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Ebrahimnezhad M, Asl SH, Rezaie M, Molavand M, Yousefi B, Majidinia M. lncRNAs: New players of cancer drug resistance via targeting ABC transporters. IUBMB Life 2024. [PMID: 39091106 DOI: 10.1002/iub.2888] [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: 04/11/2024] [Accepted: 05/30/2024] [Indexed: 08/04/2024]
Abstract
Cancer drug resistance poses a significant obstacle to successful chemotherapy, primarily driven by the activity of ATP-binding cassette (ABC) transporters, which actively efflux chemotherapeutic agents from cancer cells, reducing their intracellular concentrations and therapeutic efficacy. Recent studies have highlighted the pivotal role of long noncoding RNAs (lncRNAs) in regulating this resistance, positioning them as crucial modulators of ABC transporter function. lncRNAs, once considered transcriptional noise, are now recognized for their complex regulatory capabilities at various cellular levels, including chromatin modification, transcription, and post-transcriptional processing. This review synthesizes current research demonstrating how lncRNAs influence cancer drug resistance by modulating the expression and activity of ABC transporters. lncRNAs can act as molecular sponges, sequestering microRNAs that would otherwise downregulate ABC transporter genes. Additionally, they can alter the epigenetic landscape of these genes, affecting their transcriptional activity. Mechanistic insights reveal that lncRNAs contribute to the activity of ABC transporters, thereby altering the efflux of chemotherapeutic drugs and promoting drug resistance. Understanding these interactions provides a new perspective on the molecular basis of chemoresistance, emphasizing the regulatory network of lncRNAs and ABC transporters. This knowledge not only deepens our understanding of the biological mechanisms underlying drug resistance but also suggests novel therapeutic strategies. In conclusion, the intricate interplay between lncRNAs and ABC transporters is crucial for developing innovative solutions to combat cancer drug resistance, underscoring the importance of continued research in this field.
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Affiliation(s)
- Mohammad Ebrahimnezhad
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sanaz Hassanzadeh Asl
- Student Research Committee, Faculty of Medicine, Tabriz Azad University of Medical Sciences, Tabriz, Iran
| | - Maede Rezaie
- Immunology research center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehran Molavand
- Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Yousefi
- Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular research center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Majidinia
- Solid Tumor Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
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2
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Herbst J, Nagy SH, Vercauteren I, De Veylder L, Kunze R. The long non-coding RNA LINDA restrains cellular collapse following DNA damage in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1370-1384. [PMID: 37616189 DOI: 10.1111/tpj.16431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/04/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
The genomic integrity of every organism is endangered by various intrinsic and extrinsic stresses. To maintain genomic integrity, a sophisticated DNA damage response (DDR) network is activated rapidly after DNA damage. Notably, the fundamental DDR mechanisms are conserved in eukaryotes. However, knowledge about many regulatory aspects of the plant DDR is still limited. Important, yet little understood, regulatory factors of the DDR are the long non-coding RNAs (lncRNAs). In humans, 13 lncRNAs functioning in DDR have been characterized to date, whereas no such lncRNAs have been characterized in plants yet. By meta-analysis, we identified the putative long intergenic non-coding RNA induced by DNA damage (LINDA) that responds strongly to various DNA double-strand break-inducing treatments, but not to replication stress induced by mitomycin C. After DNA damage, LINDA is rapidly induced in an ATM- and SOG1-dependent manner. Intriguingly, the transcriptional response of LINDA to DNA damage is similar to that of its flanking hypothetical protein-encoding gene. Phylogenetic analysis of putative Brassicales and Malvales LINDA homologs indicates that LINDA lncRNAs originate from duplication of a flanking small protein-encoding gene followed by pseudogenization. We demonstrate that LINDA is not only needed for the regulation of this flanking gene but also fine-tuning of the DDR after the occurrence of DNA double-strand breaks. Moreover, Δlinda mutant root stem cells are unable to recover from DNA damage, most likely due to hyper-induced cell death.
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Affiliation(s)
- Josephine Herbst
- Department of Biology, Chemistry and Pharmacy, Molecular Genetics of Plants, Institute of Biology, Freie Universität Berlin, Berlin, D-14195, Germany
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Solveig Henriette Nagy
- Department of Biology, Chemistry and Pharmacy, Molecular Genetics of Plants, Institute of Biology, Freie Universität Berlin, Berlin, D-14195, Germany
| | - Ilse Vercauteren
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- Center for Plant Systems Biology, VIB, Ghent, B-9052, Belgium
| | - Reinhard Kunze
- Department of Biology, Chemistry and Pharmacy, Molecular Genetics of Plants, Institute of Biology, Freie Universität Berlin, Berlin, D-14195, Germany
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3
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Anchesi I, Schepici G, Mazzon E. LncRNAs and CircRNAs as Strategies against Pathological Conditions Caused by a Hypoxic/Anoxic State. Biomolecules 2023; 13:1622. [PMID: 38002304 PMCID: PMC10669691 DOI: 10.3390/biom13111622] [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: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Brain damage can be induced by oxygen deprivation. It is known that hypoxic or anoxic conditions can lead to changes in the expression levels of non-coding RNAs (ncRNAs), which, in turn, can be related to Central Nervous System (CNS) injuries. Therefore, it could be useful to investigate the involvement of non-coding RNAs (ncRNAs), as well as the underlying mechanisms which are able to modulate them in brain damage induced by hypoxic or anoxic conditions. In this review, we focused on recent research that associates these conditions with long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). The results of this review demonstrate that the expression of both lncRNAs and circRNAs can be influenced by oxygen deprivation conditions and so they can contribute to inducing damage or providing neuroprotection by affecting specific molecular pathways. Furthermore, several experimental studies have shown that ncRNA activity can be regulated by compounds, thus also modifying their transcriptomic profile and their effects on CNS damages induced by hypoxic/anoxic events.
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Affiliation(s)
| | | | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Strada Statale 113, Contrada Casazza, 98124 Messina, Italy
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4
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Ataei A, Tahsili M, Hayadokht G, Daneshvar M, Mohammadi Nour S, Soofi A, Masoudi A, Kabiri M, Natami M. Targeting long noncoding RNAs in neuroblastoma: Progress and prospects. Chem Biol Drug Des 2023; 102:640-652. [PMID: 37291742 DOI: 10.1111/cbdd.14263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 06/10/2023]
Abstract
Neuroblastoma (NB) is the third most prevalent tumor that mostly influences infants and young children. Although different treatments have been developed for the treatment of NB, high-risk patients have been reported to have low survival rates. Currently, long noncoding RNAs (lncRNAs) have shown an attractive potential in cancer research and a party of investigations have been performed to understand mechanisms underlying tumor development through lncRNA dysregulation. Researchers have just newly initiated to exhibit the involvement of lncRNAs in NB pathogenesis. In this review article, we tried to clarify the point we stand with respect to the involvement of lncRNAs in NB. Moreover, implications for the pathologic roles of lncRNAs in the development of NB have been discussed. It seems that some of these lncRNAs have promising potential to be applied as biomarkers for NB prognosis and treatment.
