression. This study will provide novel insights to explore the potential mechanisms underlying cervical cancer progression.
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Affiliation(s)
- Li Jiang
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Li Hong
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenwu Yang
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuzi Zhao
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Aili Tan
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yang Li
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, China
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Ma B, Lee TL, Hu B, Li J, Li X, Zhao X, Hou C, Zhang C, He L, Huang X, Chen X, Li J, Wu J. Molecular characteristics of early-stage female germ cells revealed by RNA sequencing of low-input cells and analysis of genome-wide DNA methylation. DNA Res 2019; 26:105-117. [PMID: 30590473 PMCID: PMC6476728 DOI: 10.1093/dnares/dsy042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/14/2018] [Indexed: 01/08/2023] Open
Abstract
High-throughput stage-specific transcriptomics provides an unbiased approach for understanding the process of cell development. Here, we report transcriptome analysis of primordial germ cell, female germline stem cell (FGSC), germinal vesicle and mature oocyte by performing RNA sequencing of freshly isolated cells in mice. As expected, these stages and gene-expression profiles are consistent with developmental timing. Analysis of genome-wide DNA methylation during female germline development was used for confirmation. By pathway analysis and blocking experiments, we demonstrate PI3K-AKT pathway is critical for FGSC maintenance. We also identify functional modules with hub genes and lncRNAs, which represent candidates for regulating FGSC self-renewal and differentiation. Remarkably, we note alternative splicing patterns change dramatically during female germline development, with the highest occurring in FGSCs. These findings are invaluable resource for dissecting the molecular pathways and processes into oogenesis and will be wider applications for other types of stem cell research.
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Affiliation(s)
- Binbin Ma
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Tin-Lap Lee
- Reproduction, Development and Endocrinology Program, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Bian Hu
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyong Li
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaodong Zhao
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Changliang Hou
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Zhang
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Lin He
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Xingxu Huang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, Nanjing, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Xuejin Chen
- Department of Laboratory Animal Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China
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Li X, Tian GG, Zhao Y, Wu J. Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells. Sci Data 2019; 6:8. [PMID: 30918261 PMCID: PMC6437644 DOI: 10.1038/s41597-019-0014-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/11/2019] [Indexed: 12/22/2022] Open
Abstract
Germline stem cells are germ cells at an early developmental stage, so their development is key to ensuring human reproduction. There is increasing evidence that long noncoding RNA (lncRNA) and circular RNA (circRNA) play important roles in the development of germ cells. This data descriptor provides unique lncRNA and circRNA transcriptomic information for mouse germline stem cells. Using the Illumina HiSeqx 2000 system, a total of 511,836,732 raw reads were generated. High-quality transcripts, lncRNAs, and circRNAs were identificated and quantified using the reads, and more precise annotations of lncRNAs (especially 9357 novel lncRNAs) and circRNAs were performed in the germline stem cells. We then analyzed the transcript structures, genetic variants, and the interaction between circRNA and microRNA to provide the basis for subsequent functional experiments. This comprehensive dataset will help advance data sharing and deepen our understanding of mouse germline stem cells, providing a theoretical foundation for research on germ cell development and human reproduction, among others.
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Affiliation(s)
- Xiaoyong Li
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Geng G Tian
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yongqiang Zhao
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ji Wu
- Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China.
- Shanghai Key Laboratory of Reproductive Medicine, Shanghai, 200025, China.
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Liu KS, Pan F, Mao XD, Liu C, Chen YJ. Biological functions of circular RNAs and their roles in occurrence of reproduction and gynecological diseases. Am J Transl Res 2019; 11:1-15. [PMID: 30787966 PMCID: PMC6357300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/23/2018] [Indexed: 06/09/2023]
Abstract
Circular RNAs (circRNAs) are a large class of non coding endogenous RNAs in eukaryotic that are formed through 3'-5' ligation of a single RNA molecule. According to the different sources of the sequences, circRNA can be divided into three types: exon circRNA (ecRNA), intron circRNA (ciRNA), and exon-intron circRNA. Accumulating studies have shown that circRNAs are abundant, diverse, stable, and cell or tissue specific expression, etc. CircRNA plays a regulating role in gene expression, and an essential role in the process of biological development, such as miRNA sponges, endogenous RNAs and biomarkers, as well as critical role in the diagnosis of diseases. Studies have verified the interplay between circRNAs and the development of embryos, sperms, ovarian epithelial tumors, endometrial cancer and preeclampsia, suggesting the potential of circRNAs to become biomarkers or therapeutical targets for human diseases. In this paper, we reviewed the researches on circRNAs' characteristics, databases of circRNA, high-throughput sequencing of circRNA, and effect on reproductive and gynecological diseases.
