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Ma Y, Dong T, Luan F, Yang J, Miao F, Wei P. Interaction of major facilitator superfamily domain containing 2A with the blood-brain barrier. Neural Regen Res 2025; 20:2133-2152. [PMID: 39248155 DOI: 10.4103/nrr.nrr-d-24-00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/08/2024] [Indexed: 09/10/2024] Open
Abstract
The functional and structural integrity of the blood-brain barrier is crucial in maintaining homeostasis in the brain microenvironment; however, the molecular mechanisms underlying the formation and function of the blood-brain barrier remain poorly understood. The major facilitator superfamily domain containing 2A has been identified as a key regulator of blood-brain barrier function. It plays a critical role in promoting and maintaining the formation and functional stability of the blood-brain barrier, in addition to the transport of lipids, such as docosahexaenoic acid, across the blood-brain barrier. Furthermore, an increasing number of studies have suggested that major facilitator superfamily domain containing 2A is involved in the molecular mechanisms of blood-brain barrier dysfunction in a variety of neurological diseases; however, little is known regarding the mechanisms by which major facilitator superfamily domain containing 2A affects the blood-brain barrier. This paper provides a comprehensive and systematic review of the close relationship between major facilitator superfamily domain containing 2A proteins and the blood-brain barrier, including their basic structures and functions, cross-linking between major facilitator superfamily domain containing 2A and the blood-brain barrier, and the in-depth studies on lipid transport and the regulation of blood-brain barrier permeability. This comprehensive systematic review contributes to an in-depth understanding of the important role of major facilitator superfamily domain containing 2A proteins in maintaining the structure and function of the blood-brain barrier and the research progress to date. This will not only help to elucidate the pathogenesis of neurological diseases, improve the accuracy of laboratory diagnosis, and optimize clinical treatment strategies, but it may also play an important role in prognostic monitoring. In addition, the effects of major facilitator superfamily domain containing 2A on blood-brain barrier leakage in various diseases and the research progress on cross-blood-brain barrier drug delivery are summarized. This review may contribute to the development of new approaches for the treatment of neurological diseases.
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Affiliation(s)
- Yilun Ma
- College of Pharmacy and First Clinical Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China
| | - Taiwei Dong
- College of Pharmacy and First Clinical Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China
| | - Fei Luan
- College of Pharmacy and First Clinical Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China
| | - Juanjuan Yang
- National Drug Clinical Trial Agency, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine/Xixian New District Central Hospital, Xi'an, Shaanxi Province, China
| | - Feng Miao
- College of Pharmacy and First Clinical Medical College, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi Province, China
| | - Peifeng Wei
- National Drug Clinical Trial Agency, The Second Affiliated Hospital of Shaanxi University of Chinese Medicine/Xixian New District Central Hospital, Xi'an, Shaanxi Province, China
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2
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Karttunen K, Patel D, Sahu B. Transposable elements as drivers of dedifferentiation: Connections between enhancers in embryonic stem cells, placenta, and cancer. Bioessays 2024; 46:e2400059. [PMID: 39073128 DOI: 10.1002/bies.202400059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
Transposable elements (TEs) have emerged as important factors in establishing the cell type-specific gene regulatory networks and evolutionary novelty of embryonic and placental development. Recently, studies on the role of TEs and their dysregulation in cancers have shed light on the transcriptional, transpositional, and regulatory activity of TEs, revealing that the activation of developmental transcriptional programs by TEs may have a role in the dedifferentiation of cancer cells to the progenitor-like cell states. This essay reviews the recent evidence of the cis-regulatory TEs (henceforth crTE) in normal development and malignancy as well as the key transcription factors and regulatory pathways that are implicated in both cell states, and presents existing gaps remaining to be studied, limitations of current technologies, and therapeutic possibilities.