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Affiliation(s)
- Ali Ataei
- School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | | | - Golsa Hayadokht
- School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | | | | | - Asma Soofi
- Department of Physical Chemistry, School of Chemistry, College of Sciences, University of Tehran, Tehran, Iran
| | - Alireza Masoudi
- Department of Laboratory Sciences, Faculty of Alied Medical Sciences, Qom University of Medical Sciences, Qom, Iran
| | - Maryam Kabiri
- Faculty of Medicine, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Mohammad Natami
- Department of Urology, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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5
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Shakhpazyan NK, Mikhaleva LM, Bedzhanyan AL, Sadykhov NK, Midiber KY, Konyukova AK, Kontorschikov AS, Maslenkina KS, Orekhov AN. Long Non-Coding RNAs in Colorectal Cancer: Navigating the Intersections of Immunity, Intercellular Communication, and Therapeutic Potential. Biomedicines 2023; 11:2411. [PMID: 37760852 PMCID: PMC10525929 DOI: 10.3390/biomedicines11092411] [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: 07/12/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
This comprehensive review elucidates the intricate roles of long non-coding RNAs (lncRNAs) within the colorectal cancer (CRC) microenvironment, intersecting the domains of immunity, intercellular communication, and therapeutic potential. lncRNAs, which are significantly involved in the pathogenesis of CRC, immune evasion, and the treatment response to CRC, have crucial implications in inflammation and serve as promising candidates for novel therapeutic strategies and biomarkers. This review scrutinizes the interaction of lncRNAs with the Consensus Molecular Subtypes (CMSs) of CRC, their complex interplay with the tumor stroma affecting immunity and inflammation, and their conveyance via extracellular vesicles, particularly exosomes. Furthermore, we delve into the intricate relationship between lncRNAs and other non-coding RNAs, including microRNAs and circular RNAs, in mediating cell-to-cell communication within the CRC microenvironment. Lastly, we propose potential strategies to manipulate lncRNAs to enhance anti-tumor immunity, thereby underlining the significance of lncRNAs in devising innovative therapeutic interventions in CRC.
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Affiliation(s)
- Nikolay K. Shakhpazyan
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Liudmila M. Mikhaleva
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Arcady L. Bedzhanyan
- Department of Abdominal Surgery and Oncology II (Coloproctology and Uro-Gynecology), Petrovsky National Research Center of Surgery, 119435 Moscow, Russia;
| | - Nikolay K. Sadykhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Konstantin Y. Midiber
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexandra K. Konyukova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Andrey S. Kontorschikov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Ksenia S. Maslenkina
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexander N. Orekhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Institute for Atherosclerosis Research, 121096 Moscow, Russia
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6
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Marques IS, Tavares V, Neto BV, Mota INR, Pereira D, Medeiros R. Long Non-Coding RNAs in Venous Thromboembolism: Where Do We Stand? Int J Mol Sci 2023; 24:12103. [PMID: 37569483 PMCID: PMC10418965 DOI: 10.3390/ijms241512103] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Venous thromboembolism (VTE), a common condition in Western countries, is a cardiovascular disorder that arises due to haemostatic irregularities, which lead to thrombus generation inside veins. Even with successful treatment, the resulting disease spectrum of complications considerably affects the patient's quality of life, potentially leading to death. Cumulative data indicate that long non-coding RNAs (lncRNAs) may have a role in VTE pathogenesis. However, the clinical usefulness of these RNAs as biomarkers and potential therapeutic targets for VTE management is yet unclear. Thus, this article reviewed the emerging evidence on lncRNAs associated with VTE and with the activity of the coagulation system, which has a central role in disease pathogenesis. Until now, ten lncRNAs have been implicated in VTE pathogenesis, among which MALAT1 is the one with more evidence. Meanwhile, five lncRNAs have been reported to affect the expression of TFPI2, an important anticoagulant protein, but none with a described role in VTE development. More investigation in this field is needed as lncRNAs may help dissect VTE pathways, aiding in disease prediction, prevention and treatment.
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Affiliation(s)
- Inês Soares Marques
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/Pathology and Laboratory Medicine Dep., Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal; (I.S.M.); (V.T.); (B.V.N.); (I.N.R.M.)
- Faculty of Sciences of University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Valéria Tavares
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/Pathology and Laboratory Medicine Dep., Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal; (I.S.M.); (V.T.); (B.V.N.); (I.N.R.M.)
- Faculty of Medicine of University of Porto (FMUP), 4200-072 Porto, Portugal
- Abel Salazar Institute for the Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Beatriz Vieira Neto
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/Pathology and Laboratory Medicine Dep., Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal; (I.S.M.); (V.T.); (B.V.N.); (I.N.R.M.)
- Research Department, Portuguese League Against Cancer (NRNorte), 4200-172 Porto, Portugal
| | - Inês N. R. Mota
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/Pathology and Laboratory Medicine Dep., Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal; (I.S.M.); (V.T.); (B.V.N.); (I.N.R.M.)
- Faculty of Sciences of University of Porto (FCUP), 4169-007 Porto, Portugal
| | - Deolinda Pereira
- Oncology Department, Portuguese Institute of Oncology of Porto (IPOP), 4200-072 Porto, Portugal;
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/Pathology and Laboratory Medicine Dep., Clinical Pathology SV/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), 4200-072 Porto, Portugal; (I.S.M.); (V.T.); (B.V.N.); (I.N.R.M.)
- Faculty of Medicine of University of Porto (FMUP), 4200-072 Porto, Portugal
- Abel Salazar Institute for the Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Research Department, Portuguese League Against Cancer (NRNorte), 4200-172 Porto, Portugal
- Faculty of Health Sciences, Fernando Pessoa University, 4200-150 Porto, Portugal
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7
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Gholizadeh O, Akbarzadeh S, Moein M, Yasamineh S, Hosseini P, Afkhami H, Amini P, Dadashpour M, Tahavvori A, Eslami M, Hossein Taherian M, Poortahmasebi V. The role of non-coding RNAs in the diagnosis of different stages (HCC, CHB, OBI) of hepatitis B infection. Microb Pathog 2023; 176:105995. [PMID: 36681203 DOI: 10.1016/j.micpath.2023.105995] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Abstract
Despite the availability of an effective hepatitis B virus (HBV) vaccine and universal immunization schedules, HBV has remained a health problem in various stages such as occult hepatitis B infection (OBI), chronic hepatitis B (CHB), and hepatocellular carcinoma (HCC), which is considered one of the possible phases during chronic HBV infection. OBI is defined as the persistence of HBV genomes in hepatocytes of patients with a negative HBV surface antigen (HBsAg) test and detectable or undetectable HBV DNA in the blood. OBI is occasionally associated with infection caused by mutant viruses that produce a modified HBsAg that is undetected by diagnostic procedures or with replication-defective variations. Many aspects of HBV (OBI more than any other stage) including prevalence, pathobiology, and clinical implications has remained controversial. According to a growing body of research, non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been linked to the development and progression of a number of illnesses, including viral infectious disorders. Despite a shortage of knowledge regarding the expression and biological activities of lncRNAs and miRNAs in HBV infection, Hepatitis B remains a major global public health concern. This review summarizes the role of lncRNAs in the diagnosis and treatment of different stages of hepatitis B infection.