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Affiliation(s)
- Kang-Sheng Liu
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Feng Pan
- Department of Andrology and Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Xiao-Dong Mao
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Chao Liu
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Ya-Jun Chen
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
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Zhang X, Shi J, Sun Y, Zhu Y, Zhang Z, Wang Y. Transcriptome analysis provides insights into differentially expressed genes and long noncoding RNAs involved in sex‐related differences in Amur sturgeon (
Acipenser schrenckii
). Mol Reprod Dev 2018; 86:132-144. [DOI: 10.1002/mrd.23065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/05/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Xin Zhang
- Department of Aquaculture, College of Animal Science, Fujian Agriculture and Forestry UniversityFuzhou China
| | - Jialong Shi
- Department of Aquaculture, College of Animal Science, Fujian Agriculture and Forestry UniversityFuzhou China
| | - Yulong Sun
- Department of Aquaculture, College of Animal Science, Fujian Agriculture and Forestry UniversityFuzhou China
| | - Youfang Zhu
- Department of Aquaculture, Putian Municipal Institute of Fisheries ResearchPutian China
| | - Ziping Zhang
- Department of Aquaculture, College of Animal Science, Fujian Agriculture and Forestry UniversityFuzhou China
| | - Yilei Wang
- Department of Aquaculture, Fisheries College, Jimei UniversityXiamen China
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García-López S, Albo-Castellanos C, Urdinguio RG, Cañón S, Sánchez-Cabo F, Martínez-Serrano A, Fraga MF, Bernad A. Deregulation of the imprinted DLK1-DIO3 locus ncRNAs is associated with replicative senescence of human adipose-derived stem cells. PLoS One 2018; 13:e0206534. [PMID: 30395586 PMCID: PMC6218046 DOI: 10.1371/journal.pone.0206534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/15/2018] [Indexed: 12/24/2022] Open
Abstract
Background Human adult adipose-derived stem cells (hADSCs) have become the most promising cell source for regenerative medicine. However the prolonged ex vivo expansion periods required to obtain the necessary therapeutic dose promotes progressive senescence, with the concomitant reduction of their therapeutic potential. Aim and scope A better understanding of the determinants of hADSC senescence is needed to improve biosafety while preserving therapeutic efficiency. Here, we investigated the association between deregulation of the imprinted DLK1-DIO3 region and replicative senescence in hADSC cultures. Methods We compared hADSC cultures at short (PS) and prolonged (PL) passages, both in standard and low [O2] (21 and 3%, respectively), in relation to replicative senescence. hADSCs were evaluated for expression alterations in the DLK1-DIO3 region on chromosome 14q32, and particularly in its main miRNA cluster. Results Comparison of hADSCs cultured at PL or PS surprisingly showed a quite significant fraction (69%) of upregulated miRNAs in PL cultures mapping to the imprinted 14q32 locus, the largest miRNA cluster described in the genome. In agreement, expression of the lncRNA MEG3 (Maternally Expressed 3; Meg3/Gtl2), cultured at 21 and 3% [O2], was also significantly higher in PL than in PS passages. During hADSC replicative senescence the AcK16H4 activating mark was found to be significantly associated with the deregulation of the entire DLK1-DIO3 locus, with a secondary regulatory role for the methylation of DMR regions. Conclusion A direct relationship between DLK1-DIO3 deregulation and replicative senescence of hADSCs is reported, involving upregulation of a very significant fraction of its largest miRNA cluster (14q32.31), paralleled by the progressive overexpression of the lncRNA MEG3, which plays a central role in the regulation of Dlk1/Dio3 activation status in mice.