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Affiliation(s)
- Konsta Karttunen
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Divyesh Patel
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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3
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Zhao X, Wu S, Yun Y, Du Z, Liu S, Bo C, Gao Y, Yang L, Song L, Bai C, Su G, Li G. Integrating Transcriptomics, Proteomics, and Metabolomics to Investigate the Mechanism of Fetal Placental Overgrowth in Somatic Cell Nuclear Transfer Cattle. Int J Mol Sci 2024; 25:9388. [PMID: 39273344 PMCID: PMC11395630 DOI: 10.3390/ijms25179388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/28/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
A major factor limiting the development of somatic cell nuclear transfer (SCNT) technology is the low success rate of pregnancy, mainly due to placental abnormalities disrupting the maternal-fetal balance during pregnancy. Although there has been some progress in research on the abnormal enlargement of cloned bovine placenta, there are still few reports on the direct regulatory mechanisms of enlarged cloned bovine placenta tissue. In this study, we conducted sequencing and analysis of transcriptomics, proteomics, and metabolomics of placental tissues from SCNT cattle (n = 3) and control (CON) cattle (n = 3). The omics analysis results indicate abnormalities in biological functions such as protein digestion and absorption, glycolysis/gluconeogenesis, the regulation of lipid breakdown, as well as glycerolipid metabolism, and arginine and proline metabolism in the placenta of SCNT cattle. Integrating these analyses highlights critical metabolic pathways affecting SCNT cattle placenta, including choline metabolism and unsaturated fatty acid biosynthesis. These findings suggest that aberrant expressions of genes, proteins, and metabolites in SCNT placentas affect key pathways in protein digestion, growth hormone function, and energy metabolism. Our results suggest that abnormal protein synthesis, growth hormone function, and energy metabolism in SCNT bovine placental tissues contribute to placental hypertrophy. These findings offer valuable insights for further investigation into the mechanisms underlying SCNT bovine placental abnormalities.
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Affiliation(s)
- Xiaoyu Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Shanshan Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yuan Yun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Zhiwen Du
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Shuqin Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Chunjie Bo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Yuxin Gao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Lei Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Lishuang Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Guanghua Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot 010070, China
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4
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Dziulko AK, Allen H, Chuong EB. An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140. Hum Mol Genet 2024; 33:1454-1464. [PMID: 38751339 PMCID: PMC11305685 DOI: 10.1093/hmg/ddae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 07/26/2024] Open
Abstract
Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn's disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family and is regulated by oncogenic mitogen-activated protein kinase (MAPK) signaling. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.
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Affiliation(s)
- Adam K Dziulko
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Holly Allen
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
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5
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Zheng W, Zhang Y, Xu P, Wang Z, Shao X, Chen C, Cai H, Wang Y, Sun MA, Deng W, Liu F, Lu J, Zhang X, Cheng D, Mysorekar IU, Wang H, Wang YL, Hu X, Cao B. TFEB safeguards trophoblast syncytialization in humans and mice. Proc Natl Acad Sci U S A 2024; 121:e2404062121. [PMID: 38968109 PMCID: PMC11253012 DOI: 10.1073/pnas.2404062121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/17/2024] [Indexed: 07/07/2024] Open
Abstract
Nutrient sensing and adaptation in the placenta are essential for pregnancy viability and proper fetal growth. Our recent study demonstrated that the placenta adapts to nutrient insufficiency through mechanistic target of rapamycin (mTOR) inhibition-mediated trophoblast differentiation toward syncytiotrophoblasts (STBs), a highly specialized multinucleated trophoblast subtype mediating extensive maternal-fetal interactions. However, the underlying mechanism remains elusive. Here, we unravel the indispensable role of the mTORC1 downstream transcriptional factor TFEB in STB formation both in vitro and in vivo. TFEB deficiency significantly impaired STB differentiation in human trophoblasts and placenta organoids. Consistently, systemic or trophoblast-specific deletion of Tfeb compromised STB formation and placental vascular construction, leading to severe embryonic lethality. Mechanistically, TFEB conferred direct transcriptional activation of the fusogen ERVFRD-1 in human trophoblasts and thereby promoted STB formation, independent of its canonical function as a master regulator of the autophagy-lysosomal pathway. Moreover, we demonstrated that TFEB directed the trophoblast syncytialization response driven by mTOR complex 1 (mTORC1) signaling. TFEB expression positively correlated with the reinforced trophoblast syncytialization in human fetal growth-restricted placentas exhibiting suppressed mTORC1 activity. Our findings substantiate that the TFEB-fusogen axis ensures proper STB formation during placenta development and under nutrient stress, shedding light on TFEB as a mechanistic link between nutrient-sensing machinery and trophoblast differentiation.