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Affiliation(s)
- Omid Gholizadeh
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | - Sama Akbarzadeh
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Masood Moein
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Saman Yasamineh
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | - Parastoo Hosseini
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamed Afkhami
- Department of Medical Microbiology, Faculty of Medicine, Shahed University of Medical Science, Tehran, Iran
| | - Paria Amini
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Dadashpour
- Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran.
| | - Amir Tahavvori
- Internal Department, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
| | - Majid Eslami
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran
| | | | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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8
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Zou Y, Guo Q, Chang Y, Zhong Y, Cheng L, Wei W. Effects of Maternal High-Fructose Diet on Long Non-Coding RNAs and Anxiety-like Behaviors in Offspring. Int J Mol Sci 2023; 24:ijms24054460. [PMID: 36901891 PMCID: PMC10003385 DOI: 10.3390/ijms24054460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
Increased fructose intake is an international issue. A maternal high-fructose diet during gestation and lactation could affect nervous system development in offspring. Long non-coding RNA (lncRNA) plays an important role in brain biology. However, the mechanism whereby maternal high-fructose diets influence offspring brain development by affecting lncRNAs is still unclear. Here, we administered 13% and 40% fructose water to establish a maternal high-fructose diet model during gestation and lactation. To determine lncRNAs and their target genes, full-length RNA sequencing was performed using the Oxford Nanopore Technologies platform, and 882 lncRNAs were identified. Moreover, the 13% fructose group and the 40% fructose group had differentially expressed lncRNA genes compared with the control group. Enrichment analyses and co-expression analyses were performed to investigate the changes in biological function. Furthermore, enrichment analyses, behavioral science experiments, and molecular biology experiments all indicated that the fructose group offspring showed anxiety-like behaviors. In summary, this study provides insight into the molecular mechanisms underlying maternal high-fructose diet-induced lncRNA expression and co-expression of lncRNA and mRNA.
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Haridevamuthu B, Guru A, Velayutham M, Snega Priya P, Arshad A, Arockiaraj J. Long non‐coding RNA, a supreme post‐transcriptional immune regulator of bacterial or virus‐driven immune evolution in teleost. REVIEWS IN AQUACULTURE 2023; 15:163-178. [DOI: 10.1111/raq.12709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/18/2022] [Indexed: 10/16/2023]
Abstract
AbstractThe global aquaculture boom, fuelled by a reduction in wild population and detection of novel viruses, has created a demanding market, hence, there is a pressing need to investigate the immune system of fish, further. As the most diverse community of vertebrates and a central contributor to the progressing global aquaculture market, teleost continues to draw vast scientific interest. Recent breakthroughs in multi‐omics technologies have provided a platform to understand the role of long non‐coding RNA (lncRNA) in the host immune system during infection. Emerging evidence shows that teleost lncRNA might have a regulatory role in immune responses, mostly through lncRNA–microRNA (miRNA) sponging. Teleost lncRNA shares a functionally active short sequence complement to target the miRNA which is conserved among the several fish species. Recent report suggests that rhabdovirus exploits a lncRNA in teleost and, to dodge the host immune mechanism and negatively regulate the immune system. This observation reveals the essentiality of lncRNA in pathogen‐driven immunity in teleost. Reports available on the function of teleost lncRNA are still in early stages and experimental verifications are a limiting factor. Unravelling the lncRNA‐mediated immune regulation in fishes could be used against the invading pathogens to strengthen the aquaculture production. This review elaborates on the experimentally identified and functionally characterized lncRNA and its regulatory role in the teleost immune response during infection and pathogen‐driven host immune evolution, which could eventually lead to achieving high standards in aquaculture productivity.
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Affiliation(s)
- B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Ajay Guru
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Manikandan Velayutham
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - P. Snega Priya
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I‐AQUAS) Universiti Putra Malaysia Port Dickson Malaysia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
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10
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Shabtai R, Tzur YB. Male-specific roles of lincRNA in C. elegans fertility. Front Cell Dev Biol 2023; 11:1115605. [PMID: 37035238 PMCID: PMC10076526 DOI: 10.3389/fcell.2023.1115605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
The testis is the mammalian tissue with the highest expression levels of long intergenic non-coding RNAs (lincRNAs). However, most in vivo models have not found significant reductions in male fertility when highly expressed lincRNA genes were removed. This suggests that certain lincRNAs may act redundantly or lack functional roles. In the genome of the nematode Caenorhabditis elegans, there is an order of magnitude fewer lincRNA genes than in mammals. This characteristic lowers the potential for redundancy, making it an ideal model to test these possibilities. We identified five highly and dynamically expressed lincRNAs in male C. elegans gonads and quantified the fertility of worm strains in which these genes were removed. In contrast to the hermaphrodites of deletion strains, which exhibited no significant reductions in broods, smaller brood sizes were observed in the progeny of males of three of the lincRNA deleted strains. This demonstrates reduced male fertility in worms with those genes removed. Interestingly, reduced brood size was statistically significant only in the last days of egg laying in two of these strains. This suggests the effect is due to early deterioration and aging of the transferred sperm. We detected a mild increase in embryonic lethality in only one of the strains, supporting the possibility that these lincRNAs do not affect fertility through critical roles in essential meiotic processes. Together our results indicate a sexually dimorphic outcome on fertility when lincRNA are removed and show that, unlike mammals, individual lincRNAs in C. elegans do play significant roles in male fertility.
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11
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COVID-19 vs. Cancer Immunosurveillance: A Game of Thrones within an Inflamed Microenviroment. Cancers (Basel) 2022; 14:cancers14174330. [PMID: 36077865 PMCID: PMC9455004 DOI: 10.3390/cancers14174330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
The COVID-19 pandemic accounts for more than 500 million confirmed infections and over 6 million deaths worldwide in the last 2 years. SARS-CoV-2 causes a highly complex form of inflammation that affects the human organism both acutely and chronically. In the same line, cancer as an inflammation-induced and immune-editing disease appears to cross-react with immune system at different levels including early interactions during carcinogenesis and later cross-talks within the tumor microenvironment. With all that in mind, a reasonable question one might address is whether the SARS-CoV-2 infection and the derived "long lasting inflammatory status" that is frequently observed in patients, might affect the cancer immunosurveillance mechanisms and consequently their risk of developing cancer, as well as the tumor and immune cell behaviors within the inflamed microenvironment. On this context, this review intends to outline and discuss the existing knowledge on SARS-CoV-2-mediated immunomodulation under the prism of changes that might be able to interfere with cancer cell immunoescape and the overall tumor progression and response to conventional therapeutics. Our goal is to highlight a potential interplay between the COVID-19 immunopathology and cancer immune-microenvironment that may pave the way for thorough investigation in the future.