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Affiliation(s)
- Silvia García-López
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Carmen Albo-Castellanos
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Rocio G. Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Hospital Universitaria Central de Asturias (HUCA) and Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo (UO), Asturias, Spain
| | - Susana Cañón
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Alberto Martínez-Serrano
- Molecular Biology Department (UAM) and Molecular Neuropathology Department, Center of Molecular Biology Severo Ochoa-CSIC, Universidad Autónoma de Madrid, Campus Cantoblanco, Madrid, Spain
| | - Mario F. Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Hospital Universitaria Central de Asturias (HUCA) and Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo (UO), Asturias, Spain
| | - Antonio Bernad
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
- * E-mail:
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Zou K, Wang J, Bi H, Zhang Y, Tian X, Tian N, Ma W, Wu J. Comparison of different in vitro differentiation conditions for murine female germline stem cells. Cell Prolif 2018; 52:e12530. [PMID: 30334302 PMCID: PMC6430485 DOI: 10.1111/cpr.12530] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/20/2018] [Accepted: 08/24/2018] [Indexed: 12/26/2022] Open
Abstract
Objectives In vitro differentiation of oocytes from female germline stem cells (FGSCs) has exciting potential applications for reproductive medicine. Some researchers have attempted to reveal the in vitro differentiation capacity of FGSCs. However, no systematic comparative study of in vitro differentiation conditions has been performed for murine FGSCs (mFGSCs). Materials and Methods mFGSCs line was cultured under five different conditions for in vitro differentiation. RT‐PCR was performed to detect the expression of Oct4, Fragilis, Blimp1, Mvh, Scp3 and Zp3. Immunofluorescence was carried out to test the expression of Mvh, Fragilis and Zp3. Two‐photon laser‐scanning microscope was used to analyze nucleus‐plasma ratio, and the proportion of chromatin of GV oocytes differentiated from mFGSCs in vitro (IVD‐GVO), GV oocytes from in vivo (GVO) and mFGSCs. Results RT‐PCR and immunofluorescence showed that mFGSC line expressed germ cell‐specific markers, but not a meiosis‐specific marker. By evaluating five different in vitro differentiation conditions, condition 5, which included a hanging drop procedure and co‐culture of mFGSCs with granulosa cells, was shown to be optimal. mFGSCs could be successfully differentiated into germinal vesicle (GV) ‐stage oocytes under this condition. 3D observation revealed that both the nucleus‐plasma ratio and proportion of chromatin were not significantly different between IVD‐GVO and GVO. Conclusion We evaluated five in vitro differentiation conditions for mFGSCs and successfully differentiate mFGSCs into GV‐stage oocytes using a three‐step differentiation process.
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Affiliation(s)
- Kang Zou
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Wang
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Haiwei Bi
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Yabin Zhang
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Xueli Tian
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing, China
| | - Ning Tian
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing, China
| | - Wanyun Ma
- State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing, China
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Bie B, Wang Y, Li L, Fang H, Liu L, Sun J. Noncoding RNAs: Potential players in the self-renewal of mammalian spermatogonial stem cells. Mol Reprod Dev 2018; 85:720-728. [PMID: 29969526 DOI: 10.1002/mrd.23041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/30/2018] [Indexed: 12/11/2022]
Abstract
Spermatogonial stem cells (SSCs), a unique population of male germ cells with self-renewal ability, are the foundation for maintenance of spermatogenesis throughout the life of the male. Although many regulatory molecules essential for SSC self-renewal have been identified, the fundamental mechanism underlying how SSCs acquire and maintain their self-renewal activity remains largely to be elucidated. In recent years, many types of noncoding RNAs (ncRNAs) have been suggested to regulate the SSC self-renewal through multiple ways, indicating ncRNAs play crucial roles in SSC self-renewal. In this paper, we mainly focus on four types of ncRNAs including microRNA, long ncRNA, piwi-interacting RNA, as well as circular RNAs, and reviewed their potential roles in SSC self-renewal that discovered recently to help us gain a better understanding of molecular mechanisms by which ncRNAs perform their function in regulating SSC self-renewal.