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Affiliation(s)
- Wanshan Zheng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Yue Zhang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Peiqun Xu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Zexin Wang
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen361102, Fujian, China
| | - Xuan Shao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing100101, China
| | - Chunyan Chen
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Han Cai
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Yinan Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou225009, Jiangsu, China
| | - Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Fan Liu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Jinhua Lu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Xueqin Zhang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Dunjin Cheng
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou510140, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou510140, Guangdong, China
| | - Indira U. Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston77030, TX
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston77030, TX
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
| | - Yan-Ling Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing100101, China
| | - Xiaoqian Hu
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen361102, Fujian, China
| | - Bin Cao
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen 361102, Fujian, China
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6
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Li Y, Lyu R, Chen S, Wang Y, Sun MA. TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms. Nucleic Acids Res 2024; 52:W126-W131. [PMID: 38747349 PMCID: PMC11223789 DOI: 10.1093/nar/gkae411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 07/06/2024] Open
Abstract
Transposable elements (TEs) are abundant in the genomes of various eukaryote organisms. Increasing evidence suggests that TEs can play crucial regulatory roles-usually by creating cis-elements (e.g. enhancers and promoters) bound by distinct transcription factors (TFs). TE-derived cis-elements have gained unprecedented attentions recently, and one key step toward their understanding is to identify the enriched TEs in distinct genomic intervals (e.g. a set of enhancers or TF binding sites) as candidates for further study. Nevertheless, such analysis remains challenging for researchers unfamiliar with TEs or lack strong bioinformatic skills. Here, we present TEENA (Transposable Element ENrichment Analyzer) to streamline TE enrichment analysis in various organisms. It implements an optimized pipeline, hosts the genome/gene/TE annotations of almost one hundred species, and provides multiple parameters to enable its flexibility. Taking genomic interval data as the only user-supplied file, it can automatically retrieve the corresponding annotations and finish a routine analysis in a couple minutes. Multiple case studies demonstrate that it can produce highly reliable results matching previous knowledge. TEENA can be freely accessed at: https://sun-lab.yzu.edu.cn/TEENA. Due to its easy-to-use design, we expect it to facilitate the studies of the regulatory function of TEs in various model and non-model organisms.
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Affiliation(s)
- Yuzhuo Li
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009 Jiangsu, China
| | - Renzhe Lyu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009 Jiangsu, China
| | - Shuai Chen
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009 Jiangsu, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009 Jiangsu, China
- Joint International Research Laboratory of Important Animal Infectious Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009 Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009 Jiangsu, China
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7
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Guo X, Zhao Y, You F. Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection. Front Immunol 2024; 15:1294020. [PMID: 38646531 PMCID: PMC11026653 DOI: 10.3389/fimmu.2024.1294020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/14/2024] [Indexed: 04/23/2024] Open
Abstract
Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2. We identified 405, 283, and 206 significantly up-regulated transposable elements (TEs) in hPBMCs, monkeys, and mice, respectively. This included 254, 119, 68, and 28 ERVs found in hPBMCs from severe and mild COVID-19 patients, monkeys, and transgenic mice expressing the human ACE2 receptor (hACE2) and infected with SARS-CoV-2. Furthermore, analysis using the Genomic Regions Enrichment of Annotations Tool (GREAT) revealed certain parental genomic sequences of these up-regulated ERVs in COVID-19 patients may be involved in various biological processes, including histone modification and viral replication. Of particular interest, we identified 210 ERVs specifically up-regulated in the severe COVID-19 group. The genes associated with these differentially expressed ERVs were enriched in processes such as immune response activation and histone modification. HERV1_I-int: ERV1:LTR and LTR7Y: ERV1:LTR were highlighted as potential biomarkers for evaluating the severity of COVID-19. Additionally, validation of our findings using RT-qPCR in Bone Marrow-Derived Macrophages (BMDMs) from mice infected by HSV-1 and VSV provided further support to our results. This study offers insights into the expression patterns and potential roles of ERVs following viral infection, providing a valuable resource for future studies on ERVs and their interaction with SARS-CoV-2.