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12
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Chen W, Liu Y, Kang S, Lv X, Fu W, Zhang J, Song C. LINC00092 Modulates Oxidative Stress and Glycolysis of Breast Cancer Cells via Pyruvate Carboxylase-Mediated AKT/mTOR Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5215748. [PMID: 35799892 PMCID: PMC9256459 DOI: 10.1155/2022/5215748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022]
Abstract
Background The discovery of noncoding RNAs (ncRNAs) offers new options for cancer-targeted therapy. This study is aimed at exploring the regulatory function of LINC00092 on breast cancer (BC) oxidative stress and glycolysis, along with internal mechanism concerning pyruvate carboxylase (PC). Methods Bioinformatics analysis was used to explore LINC00092 (or friend leukemia virus integration 1 (FLI1)) expression on BC progression, as well as oxidative stress and glycolysis in BC. After LINC00092 overexpression or silence, BC cell viability, proliferation, migration, invasion, oxidative stress, glycolysis, and AKT/mTOR pathway were detected. Following 2-DG, SC79, or MK2206 treatment, effects of LINC00092 on BC cells were measured. Moreover, regulatory activity of LINC00092 in PC expression was analyzed. Whether PC participated in the modulation of LINC00092 on BC cell functions was explored. Results LINC00092 was lowly expressed in BC and negatively related to BC progression. FLI1 bound to LINC00092 promoter to positively modulate LINC00092. LINC00092 overexpression inhibited BC cell proliferation, migration, invasion, oxidative stress, glycolysis, and AKT/mTOR pathway and likewise suppressed BC growth in vivo. Silence of LINC00092 had opposite influences. 2-DG partially reversed the LINC00092 silence-resulted increase of BC cell proliferation. SC79 alleviated the function of LINC00092 overexpression on BC cell functions. MK2206 had the contrary influence of SC79. Besides, LINC00092 bound to PC to modulate ubiquitination degradation of PC protein. PC took part in the influences of LINC00092 on BC cell functions. Conclusions LINC0092 modulates oxidative stress and glycolysis of BC cells via the PC-mediated AKT/mTOR pathway, which is possibly a target for BC diagnosis and therapy.
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Affiliation(s)
- Wei Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Yushan Liu
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Shaohong Kang
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Xinying Lv
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Wenfen Fu
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Jie Zhang
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province 350001, China
| | - Chuangui Song
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province 350001, China
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Santoleri D, Lim HW, Emmett MJ, Stoute J, Gavin MJ, Sostre-Colón J, Uehara K, Welles JE, Liu KF, Lazar MA, Titchenell PM. Global-run on sequencing identifies Gm11967 as an Akt-dependent long noncoding RNA involved in insulin sensitivity. iScience 2022; 25:104410. [PMID: 35663017 PMCID: PMC9156944 DOI: 10.1016/j.isci.2022.104410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/18/2022] [Accepted: 05/11/2022] [Indexed: 01/07/2023] Open
Abstract
The insulin responsive Akt and FoxO1 signaling axis is a key regulator of the hepatic transcriptional response to nutrient intake. Here, we used global run-on sequencing (GRO-seq) to measure the nascent transcriptional response to fasting and refeeding as well as define the specific role of hepatic Akt and FoxO1 signaling in mediating this response. We identified 599 feeding-regulated transcripts, as well as over 6,000 eRNAs, and mapped their dependency on Akt and FoxO1 signaling. Further, we identified several feeding-regulated lncRNAs, including the lncRNA Gm11967, whose expression was dependent upon the liver Akt-FoxO1 axis. Restoring Gm11967 expression in mice lacking liver Akt improved insulin sensitivity and induced glucokinase protein expression, indicating that Akt-dependent control of Gm11967 contributes to the translational control of glucokinase. More broadly, we have generated a unique genome-wide dataset that defines the feeding and Akt/FoxO1-dependent transcriptional changes in response to nutrient availability.
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Affiliation(s)
- Dominic Santoleri
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew J. Emmett
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julian Stoute
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew J. Gavin
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Jaimarie Sostre-Colón
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Kahealani Uehara
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Jaclyn E. Welles
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mitchell A. Lazar
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul M. Titchenell
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Biomedical Graduate Studies, Philadelphia, PA 19104, USA
- Institute of Diabetes, Obesity and Metabolism, Smilow Center for Translational Research, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Building 421, Philadelphia, PA 19104, USA
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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Abstract
The tumor microenvironment (TME) is a well-recognized system that plays an essential role in tumor initiation, development, and progression. Intense intercellular communication between tumor cells and other cells (especially macrophages) occurs in the TME and is mediated by cell-to-cell contact and/or soluble messengers. Emerging evidence indicates that noncoding RNAs (ncRNAs) are critical regulators of the relationship between cells within the TME. In this review, we provide an update on the regulation of ncRNAs (primarily micro RNAs [miRNAs], long ncRNAs [lncRNAs], and circular RNAs [circRNAs]) in the crosstalk between macrophages and tumor cells in hepatocellular carcinoma (HCC). These ncRNAs are derived from macrophages or tumor cells and act as oncogenes or tumor suppressors, contributing to tumor progression not only by regulating the physiological and pathological processes of tumor cells but also by controlling macrophage infiltration, activation, polarization, and function. Herein, we also explore the options available for clinical therapeutic strategies targeting crosstalk-related ncRNAs to treat HCC. A better understanding of the relationship between macrophages and tumor cells mediated by ncRNAs will uncover new diagnostic biomarkers and pharmacological targets in cancer.
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Xu Y, Sun X, Chen J, Xu J, Wei J. Knockdown of lncRNA ENST00000603829 Inhibits the Proliferation and Invasion of Salivary Gland Pleomorphic Adenoma through Regulating Cyclin D1. Appl Bionics Biomech 2022; 2022:8805305. [PMID: 35528529 PMCID: PMC9068327 DOI: 10.1155/2022/8805305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/02/2022] [Accepted: 04/09/2022] [Indexed: 11/17/2022] Open
Abstract
Objective Salivary gland pleomorphic adenoma (SPA) is a benign neoplasm that can still recur even after radical surgery. To investigate its underlying pathogenesis, here, we examined the significance of lncRNA ENST00000603829 in the proliferation and invasion of SPA. Methods SPA tissues (n = 30) and adjacent normal tissues (NC; n = 30) were collected from SPA patients treated at our hospital from June 2017 to December 2019. The human normal salivary gland epithelial cell line (HSG) and SPA cells (PA30, PA37, and PA116) were cultured. qRT-PCR was used for detecting the expression of cyclin D1 and lncRNA ENST00000603829 in tissues and cells. lncRNA ENST00000603829/cyclin D1 was knocked down or overexpressed in PA116 cells. The expression of cyclin D1 and lncRNA ENST00000603829 in different cell lines was examined using qRT-PCR. Transwell assays and cell counting kit-8 (CCK-8) were used to assess cellular invasion and proliferation. The testing result regarding the apoptosis rate and cell cycle was obtained via flow cytometry. Western blot provided the measurement of cyclin D1 expression in cells. Results We observed an upregulation of lncRNA ENST00000603829 and cyclin D1 expression in SPA tissues and cells. Knockdown of lncRNA ENST00000603829 inhibited cell invasion and proliferation, promoting apoptosis and retaining the cells during the G0/G1 phase. However, such effects of lncRNA ENST00000603829 knockdown were inhibited when cyclin D1 was overexpressed. Conclusion lncRNA ENST00000603829 can promote the occurrence and development of SPA through increasing cyclin D1 expression.