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Affiliation(s)
- Beibei Bie
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Ya Wang
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Liang Li
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Huanle Fang
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Libing Liu
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Jin Sun
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
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39
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Analysis of the Coding and Non-Coding RNA Transcriptomes in Response to Bell Pepper Chilling. Int J Mol Sci 2018; 19:ijms19072001. [PMID: 29987249 PMCID: PMC6073856 DOI: 10.3390/ijms19072001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/25/2018] [Accepted: 06/27/2018] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence suggests that long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have roles during biotic and abiotic stress, though their exact contributions remain unclear. To explore their biological functions in response to chilling in bell pepper, we examined their accumulation profiles by deep sequencing and identified 380 lncRNAs, 36 circRNAs, 18 miRNAs, and 4128 differentially expressed mRNAs in the chilled versus the non-chilled fruit. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed differentially expressed genes and putative ncRNA targets, including transcription factors of multiple classes, such as myeloblastosis (MYB), basic helix-loop-helix (bHLH), and ethylene response factor (ERF) transcription factors (TFs), enzymes involved in bio-oxidation and oxidative phosphorylation (serine/threonine-protein kinase, polyphenol oxidase, catalase, peroxidase, lipoxygenase, and ATPase), and cell wall metabolism-related enzymes (beta-galactosidase, pectate lyase, pectinesterase, and polygalacturonase). On the basis of the accumulation profiles, a network of putatively interacting RNAs associated with bell pepper chilling was developed, which pointed to ncRNAs that could provide the foundation for further developing a more refined understanding of the molecular response to chilling injury.
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Lecluze E, Jégou B, Rolland AD, Chalmel F. New transcriptomic tools to understand testis development and functions. Mol Cell Endocrinol 2018; 468:47-59. [PMID: 29501799 DOI: 10.1016/j.mce.2018.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 12/16/2022]
Abstract
The testis plays a central role in the male reproductive system - secreting several hormones including male steroids and producing male gametes. A complex and coordinated molecular program is required for the proper differentiation of testicular cell types and maintenance of their functions in adulthood. The testicular transcriptome displays the highest levels of complexity and specificity across all tissues in a wide range of species. Many studies have used high-throughput sequencing technologies to define the molecular dynamics and regulatory networks in the testis as well as to identify novel genes or gene isoforms expressed in this organ. This review intends to highlight the complementarity of these transcriptomic studies and to show how the use of different sequencing protocols contribute to improve our global understanding of testicular biology.
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Affiliation(s)
- Estelle Lecluze
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France.
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Genome-wide analysis of circular RNAs in bovine cumulus cells treated with BMP15 and GDF9. Sci Rep 2018; 8:7944. [PMID: 29786687 PMCID: PMC5962577 DOI: 10.1038/s41598-018-26157-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/08/2018] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) are important members of the non-coding RNA family, and those relating to animal physiologies have been widely studied in recent years. This study aimed to explore the roles of circRNAs in the regulation of follicular development. We constructed four bovine cumulus cell cDNA libraries, including a negative control group (NC) and groups treated with BMP15, GDF9 and BMP15 + GDF9, and we sequenced the libraries on the Illumina HiSeq Xten platform. We identified 1706 circRNAs and screened for differential circRNA expression. We conducted a bioinformatics analysis of these circRNAs and screened for differential circRNAs. Functional annotation and enrichment analysis of the host genes showed that the differential circRNAs were related to locomotion, reproduction, biological adhesion, growth, rhythmic processes, biological phases and hormone secretion. According to the differential expression of circRNA between groups, there were 3 up-regulated and 6 down-regulated circRNAs in the BMP15 group as well as 12 up-regulated and 24 down-regulated circRNAs in the GDF9 group. Co-addition of both BMP15 and GDF9 resulted in 15 up-regulated and 13 down-regulated circRNAs. circ_n/a_75,circ_12691_1 and circ_n/a_303 were altered in both the BMP15 and GDF9 groups as well as in the BMP15 + GDF9 combination group. We focused on these three circRNAs because they were potentially associated with the additive effect of BMP15 and GDF9. Quantitative PCR analysis showed that the expression levels of these three circRNAs were consistent with the sequencing results. In addition, the target miRNAs of circ_n/a_75 and circ_n/a_303, miR-339a, miR-2400 and miR-30c, were down-regulated in the experimental group, which was in contrast to the circRNAs trend. These findings demonstrated that BMP15 and GDF9 may regulate the target gene through circRNA, as a miRNA sponge, in order to regulate the status of bovine cumulus cells and affect follicular development.