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Wang J, Lu X, Zhang W, Liu GH. Endogenous retroviruses in development and health. Trends Microbiol 2024; 32:342-354. [PMID: 37802660 DOI: 10.1016/j.tim.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 10/08/2023]
Abstract
Endogenous retroviruses (ERVs) are evolutionary remnants of retroviral infections in which the viral genome became embedded as a dormant regulatory element within the host germline. When ERVs become activated, they comprehensively rewire genomic regulatory networks of the host and facilitate critical developmental events, such as preimplantation development and placentation, in a manner specific to species, developmental stage, and tissues. However, accumulating evidence suggests that aberrant ERV transcription compromises genome stability and has been implicated in cellular senescence and various pathogenic processes, underscoring the significance of host genomic surveillance mechanisms. Here, we revisit the prominent functions of ERVs in early development and highlight their emerging roles in mammalian post-implantation development and organogenesis. We also discuss their implications for aging and pathological processes such as microbial infection, immune response. Furthermore, we discuss recent advances in stem-cell-based models, single-cell omics, and genome editing technologies, which serve as beacons illuminating the versatile nature of ERVs in mammalian development and health.
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Affiliation(s)
- Jichang Wang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, China.
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China.
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9
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Yi C, Song H, Liang H, Ran Y, Tang J, Chen E, Li F, Fu L, Wang Y, Chen F, Wang Y, Ding Y, Xie Y. TBX3 reciprocally controls key trophoblast lineage decisions in villi during human placenta development in the first trimester. Int J Biol Macromol 2024; 263:130220. [PMID: 38368983 DOI: 10.1016/j.ijbiomac.2024.130220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/20/2024]
Abstract
Human trophoblastic lineage development is intertwined with placental development and pregnancy outcomes, but the regulatory mechanisms underpinning this process remain inadequately understood. In this study, based on single-nuclei RNA sequencing (snRNA-seq) analysis of the human early maternal-fetal interface, we compared the gene expression pattern of trophoblast at different developmental stages. Our findings reveal a predominant upregulation of TBX3 during the transition from villous cytotrophoblast (VCT) to syncytiotrophoblast (SCT), but downregulation of TBX3 as VCT progresses into extravillous trophoblast cells (EVT). Immunofluorescence analysis verified the primary expression of TBX3 in SCT, partial expression in MKi67-positive VCT, and absence in HLA-G-positive EVT, consistent with our snRNA-seq results. Using immortalized trophoblastic cell lines (BeWo and HTR8/SVneo) and human primary trophoblast stem cells (hTSCs), we observed that TBX3 knockdown impedes SCT formation through RAS-MAPK signaling, while TBX3 overexpression disrupts the cytoskeleton structure of EVT and hinders EVT differentiation by suppressing FAK signaling. In conclusion, our study suggests that the spatiotemporal expression of TBX3 plays a critical role in regulating trophoblastic lineage development via distinct signaling pathways. This underscores TBX3 as a key determinant during hemochorial placental development.
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Affiliation(s)
- Cen Yi
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Honglan Song
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Hongxiu Liang
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yujie Ran
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Jing Tang
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Enxiang Chen
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Fangfang Li
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Lijuan Fu
- Department of Gynecology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China 400021; Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, School of Traditional Chinese Medicine, Chongqing Medical University, Chongqing 400016, China; Department of Basic Medical Sciences, Changsha Medical University, Hunan 410219, China
| | - Yaqi Wang
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Fengming Chen
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, 410129, China
| | - Yingxiong Wang
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Yubin Ding
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China
| | - Youlong Xie
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing 400016, China.