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Affiliation(s)
- Yi Xu
- Department of Stomatology, Taizhou First People's Hospital, Taizhou, Zhejiang 318020, China
| | - Xin Sun
- Department of Stomatology, Taizhou First People's Hospital, Taizhou, Zhejiang 318020, China
| | - Jing Chen
- Department of Stomatology, Taizhou First People's Hospital, Taizhou, Zhejiang 318020, China
| | - Jinbiao Xu
- Department of Stomatology, Taizhou First People's Hospital, Taizhou, Zhejiang 318020, China
| | - Junshui Wei
- Department of Stomatology, Taizhou First People's Hospital, Taizhou, Zhejiang 318020, China
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Han T, Liao A. CASC7: a LncRNA with potential clinical application. Int J Radiat Biol 2022; 98:1510-1518. [PMID: 35311616 DOI: 10.1080/09553002.2022.2055801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AIM To explore the novel lncRNA CASC7 and its potential clinical applications.Long non-coding RNAs (IncRNAs) are defined as non-coding genes with a length exceeding 200 nt. As transcripts of RNA polymerase Il, they have limited coding potential due to the lack of an open reading frame in the gene segment. Research has confirmed that lncRNAs are important biological factors that regulate many life processes in the human body through different mechanisms. This work focused on Cancer Susceptibility Candidate 7 (CASC7), a lncRNA with nuclear and cytoplasmic localization. Publicly available databases show that CASC7 is differentially expressed in human organs as well as in tumor tissues. A study confirmed that CASC7 is abnormally expressed in colorectal cancer, glioma, breast cancer, non-small cell lung cancer and thyroid cancer. In male infertility, asthma and heart failure, it may also be a potential therapeutic target and promising biomarker. CASC7 mainly plays a biological effect through direct or indirect effects of promoting or inhibiting the expression of related genes. Currently, only few studies have assessed CASC7, and its mechanisms are not clear. The main purpose of this review was to examine CASC7 and its possible molecular mechanisms and clinical significance in cancer. CONCLUSION We reviewed the recent research progress of CASC7 and its potential as a diagnostic marker and therapeutic target, and provide an outlook on its future application in terms of mechanism.Key points:CASC7 is a novel lncRNA, for which there are few reports.Aberrant expression of CASC7 may be associated with the emergence and treatment of many clinical diseases, including malignancy.
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Affiliation(s)
- Tao Han
- The First Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Aijun Liao
- The First Affiliated Hospital, Department of Gastroenterology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
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17
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Shapiro JA. What we have learned about evolutionary genome change in the past 7 decades. Biosystems 2022; 215-216:104669. [DOI: 10.1016/j.biosystems.2022.104669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/12/2022]
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18
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Rappaport Y, Falk R, Achache H, Tzur YB. linc-20 and linc-9 do not have compensatory fertility roles in C. elegans. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000524. [PMID: 35169683 PMCID: PMC8837906 DOI: 10.17912/micropub.biology.000524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/15/2022]
Abstract
Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides which are transcribed from regions that do not overlap with protein coding sequences. Reproductive organs express high levels of lincRNAs, yet removal of many lincRNA genes with high and dynamic germline expression did not lead to fertility defects. It was previously suggested this stems from redundant roles of different lincRNA genes. We previously reported engineering C. elegans strains in which we deleted lincRNA genes with high and dynamic expression in the gonad. The individual mutations did not lead to major effects on fertility. Two of those lincRNA genes, linc-9 and linc-20, are highly homologous, suggesting they could perform redundant roles. Here we report that in the double mutant linc-9; linc-20 the brood size and embryonic lethality do not significantly differ from wild-type worms. This could be explained by either lack of fertility roles, or redundancy with other lincRNA genes.
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Affiliation(s)
- Yisrael Rappaport
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Roni Falk
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Hanna Achache
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yonatan B. Tzur
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel,
Correspondence to: Yonatan B. Tzur ()
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19
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Klapproth C, Sen R, Stadler PF, Findeiß S, Fallmann J. Common Features in lncRNA Annotation and Classification: A Survey. Noncoding RNA 2021; 7:77. [PMID: 34940758 PMCID: PMC8708962 DOI: 10.3390/ncrna7040077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are widely recognized as important regulators of gene expression. Their molecular functions range from miRNA sponging to chromatin-associated mechanisms, leading to effects in disease progression and establishing them as diagnostic and therapeutic targets. Still, only a few representatives of this diverse class of RNAs are well studied, while the vast majority is poorly described beyond the existence of their transcripts. In this review we survey common in silico approaches for lncRNA annotation. We focus on the well-established sets of features used for classification and discuss their specific advantages and weaknesses. While the available tools perform very well for the task of distinguishing coding sequence from other RNAs, we find that current methods are not well suited to distinguish lncRNAs or parts thereof from other non-protein-coding input sequences. We conclude that the distinction of lncRNAs from intronic sequences and untranslated regions of coding mRNAs remains a pressing research gap.
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Affiliation(s)
- Christopher Klapproth
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; (C.K.); (P.F.S.); (S.F.)
| | - Rituparno Sen
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), D-97080 Würzburg, Germany;
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; (C.K.); (P.F.S.); (S.F.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig, D-04103 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
- Facultad de Ciencias, Universidad National de Colombia, Bogotá CO-111321, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Sven Findeiß
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; (C.K.); (P.F.S.); (S.F.)
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; (C.K.); (P.F.S.); (S.F.)
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20
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Liao Y, Kuang C, Bao Z, He Y, Gu L, Tao Q, Qiu X, Dipritu G, Kong X, Zhang L, Peng J, Jiang Y, Yin S. Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment. RNA Biol 2021; 18:866-880. [PMID: 34843419 DOI: 10.1080/15476286.2021.2004684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Subcellular localization of transcripts is highly associated with regulation of gene expression, synthesis of protein, and also the development of the human brain cortex. Although many mechanisms are prevalent in the occurrence of neuroinflammation, the mechanisms based on differences in subcellular localization of transcripts have not been explored. To characterize the dynamic profile of nuclear and cytoplasmic transcripts during the progress of haemorrhage-induced neuroinflammation, we isolated nucleo-cytoplasmic RNA fractions of oxyhaemoglobin (oxy-Hb) treated microglia cells and sequenced both fractions. We discovered that cytoplasmic retained genes were the major forces to maintain the neuroinflammatory microenvironment with 10 hub genes and 40 conserved genes were identified. Moreover, antisense RNA Gm44096 and lincRNA Gm47270, which co-expressed with a crowd of inflammatory genes in the cytoplasm, were discovered as regulatory strategies for sustaining the neuroinflammatory microenvironment. Thus, our study provides a new perspective on understanding haemorrhage-induced neuroinflammation and also reveals a mechanism of lncRNA responsible for maintaining the neuroinflammatory microenvironment.