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Zhang X, Yang Y, Xia Q, Song H, Wei R, Wang J, Zou K. Cadherin 22 participates in the self-renewal of mouse female germ line stem cells via interaction with JAK2 and β-catenin. Cell Mol Life Sci 2018; 75:1241-1253. [PMID: 29063123 PMCID: PMC11105442 DOI: 10.1007/s00018-017-2689-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/12/2017] [Accepted: 10/18/2017] [Indexed: 02/03/2023]
Abstract
The self-renewal capacity of the stem cell pool determines tissue function and health. Cadherin-22 (Cdh22), a member of the cadherin superfamily, has two splicing patterns in rats, and the short type that lacks a catenin binding domain is closely related to spermatogonial stem cell self-renewal. Previously, we reported that CDH22 was highly expressed in mouse ovary germ cells, especially in female germ line stem cells (FGSCs). However, its underlying function in FGSCs is still not clear. Here, we found that Cdh22 encodes only one type of protein product in mice and demonstrated that CDH22 was required for FGSC self-renewal. In addition, JAK2 and β-catenin were found to interact with CDH22 and be involved in CDH22 signaling in mouse FGSCs. Moreover, extrinsic CDH22 was identified as a potential molecule that participates in FGSC adhesion and is pivotal for FGSC maintenance and self-renewal. These results reveal that CDH22 functions as an essential molecule in FGSC maintenance and self-renewal via different mechanisms, including interaction with the JAK-STAT signaling pathway and β-catenin.
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Affiliation(s)
- Xiaoyu Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qin Xia
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongfei Song
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rui Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jingjing Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kang Zou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Long noncoding RNA growth arrest-specific 5 promotes proliferation and survival of female germline stem cells in vitro. Gene 2018; 653:14-21. [PMID: 29428796 DOI: 10.1016/j.gene.2018.02.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/28/2018] [Accepted: 02/07/2018] [Indexed: 11/23/2022]
Abstract
Female germline stem cells (FGSCs) are proposed to be a key factor for ameliorating female infertility. Previously we have shown that neonatal and adult FGSCs could be isolated and purified from mouse ovarian tissues. The long noncoding (lnc) RNA growth arrest-specific 5 sequence (GAS5) transcribed from mammalian genomes plays important regulatory roles in various developmental processes. However, there is no study on the relationship between GAS5 and FGSC development in vitro. In this study, we showed that GAS5 was highly expressed in the neonatal mouse ovary and was located in both FGSCs and oocytes. GAS5 facilitated FGSC proliferation and promoted their survival in vitro. Moreover, GAS5 also inhibited apoptosis of cultured FGSCs. These findings indicate that GAS5 is a crucial regulator of FGSC development. This might serve as a foundation for a strategy of lncRNA-directed diagnosis or treatment of female infertility.