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10
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Chen M, Huang X, Wang C, Wang S, Jia L, Li L. Endogenous retroviral solo-LTRs in human genome. Front Genet 2024; 15:1358078. [PMID: 38606358 PMCID: PMC11007075 DOI: 10.3389/fgene.2024.1358078] [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: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 04/13/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are derived from the infection and integration of exogenetic retroviruses. HERVs account for 8% of human genome, and the majority of HERVs are solitary LTRs (solo-LTRs) due to homologous recombination. Multiple findings have showed that solo-LTRs could provide an enormous reservoir of transcriptional regulatory sequences involved in diverse biological processes, especially carcinogenesis and cancer development. The link between solo-LTRs and human diseases still remains poorly understood. This review focuses on the regulatory modules of solo-LTRs, which contribute greatly to the diversification and evolution of human genes. More importantly, although inactivating mutations, insertions and deletions have been identified in solo-LTRs, the inherited regulatory elements of solo-LTRs initiate the expression of chimeric lncRNA transcripts, which have been reported to play crucial roles in human health and disease. These findings provide valuable insights into the evolutionary and functional mechanisms underlying the presence of HERVs in human genome. Taken together, in this review, we will present evidences showing the regulatory and encoding capacity of solo-LTRs as well as the significant impact on various aspects of human biology.
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Affiliation(s)
- Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Xiaolong Huang
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Chunlei Wang
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Shibo Wang
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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11
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Kong X, Li R, Chen M, Zheng R, Wang J, Sun C, Qu Y. Endogenous retrovirus HERVH-derived lncRNA UCA1 controls human trophoblast development. Proc Natl Acad Sci U S A 2024; 121:e2318176121. [PMID: 38483994 PMCID: PMC10962953 DOI: 10.1073/pnas.2318176121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Endogenous retroviruses (ERVs) are frequently reactivated in mammalian placenta. It has been proposed that ERVs contribute to shaping the gene regulatory network of mammalian trophoblasts, dominantly acting as species- and placental-specific enhancers. However, whether and how ERVs control human trophoblast development through alternative pathways remains poorly understood. Besides the well-recognized function of human endogenous retrovirus-H (HERVH) in maintaining pluripotency of early human epiblast, here we present a unique role of HERVH on trophoblast lineage development. We found that the LTR7C/HERVH subfamily exhibits an accessible chromatin state in the human trophoblast lineage. Particularly, the LTR7C/HERVH-derived Urothelial Cancer Associated 1 (UCA1), a primate-specific long non-coding RNA (lncRNA), is transcribed in human trophoblasts and promotes the proliferation of human trophoblast stem cells (hTSCs), whereas its ectopic expression compromises human trophoblast syncytialization coinciding with increased interferon signaling pathway. Importantly, UCA1 upregulation is detectable in placental samples from early-onset preeclampsia (EO-PE) patients and the transcriptome of EO-PE placenta exhibits considerable similarities to that of the syncytiotrophoblasts differentiated from UCA1-overexpressing hTSCs, supporting up-regulated UCA1 as a potential biomarker of this disease. Altogether, our data shed light on the versatile regulatory role of HERVH in early human development and provide a unique mechanism whereby ERVs exert a function in human placentation and placental syndromes.
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Affiliation(s)
- Xuhui Kong
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
| | - Ruiqi Li
- Reproductive and Genetic Hospital of Kapok, Hainan571400, China
- Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou510120, China
- The First People’s Hospital of Kashgar, Kashgar844000, China
| | - Manqi Chen
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
| | - Rongyan Zheng
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
| | - Jichang Wang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou510623, China
| | - Yuliang Qu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou510080, China
- Key Laboratory for Stem Cells and Tissue Engineering, Sun Yat-sen University, Ministry of Education, Guangzhou510080, China