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Affiliation(s)
- Yuyan Liao
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chenghao Kuang
- Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zheng Bao
- Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yijing He
- Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Long Gu
- Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qianke Tao
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiancheng Qiu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ghosh Dipritu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xi Kong
- Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lifang Zhang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Sichuan Clinical Research Center for Neurosurgery, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jianhua Peng
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yong Jiang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Sichuan Clinical Research Center for Neurosurgery, the Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shigang Yin
- Laboratory of Neurological Diseases and Brain Function, the Affiliated Hospital of Southwest Medical University, Luzhou, China.,Institute of Epigenetics and Brain Science, Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, the Affiliated Hospital of Southwest Medical University, Luzhou, China
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Li L, Wei H, Zhang YW, Zhao S, Che G, Wang Y, Chen L. Differential expression of long non-coding RNAs as diagnostic markers for lung cancer and other malignant tumors. Aging (Albany NY) 2021; 13:23842-23867. [PMID: 34670194 PMCID: PMC8580341 DOI: 10.18632/aging.203523] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/02/2021] [Indexed: 02/05/2023]
Abstract
Due to advances in chip and sequencing technology, several types and numbers of long non-coding RNAs (lncRNAs) have been identified. LncRNAs are defined as non-protein-coding RNA molecules longer than 200 nucleotides, and are now thought as a new frontier in the study of human malignant diseases including NSCLC. Diagnosis of numerous malignant tumors has been closely linked to the differential expression of certain lncRNAs. LncRNAs are involved in gene expression regulation at multiple levels of epigenetics, transcriptional regulation, and post-transcriptional regulation. Mutations, deletions, or abnormal expression levels lead to physiological abnormalities, disease occurrence and are closely associated with human tumor diseases. LncRNAs play a crucial role in cancerous processes as either oncogenes or tumor suppressor genes. The expression of lncRNAs can regulate tumor cell in the proliferation, migration, apoptosis, cycle, invasion, and metastasis. As such, lncRNAs are potential diagnostic and treatment targets for cancer. And that, tumor biomarkers need to be detectable in easily accessible body samples, should be characterized by high specificity and sufficient sensitivity. Herein, it is significant clinical importance to screen and supplement new biomarkers for early diagnosis of lung cancer. This study aimed at systematically describing lncRNAs from five aspects based on recent studies: concepts, classification, structure, molecular mechanism, signal pathway, as well as review lncRNA implications in malignant tumor.
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Affiliation(s)
- Li Li
- College of Nursing and Health, Henan University, Kaifeng, Henan 475004, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Haitao Wei
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.,Department of Thoracic Surgery, Huaihe Hospital, Henan University, Kaifeng, Henan 475001, China
| | - Yi Wei Zhang
- College of Nursing and Health, Henan University, Kaifeng, Henan 475004, China
| | - Shizhe Zhao
- Basic Medical College of Henan University, Kaifeng, Henan 475004, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yun Wang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Longqi Chen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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22
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Tian C, Yang Y, Ke Y, Yang L, Zhong L, Wang Z, Huang H. Integrative Analyses of Genes Associated With Right Ventricular Cardiomyopathy Induced by Tricuspid Regurgitation. Front Genet 2021; 12:708275. [PMID: 34603374 PMCID: PMC8485137 DOI: 10.3389/fgene.2021.708275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/06/2021] [Indexed: 12/14/2022] Open
Abstract
Tricuspid regurgitation (TR) induces right ventricular cardiomyopathy, a common heart disease, and eventually leads to severe heart failure and serious clinical complications. Accumulating evidence shows that long non-coding RNAs (lncRNAs) are involved in the pathological process of a variety of cardiovascular diseases. However, the regulatory mechanisms and functional roles of RNA interactions in TR-induced right ventricular cardiomyopathy are still unclear. Accordingly, we performed integrative analyses of genes associated with right ventricular cardiomyopathy induced by TR to study the roles of lncRNAs in the pathogenesis of this disease. In this study, we used high-throughput sequencing data of tissue samples from nine clinical cases of right ventricular myocardial cardiomyopathy induced by TR and nine controls with normal right ventricular myocardium from the Genotype-Tissue Expression database. We identified differentially expressed lncRNAs and constructed a protein-protein interaction and lncRNA-messenger RNA (mRNA) co-expression network. Furthermore, we determined hub lncRNA-mRNA modules related to right ventricular myocardial disease induced by TR and constructed a competitive endogenous RNA network for TR-induced right ventricular myocardial disease by integrating the interaction of lncRNA-miRNA-mRNA. In addition, we analyzed the immune infiltration using integrated data and the correlation of each immune-related gene with key genes of the integrated expression matrix. The present study identified 648 differentially expressed mRNAs, 201 differentially expressed miRNAs, and 163 differentially expressed lncRNAs. Protein-protein interaction network analysis confirmed that ADRA1A, AVPR1B, OPN4, IL-1B, IL-1A, CXCL4, ADCY2, CXCL12, GNB4, CCL20, CXCL8, and CXCL1 were hub genes. CTD-2314B22.3, hsa-miR-653-5p, and KIF17ceRNA; SRGAP3-AS2, hsa-miR-539-5p, and SHANK1; CERS6-AS1, hsa-miR-497-5p, and OPN4; INTS6-AS1, hsa-miR-4262, and NEURL1B; TTN-AS1, hsa-miR-376b-3p, and TRPM5; and DLX6-AS1, hsa-miR-346, and BIRC7 axes were obtained by constructing the ceRNA networks. Through the immune infiltration analysis, we found that the proportion of CD4 and CD8 T cells was about 20%, and the proportion of fibroblasts and endothelial cells was high. Our findings provide some insights into the mechanisms of RNA interaction in TR-induced right ventricular cardiomyopathy and suggest that lncRNAs are a potential therapeutic target for treating right ventricular myocardial disease induced by TR.
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Affiliation(s)
- Chengnan Tian
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China.,The First Affiliated Hospital, Gannan Medical University, Ganzhou, China
| | - Yanchen Yang
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Yingjie Ke
- Nanhai Hospital of Guangdong Provincial People's Hospital, Foshan, China
| | - Liang Yang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Lishan Zhong
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Zhenzhong Wang
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China.,School of Medicine, South China University of Technology, Guangzhou, China
| | - Huanlei Huang
- Department of Cardiovascular Surgery, Guangdong Provincial People's Hospital, Guangzhou, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
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23
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Yousefi L, Osquee HO, Ghotaslou R, Rezaee MA, Pirzadeh T, Sadeghi J, Hemmati F, Yousefi B, Moaddab SY, Yousefi M, Shirmohammadi M, Somi MH, Ganbarov K, Kafil HS. Dysregulation of lncRNA in Helicobacter pylori-Infected Gastric Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6911734. [PMID: 34337048 PMCID: PMC8286195 DOI: 10.1155/2021/6911734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/31/2022]
Abstract
Helicobacter pylori (H. pylori) infection is the most common cause of gastric cancer (GC). This microorganism is genetically diverse; GC is caused by several genetic deregulations in addition to environmental factors and bacterial virulence factors. lncRNAs (long noncoding RNAs) are significant biological macromolecules in GC, have specific functions in diseases, and could be therapeutic targets. Altered lncRNAs can lead to the abnormal expression of adjacent protein-coding genes, which may be important in cancer development. Their mechanisms have not been well understood, so we are going to investigate the risk of GC in a population with both high lncRNA and H. pylori infection.