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Pan T, Sun X, Liu Y, Li H, Deng G, Lin H, Wang S. Heat stress alters genome-wide profiles of circular RNAs in Arabidopsis. PLANT MOLECULAR BIOLOGY 2018; 96:217-229. [PMID: 29177640 DOI: 10.1007/s11103-017-0684-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/18/2017] [Indexed: 05/19/2023]
Abstract
1599 novel circRNAs and 1583 heat stress-specific circRNAs were identified in Arabidopsis. Heat stress enhanced accumulation of circRNAs remarkably. Heat stress altered the sizes of circRNAs, numbers of circularized exons and alterative circularization events. A putative circRNA-mediated ceRNA networks under heat stress was established. Heat stress retards plant growth and destabilizes crop yield. The noncoding RNAs were demonstrated to be involved in plant response to heat stress. As a newly-characterized class of noncoding RNAs, circular RNAs (circRNAs) play important roles in transcriptional and post-transcriptional regulation. A few recent investigations indicated that plant circRNAs were differentially expressed under abiotic stress. However, little is known about how heat stress mediates biogenesis of circRNAs in plants. Here, we uncovered 1599 previously-unknown circRNAs and 1583 heat-specific circRNAs, by RNA-sequencing and bioinformatic analysis. Our results indicated that much more circRNAs were expressed under heat stress than in control condition. Besides, heat stress also increased the length of circRNAs, the quantity of circularized exons, and alternative circularization events. Moreover, we observed a positive correlation between expression patterns of some circRNAs and their parental genes. The prediction of ceRNA (competing endogenous RNA) networks indicated that differentially-expressed circRNAs could influence expression of many important genes, that participate in response to heat stress, hydrogen peroxide, and phytohormone signaling pathways, by interacting with the corresponding microRNAs. Together, our observations indicated that heat stress had great impacts on the biogenesis of circRNAs. Heat-induced circRNAs might participate in plant response to heat stress through the circRNA-mediated ceRNA networks.
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Affiliation(s)
- Ting Pan
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Ministry of Education, Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiuqiang Sun
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangxuan Liu
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Li
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Guangbin Deng
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Honghui Lin
- Ministry of Education, Key Laboratory for Bio-Resource and Eco-Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
| | - Songhu Wang
- CAS Center for Excellence in Molecular Plant Sciences, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhu X, Tian GG, Yu B, Yang Y, Wu J. Effects of bisphenol A on ovarian follicular development and female germline stem cells. Arch Toxicol 2018; 92:1581-1591. [PMID: 29380011 DOI: 10.1007/s00204-018-2167-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/25/2018] [Indexed: 01/07/2023]
Abstract
Bisphenol A (BPA), one of the most frequently detected emerging pollutants in the environment, has been implicated in adverse effects in male and female reproduction at extremely low concentrations. This study aimed to investigate the effects and potential mechanism of BPA on mouse ovarian follicular development and female germline stem cells (FGSCs). Female CD-1 adult mice were administered gradient concentrations of BPA (12.5, 25, and 50 mg/kg/day) by intraperitoneal injection. We found that the number of atretic ovarian follicles was significantly increased at high BPA concentrations. Additionally, the numbers of primordial follicles, primary follicles, and corpus luteum (CL) were significantly reduced at high BPA concentrations. Interestingly, the number of FGSCs was remarkably reduced in BPA-treated ovaries. Furthermore, the increased apoptotic rate of FGSCs in vitro was triggered by BPA accompanied by increased BPA concentrations. To investigate the mechanism of BPA in ovarian follicular development, 193 differentially expressed proteins were identified in BPA-treated ovaries by the isobaric tags for relative and absolute quantification-coupled 2D liquid chromatography-mass spectrometry technique. A total of 106 proteins were downregulated and 85 proteins were upregulated. Among these proteins, the apoptosis-related protein SAFB-like transcriptional modulator (SLTM) was remarkably upregulated, and this result was consistent with western blotting. Taken together, our results suggest that an ovarian follicular development, especially, the development of primordial follicles, primary follicles, and the CL, is inhibited by high BPA concentrations, and the ovarian follicle atresia is initiated by BPA through upregulated expression of SLTM. Furthermore, BPA induces apoptosis of cultured FGSCs. The effect of BPA on ovarian follicular development and FGSCs, especially the effect on FGSCs, suggests a novel mechanism of how BPA causes female infertility.
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Affiliation(s)
- Xiaoqin Zhu
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Geng G Tian
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Baoli Yu
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yanzhou Yang
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China
| | - Ji Wu
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, No. 800. Dongchuan Road, Minhang District, Shanghai, 200240, China. .,Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China.