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12
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Wu X, Liu L, Xue X, Li X, Zhao K, Zhang J, Li W, Yao W, Ding S, Jia C, Zhu F. Captive ERVWE1 triggers impairment of 5-HT neuronal plasticity in the first-episode schizophrenia by post-transcriptional activation of HTR1B in ALKBH5-m6A dependent epigenetic mechanisms. Cell Biosci 2023; 13:213. [PMID: 37990254 PMCID: PMC10664518 DOI: 10.1186/s13578-023-01167-4] [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: 07/27/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Abnormalities in the 5-HT system and synaptic plasticity are hallmark features of schizophrenia. Previous studies suggest that the human endogenous retrovirus W family envelope (ERVWE1) is an influential risk factor for schizophrenia and inversely correlates with 5-HT4 receptor in schizophrenia. To our knowledge, no data describes the effect of ERVWE1 on 5-HT neuronal plasticity. N6-methyladenosine (m6A) regulates gene expression and impacts synaptic plasticity. Our research aims to systematically investigate the effects of ERVWE1 on 5-HT neuronal plasticity through m6A modification in schizophrenia. RESULTS HTR1B, ALKBH5, and Arc exhibited higher levels in individuals with first-episode schizophrenia compared to the controls and showed a strong positive correlation with ERVWE1. Interestingly, HTR1B was also correlated with ALKBH5 and Arc. Further analyses confirmed that ALKBH5 may be an independent risk factor for schizophrenia. In vitro studies, we discovered that ERVWE1 enhanced HTR1B expression, thereby activating the ERK-ELK1-Arc pathway and reducing the complexity and spine density of 5-HT neurons. Furthermore, ERVWE1 reduced m6A levels through ALKBH5 demethylation. ERVWE1 induced HTR1B upregulation by improving its mRNA stability in ALKBH5-m6A-dependent epigenetic mechanisms. Importantly, ALKBH5 mediated the observed alterations in 5-HT neuronal plasticity induced by ERVWE1. CONCLUSIONS Overall, HTR1B, Arc, and ALKBH5 levels were increased in schizophrenia and positively associated with ERVWE1. Moreover, ALKBH5 was a novel risk gene for schizophrenia. ERVWE1 impaired 5-HT neuronal plasticity in ALKBH5-m6A dependent mechanism by the HTR1B-ERK-ELK1-Arc pathway, which may be an important contributor to aberrant synaptic plasticity in schizophrenia.
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Affiliation(s)
- Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | | | - Xing Xue
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xuhang Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Kexin Zhao
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jiahang Zhang
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenshi Li
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wei Yao
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Shuang Ding
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Chen Jia
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan, 430071, China.
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Chilosi M, Doglioni C, Ravaglia C, Piciucchi S, Dubini A, Stefanizzi L, Poletti V. COVID-19. Biology, pathophysiology, and immunology: a pathologist view. Pathologica 2023; 115:248-256. [PMID: 38054899 DOI: 10.32074/1591-951x-954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 12/07/2023] Open
Abstract
Even if the SARS-CoV-2 pandemic has been declared over, several risks and clinical problems remain to be faced, including long-COVID sequelae and possible outbreaks of pathogenic variants. Intense research on COVID-19 has provided in these few years a striking amount of data covering different fields and disciplines, which can help to provide a knowledge shield against new potential infective spreads, and may also potentially be applied to other fields of medicine, including oncology and neurology. Nevertheless, areas of uncertainty still remain regarding the pathogenic mechanisms that subtend the multifaceted manifestations of the disease. To better clarify the pathogenesis of the disease, a systematic multidisciplinary evaluation of the many mechanisms involved in COVID-19 is mandatory, including clinical, physiological, radiological, immunological and pathological studies. In COVID-19 syndrome the pathological studies have been mainly performed on autopsy cases, and only a few studies are available on biopsies. Nevertheless, these studies have provided relevant information that can substantially contribute to decipher the complex scenario characterizing the different forms of COVID-19 and long-COVID-19. In this review the data provided by pathological investigations are recapitulated and discussed, in the light of different hypothesis and data provided by clinical, physiological and immunological data.