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Affiliation(s)
- Leila Yousefi
- Student Research Committee, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamid Owaysee Osquee
- Pharmaceutical Nanotechnology Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Pharmaceutical Nanotechnology Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Tahereh Pirzadeh
- Immunology Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadeghi
- Immunology Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Hemmati
- Student Research Committee, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Yousefi
- Stem Cell Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Yaghoub Moaddab
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Stem Cell Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Shirmohammadi
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Somi
- Liver and Gastrointestinal Diseases Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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24
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Li G, Liu X, Smagghe G, Niu J, Wang J. Genome-Wide Characterization and Identification of Long Non-Coding RNAs during the Molting Process of a Spider Mite, Panonychus citri. Int J Mol Sci 2021; 22:6909. [PMID: 34199120 PMCID: PMC8269015 DOI: 10.3390/ijms22136909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 01/26/2023] Open
Abstract
Molting is essential for arthropods to grow. As one of the important arthropod pests in agriculture, key spider mite species (Tetranychus and Panonychus) can normally molt three times from the larva to adult stage within a week. This physiological strategy results in the short lifecycle of spider mites and difficulties in their control in the field. Long non-coding RNAs (lncRNAs) regulate transcriptional editing, cellular function, and biological processes. Thus, analysis of the lncRNAs in the spider mite molting process may provide new insights into their roles in the molting mechanism. For this purpose, we used high-throughput RNA-seq to examine the expression dynamics of lncRNAs and mRNAs in the molting process of different development stages in Panonychus citri. We identified 9199 lncRNAs from 18 transcriptomes. Analysis of the lncRNAs suggested that they were shorter and had fewer exons and transcripts than mRNAs. Among these, 356 lncRNAs were differentially expressed during three molting processes: late larva to early protonymph, late protonymph to early deutonymph, and late deutonymph to early adult. A time series profile analysis of differentially expressed lncRNAs showed that 77 lncRNAs were clustered into two dynamic expression profiles (Pattern a and Pattern c), implying that lncRNAs were involved in the molting process of spider mites. Furthermore, the lncRNA-mRNA co-expression networks showed that several differentially expressed hub lncRNAs were predicted to be functionally associated with typical molting-related proteins, such as cuticle protein and chitin biosynthesis. These data reveal the potential regulatory function of lncRNAs in the molting process and provide datasets for further analysis of lncRNAs and mRNAs in spider mites.
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Affiliation(s)
- Gang Li
- Provincial Key Laboratory of Agricultural Pest Management of Mountainous Regions, Institute of Entomology, Guizhou University, Guiyang 550025, China;
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
| | - Xunyan Liu
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
| | - Guy Smagghe
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Jinzhi Niu
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
| | - Jinjun Wang
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China; (X.L.); (G.S.); (J.N.)
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25
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Yang X, Song D, Zhang J, Yang X, Feng H, Guo J. PRR34-AS1 sponges miR-498 to facilitate TOMM20 and ITGA6 mediated tumor progression in HCC. Exp Mol Pathol 2021; 120:104620. [PMID: 33609562 DOI: 10.1016/j.yexmp.2021.104620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/03/2021] [Accepted: 02/12/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The researches on PRR34 antisense RNA 1 (PRR34-AS1) have been limited. Both translocase of outer mitochondrial membrane 20 (TOMM20) and integrin subunit alpha 6 (ITGA6) have been proven to facilitate cancer progression. Whether TOMM20 or ITGA6 affects hepatocellular carcinoma (HCC) progression has never been investigated. Some studies showed that microRNA 498 (miR-498) can suppress HCC progression. Additionally, the influence of ceRNA network (including PRR34-AS1, miR-498, and TOMM20 or ITGA6) on HCC progression has not been inquired into yet. METHODS The knockdown or overexpression efficiency was validated via RT-qPCR. Also, RT-qPCR was applied to detect the expression of PRR34-AS1, miR-498, TOMM20, and ITGA6. Cell proliferation in HCC was tested via EdU and colony formation assays. Transwell assays presented the migratory and invasive capabilities of HCC cells. Subcellular fractionation and FISH assays showed the subcellular localization of PRR34-AS1. RNA pull down and luciferase reporter assays were performed to explore whether miR-498 combines with PRR34-AS1, TOMM20 or ITGA6. Western blot was conducted to detect protein expression. Rescue experiments were conducted to verify the relationship among PRR34-AS1, miR-498, TOMM20, and ITGA6. RESULTS The expressions of PRR34-AS1, TOMM20, and ITGA6 were markedly high in HCC cell lines while miR-498 was lowly expressed. PRR34-AS1, TOMM20, and ITGA6 promoted HCC progression while miR-498 suppressed cell proliferation, migration, and invasion in HCC. Furthermore, PRR34-AS1, TOMM20, and ITGA6 combined with miR-498. CONCLUSION PRR34-AS1 facilitates HCC progression by regulating miR-498/TOMM20/ITGA6 axis.
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Affiliation(s)
- Xuejing Yang
- Department of Medical Oncology, Shanxi Bethune Hospital& Shanxi Academy of Medical Sciences, Taiyuan 030032, China
| | - Dong Song
- Department of Medical Oncology, Shanxi Bethune Hospital& Shanxi Academy of Medical Sciences, Taiyuan 030032, China
| | - Junping Zhang
- Department of Medical Oncology, Shanxi Bethune Hospital& Shanxi Academy of Medical Sciences, Taiyuan 030032, China
| | - Xuejing Yang
- Department of Medical Oncology, Shanxi Bethune Hospital& Shanxi Academy of Medical Sciences, Taiyuan 030032, China
| | - Huijing Feng
- Department of Medical Oncology, Shanxi Bethune Hospital& Shanxi Academy of Medical Sciences, Taiyuan 030032, China
| | - Jianian Guo
- Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China.
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26
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Zheng W, Chu Q, Xu T. The long noncoding RNA NARL regulates immune responses via microRNA-mediated NOD1 downregulation in teleost fish. J Biol Chem 2021; 296:100414. [PMID: 33581111 PMCID: PMC7966872 DOI: 10.1016/j.jbc.2021.100414] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
Increasing evidence shows that the long noncoding RNA (lncRNA) is a major regulator and participates in the regulation of various physiological and pathological processes, such as cell proliferation, differentiation, metastasis, and apoptosis. Unlike mammals, however, the study of lncRNA in lower invertebrates is just beginning and the extent of lncRNA-mediate regulation remains unclear. Here, we for the first time identify an lncRNA, termed nucleotide oligomerization domain 1 (NOD1) antibacterial and antiviral-related lncRNA (NARL), as a key regulator for innate immunity in teleost fish. We found that NOD1 plays an important role in the antibacterial and antiviral process in fish and that the microRNA miR-217-5p inhibits NOD1 expression and thus weakens the NF-κB and the IRF3-driven signaling pathway. Furthermore, our results indicated that NARL functions as a competing endogenous RNA (ceRNA) for miR-217-5p to regulate protein abundance of NOD1; thus, invading microorganisms are eliminated and immune responses are promoted. Our study also demonstrates the regulation mechanism that lncRNA NARL can competitive adsorption miR-217-5p to regulate the miR-217-5p/NOD1 axis is widespread in teleost fish. Taken together, our results reveal that NARL in fish is a critical positive regulator of innate immune responses to viral and bacterial infection by suppressing a feedback to NOD1-NF-κB/IRF3-mediated signaling.
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Affiliation(s)
- Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qing Chu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China.