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Hou L, Wang J, Wang Y, Hua X, Wu J. Compared proteomic analysis of 8- and 32-week-old postnatal porcine ovaries. Cell Biochem Funct 2017; 36:34-42. [PMID: 29282749 DOI: 10.1002/cbf.3315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/24/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022]
Abstract
Pigs share many anatomical and physiological features with humans, offering a unique and viable model for biomedical research. Tandem mass tag method followed by mass spectrometry analysis was utilized to identify peptides (47,405), proteins (14,701), and protein groups (7634) in ovaries of 8- and 32-week-old postnatal Banna miniature pigs. After annotation and analysis by Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology, the proteins were identified as being involved in hormone metabolic pathways and maintenance, proliferation, and regulation of stem cells. In addition, we found 638 differentially expressed proteins between ovaries of 8- and 32-week-old postnatal Banna miniature pigs. We used Interactive Pathway Explorer to produce an overview of pig ovarian proteomics. Compared with those of the 8-week-old group, the proteins enriched in metabolism of steroid hormones, metabolism of lipids, and energy metabolism pathway were upregulated in the 32-week-old group, indicating physiological characteristics of sexual maturity. These findings have implications in applications of biomedicine. SIGNIFICANCE OF THE STUDY Pigs share many anatomical and physiological features with humans, offering a unique and viable model for biomedical research. In this study, we used tandem mass tag quantitative proteomics to describe, for the first time, protein expression patterns of postnatal pig ovaries. Proteins involved in hormone metabolic pathways and maintenance, proliferation, and regulation of stem cells were identified. With further analysis by Interactive Pathway Explorer, proteins enriched in metabolism of steroid hormones, metabolism of lipids, and energy metabolism pathway were upregulated in the 32-week-old group, indicating physiological characteristics of sexual maturity. These findings have implications in applications of biomedicine.
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Affiliation(s)
- Lin Hou
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), School of Medicine, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Wang
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), School of Medicine, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Yinjuan Wang
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), School of Medicine, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuguo Hua
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), School of Medicine, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, China.,Shanghai Key Laboratory of Reproductive Medicine, Shanghai, China
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Gu X, Li M, Jin Y, Liu D, Wei F. Identification and integrated analysis of differentially expressed lncRNAs and circRNAs reveal the potential ceRNA networks during PDLSC osteogenic differentiation. BMC Genet 2017; 18:100. [PMID: 29197342 PMCID: PMC5712120 DOI: 10.1186/s12863-017-0569-4] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 11/16/2017] [Indexed: 02/06/2023] Open
Abstract
Background Researchers have been exploring the molecular mechanisms underlying the control of periodontal ligament stem cell (PDLSC) osteogenic differentiation. Recently, long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) were shown to function as competitive endogenous RNAs (ceRNAs) to regulate the effect of microRNAs (miRNAs) on their target genes during cell differentiation. However, comprehensive identification and integrated analysis of lncRNAs and circRNAs acting as ceRNAs during PDLSC osteogenic differentiation have not been performed. Results PDLSCs were derived from healthy human periodontal ligament and cultured separately with osteogenic induction and normal media for 7 days. Cultured PDLSCs were positive for STRO-1 and CD146 and negative for CD31 and CD45. Osteo-induced PDLSCs showed increased ALP (alkaline phosphatase) activity and up-regulated expression levels of the osteogenesis-related markers ALP, Runt-related transcription factor 2 and osteocalcin. Then, a total of 960 lncRNAs and 1456 circRNAs were found to be differentially expressed by RNA sequencing. The expression profiles of eight lncRNAs and eight circRNAs were measured with quantitative real-time polymerase chain reaction and were shown to agree with the RNA-seq results. Furthermore, the potential functions of lncRNAs and circRNAs as ceRNAs were predicted based on miRanda and were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. In total, 147 lncRNAs and 1382 circRNAs were predicted to combine with 148 common miRNAs and compete for miRNA binding sites with 744 messenger RNAs. These mRNAs