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Affiliation(s)
- Marco Chilosi
- Department of Pathology, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Claudio Doglioni
- Department of Pathology, San Raffaele Scientific Institute. Milan, Italy
| | - Claudia Ravaglia
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Sara Piciucchi
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | | | | | - Venerino Poletti
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
- Department of Pathology, Ospedale GB Morgagni, Forlì, Italy
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14
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Koga A, Nishihara H, Tanabe H, Tanaka R, Kayano R, Matsumoto S, Endo T, Srikulnath K, O'Neill RJ. Kangaroo endogenous retrovirus (KERV) forms megasatellite DNA with a simple repetition pattern in which the provirus structure is retained. Virology 2023; 586:56-66. [PMID: 37487326 DOI: 10.1016/j.virol.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023]
Abstract
The kangaroo endogenous retrovirus (KERV) was previously reported to have undergone a rapid copy number increase in the red-necked wallaby; however, the mode of amplification was left to be clarified. The present study revealed that the long terminal repeat (LTR) (0.6 kb) and internal region (2.0 kb) of a provirus are repeated alternately, forming megasatellite DNA which we named kervRep. This repetition pattern was the same as that observed for walbRep, megasatellite DNA originating from another endogenous retrovirus. Their formation process can be explained using a simple model: pairing slippage followed by homologous recombination. This model features that the initial step is triggered by the presence of two identical sequences within a short distance; the possession of LTRs by endogenous retroviruses fulfills this condition. The discovery of two cases suggests that formation of this type of satellite DNA is one of non-negligible effects of endogenous retroviruses on their host genomes.
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Affiliation(s)
- Akihiko Koga
- Center for Evolutionary Origins of Human Behavior, Kyoto University, Inuyama 484-8506, Japan; Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Hideyuki Tanabe
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Hayama 240-0193, Japan
| | - Rieko Tanaka
- Saitama Children's Zoo, Higashimatsuyama 355-0065, Japan
| | - Rika Kayano
- Saitama Children's Zoo, Higashimatsuyama 355-0065, Japan
| | | | | | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
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15
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Dawson T, Rentia U, Sanford J, Cruchaga C, Kauwe JSK, Crandall KA. Locus specific endogenous retroviral expression associated with Alzheimer's disease. Front Aging Neurosci 2023; 15:1186470. [PMID: 37484691 PMCID: PMC10359044 DOI: 10.3389/fnagi.2023.1186470] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Human endogenous retroviruses (HERVs) are transcriptionally-active remnants of ancient retroviral infections that may play a role in Alzheimer's disease. Methods We combined two, publicly available RNA-Seq datasets with a third, novel dataset for a total cohort of 103 patients with Alzheimer's disease and 45 healthy controls. We use telescope to perform HERV quantification for these samples and simultaneously perform gene expression analysis. Results We identify differentially expressed genes and differentially expressed HERVs in Alzheimer's disease patients. Differentially expressed HERVs are scattered throughout the genome; many of them are members of the HERV-K superfamily. A number of HERVs are correlated with the expression of dysregulated genes in Alzheimer's and are physically proximal to genes which drive disease pathways. Discussion Dysregulated expression of ancient retroviral insertions in the human genome are present in Alzheimer's disease and show localization patterns that may explain how these elements drive pathogenic gene expression.
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Affiliation(s)
- Tyson Dawson
- Computational Biology Institute, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Uzma Rentia
- Computational Biology Institute, The George Washington University, Washington, DC, United States
| | - Jessie Sanford
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, United States
| | - John S. K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Keith A. Crandall
- Computational Biology Institute, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
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16
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Zuo Z. THE1B may have no role in human pregnancy due to ZNF430-mediated silencing. Mob DNA 2023; 14:6. [PMID: 37217947 DOI: 10.1186/s13100-023-00294-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
THE1-family retrovirus invaded the primate genome more than 40 million years ago. Dunn-Fletcher et al. reported one THE1B element upstream of CRH gene alters gestation length by upregulating corticotropin-releasing hormone expression in transgenic mice and concluded it has the same role in human as well. However, no promoter or enhancer mark has been detected around this CRH-proximal element in any human tissue or cell, so probably some anti-viral factor exists in primates to prevents it from wreaking havoc. Here I report two paralogous zinc finger genes, ZNF430 and ZNF100, that emerged during the simian lineage to specifically silence THE1B and THE1A, respectively. Contact residue changes in one finger confers each ZNF the unique ability to preferentially repress one THE1 sub-family over the other. The reported THE1B element contains an intact ZNF430 binding site, thus under the repression of ZNF430 in most tissues including placenta, it is questionable whether or not this retrovirus has any role in human pregnancy. Overall, this analysis highlights the need to study human retroviruses' functions in suitable model system.
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Affiliation(s)
- Zheng Zuo
- Shenzhen University, Shenzhen, Guangdong, China.
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