were predicted to significantly participate in osteoblast differentiation, the MAPK pathway, the Wnt pathway and the signaling pathways regulating pluripotency of stem cells. Among them, lncRNAs coded as TCONS_00212979 and TCONS_00212984, as well as circRNA BANP and circRNA ITCH, might interact with miRNA34a and miRNA146a to regulate PDLSC osteogenic differentiation via the MAPK pathway. Conclusions This study comprehensively identified lncRNAs/circRNAs and first integrated their potential ceRNA function during PDLSC osteogenic differentiation. These findings suggest that specific lncRNAs and circRNAs might function as ceRNAs to promote PDLSC osteogenic differentiation and periodontal regeneration. Electronic supplementary material The online version of this article (10.1186/s12863-017-0569-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiuge Gu
- Department of Orthodontics, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Wenhua Xi Road No. 44-1, Jinan, Shandong, 250012, People's Republic of China.,Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China
| | - Mengying Li
- Department of Orthodontics, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Wenhua Xi Road No. 44-1, Jinan, Shandong, 250012, People's Republic of China.,Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China
| | - Ye Jin
- Department of Orthodontics, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Wenhua Xi Road No. 44-1, Jinan, Shandong, 250012, People's Republic of China.,Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China
| | - Dongxu Liu
- Department of Orthodontics, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Wenhua Xi Road No. 44-1, Jinan, Shandong, 250012, People's Republic of China. .,Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China.
| | - Fulan Wei
- Department of Orthodontics, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Wenhua Xi Road No. 44-1, Jinan, Shandong, 250012, People's Republic of China. .,Shandong Provincial Key Laboratory of Oral Tissue Regeneration, School of Stomatology, Shandong University, Jinan, People's Republic of China.
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Zhang X, Zhu M, Yang R, Zhao W, Hu X, Gan J. Identification and comparison of novel circular RNAs with associated co-expression and competing endogenous RNA networks in pulmonary tuberculosis. Oncotarget 2017; 8:113571-113582. [PMID: 29371930 PMCID: PMC5768347 DOI: 10.18632/oncotarget.22710] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/27/2017] [Indexed: 12/11/2022] Open
Abstract
Pulmonary tuberculosis (PTB) is caused by Mycobacterium tuberculosis and is one of the most serious diseases worldwide. Circular RNAs (circRNAs) are a large class of non-coding RNAs that were identified with potential regulatory roles in disease pathogenesis and progression. In this study, we used whole transcriptome sequencing to identify circRNAs from 3 PTB patients and 3 healthy individuals to determine the expression pattern of circRNAs in blood and the circRNA molecular regulatory networks in PTB pathogenesis. One hundred and seventy differentially expressed (≥ 2-fold change) circRNAs were dysregulated in PTB, compared with in healthy individuals. Quantitative real-time polymerase chain reaction was used to validate the RNA sequencing analysis from 20 PTB patients, and the results were consistent with the sequencing data. Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway analysis were applied to explore the potential circRNA functions of the significantly deregulated genes. Several immunity pathways, including endocytosis pathways in cancer, mitogen-activated protein kinase signaling pathway, human T-lymphotropic virus type 1 infection, and ubiquitin-mediated proteolysis, were involved in PTB pathogenesis. Competing endogenous RNAs (ceRNA) were constructed and inferred that aberrant expression of circRNA-associated ceRNA resulted in extensive variation in gene expression by miRNA-mediated circRNA-mRNA crosstalk interactions. Our study revealed that the circRNA-miRNA-mRNA network may shed light on the biological functions of circRNAs in PTB and provide useful information for exploring potential roles of circRNA in PTB.
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Affiliation(s)
- Xing Zhang
- Department of Infectious Disease, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215006, China
| | - Min Zhu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Rong Yang
- Department of Infectious Disease, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215006, China
| | - Weifeng Zhao
- Department of Infectious Disease, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215006, China
| | - Xiaolong Hu
- School of Biology and Basic Medical Science, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Jianhe Gan
- Department of Infectious Disease, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215006, China
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