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27
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Gao Q, Xiong Z, Larsen RS, Zhou L, Zhao J, Ding G, Zhao R, Liu C, Ran H, Zhang G. High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis. Gigascience 2020; 9:6034789. [PMID: 33319913 PMCID: PMC7736795 DOI: 10.1093/gigascience/giaa143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/11/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
Background Ants with complex societies have fascinated scientists for centuries. Comparative genomic and transcriptomic analyses across ant species and castes have revealed important insights into the molecular mechanisms underlying ant caste differentiation. However, most current ant genomes and transcriptomes are highly fragmented and incomplete, which hinders our understanding of the molecular basis for complex ant societies. Findings By hybridizing Illumina, Pacific Biosciences, and Hi-C sequencing technologies, we de novo assembled a chromosome-level genome for Monomorium pharaonis, with a scaffold N50 of 27.2 Mb. Our new assembly provides better resolution for the discovery of genome rearrangement events at the chromosome level. Analysis of full-length isoform sequencing (ISO-seq) suggested that ∼15 Gb of ISO-seq data were sufficient to cover most expressed genes, but the number of transcript isoforms steadily increased with sequencing data coverage. Our high-depth ISO-seq data greatly improved the quality of gene annotation and enabled the accurate detection of alternative splicing isoforms in different castes of M. pharaonis. Comparative transcriptome analysis across castes based on the ISO-seq data revealed an unprecedented number of transcript isoforms, including many caste-specific isoforms. We also identified a number of conserved long non-coding RNAs that evolved specifically in ant lineages and several that were conserved across insect lineages. Conclusions We produced a high-quality chromosome-level genome for M. pharaonis, which significantly improved previous short-read assemblies. Together with full-length transcriptomes for all castes, we generated a highly accurate annotation for this ant species. These long-read sequencing results provide a useful resource for future functional studies on the genetic mechanisms underlying the evolution of social behaviors and organization in ants.
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Affiliation(s)
- Qionghua Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zijun Xiong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Rasmus Stenbak Larsen
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Long Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Jie Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guo Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.,Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Chengyuan Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Hao Ran
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.,Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
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28
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Chen C, Shi X, Zhou T, Li W, Li S, Bai G. Full-length transcriptome analysis and identification of genes involved in asarinin and aristolochic acid biosynthesis in medicinal plant Asarum sieboldii. Genome 2020; 64:639-653. [PMID: 33320770 DOI: 10.1139/gen-2020-0095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Asarum sieboldii, a well-known traditional Chinese medicinal herb, is used for curing inflammation and ache. It contains both the bioactive ingredient asarinin and the toxic compound aristolochic acid. To address further breeding demand, genes involved in the biosynthetic pathways of asarinin and aristolochic acid should be explored. Therefore, the full-length transcriptome of A. sieboldii was sequenced using PacBio Iso-Seq to determine the candidate transcripts that encode the biosynthetic enzymes of asarinin and aristolochic acid. In this study, 63 023 full-length transcripts were generated with an average length of 1371 bp from roots, stems, and leaves, of which 49 593 transcripts (78.69%) were annotated against public databases. Furthermore, 555 alternative splicing (AS) events, 10 869 long noncoding RNAs (lncRNAs) as well as their 11 291 target genes, and 17 909 simple sequence repeats (SSRs) were identified. The data also revealed 97 candidate transcripts related to asarinin metabolism, of which six novel genes that encoded enzymes involved in asarinin biosynthesis were initially reported. In addition, 56 transcripts related to aristolochic acid biosynthesis were also identified, including CYP81B. In summary, these transcriptome data provide a useful resource to study gene function and genetic engineering in A. sieboldii.
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Affiliation(s)
- Chen Chen
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Xinwei Shi
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Tao Zhou
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76 Yanta West Road, 710061, Xi'an City, Shaanxi Province, China
| | - Weimin Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Sifeng Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Guoqing Bai
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
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29
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Palazzo AF, Koonin EV. Functional Long Non-coding RNAs Evolve from Junk Transcripts. Cell 2020; 183:1151-1161. [PMID: 33068526 DOI: 10.1016/j.cell.2020.09.047] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/20/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022]
Abstract
Transcriptome studies reveal pervasive transcription of complex genomes, such as those of mammals. Despite popular arguments for functionality of most, if not all, of these transcripts, genome-wide analysis of selective constraints indicates that most of the produced RNA are junk. However, junk is not garbage. On the contrary, junk transcripts provide the raw material for the evolution of diverse long non-coding (lnc) RNAs by non-adaptive mechanisms, such as constructive neutral evolution. The generation of many novel functional entities, such as lncRNAs, that fuels organismal complexity does not seem to be driven by strong positive selection. Rather, the weak selection regime that dominates the evolution of most multicellular eukaryotes provides ample material for functional innovation with relatively little adaptation involved.
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Affiliation(s)
- Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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30
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Long noncoding RNA AANCR modulates innate antiviral responses by blocking miR-210-dependent MITA downregulation in teleost fish, Miichthys miiuy. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1131-1148. [PMID: 32997329 DOI: 10.1007/s11427-020-1789-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/03/2020] [Indexed: 01/17/2023]
Abstract
Viral infection induces the initiation of antiviral effectors and cytokines which are critical mediators of innate antiviral responses. The critical molecular determinants are responsible for triggering an appropriate immune response. Long noncoding RNAs (lncRNAs) have emerged as new gene modulators involved in various biological processes, while how lncRNAs operate in lower vertebrates are still unknown. Here, we discover a long noncoding RNA, termed antiviral-associated long noncoding RNA (AANCR), as a novel regulator for innate antiviral responses in teleost fish. The results indicate that fish MITA plays an essential role in host antiviral responses and inhibition of Siniperca chuatsi rhabdovirus (SCRV) production. miR-210 reduces MITA expression and suppress MITA-mediated antiviral responses, which may help viruses evade host antiviral responses. Further, AANCR functions as a competing endogenous RNA (ceRNA) for miR-210 to control protein abundance of MITA, thereby inhibiting SCRV replication and promoting antiviral responses. Our data not only shed new light on understanding the function role of lncRNA in biological processes in teleost fish, but confirmed the hypothesis that ceRNA networks exist widely in vertebrates.
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31
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Kyriazi AA, Papiris E, Kitsos Kalyvianakis K, Sakellaris G, Baritaki S. Dual Effects of Non-Coding RNAs (ncRNAs) in Cancer Stem Cell Biology. Int J Mol Sci 2020; 21:ijms21186658. [PMID: 32932969 PMCID: PMC7556003 DOI: 10.3390/ijms21186658] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of cancer stem cells (CSCs) as initiators of carcinogenesis has revolutionized the era of cancer research and our perception for the disease treatment options. Additional CSC features, including self-renewal and migratory and invasive capabilities, have further justified these cells as putative diagnostic, prognostic, and therapeutic targets. Given the CSC plasticity, the identification of CSC-related biomarkers has been a serious burden in CSC characterization and therapeutic targeting. Over the past decades, a compelling amount of evidence has demonstrated critical regulatory functions of non-coding RNAs (ncRNAs) on the exclusive features of CSCs. We now know that ncRNAs may interfere with signaling pathways, vital for CSC phenotype maintenance, such as Notch, Wnt, and Hedgehog. Here, we discuss the multifaceted contribution of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), as representative ncRNA classes, in sustaining the CSC-like traits, as well as the underlying molecular mechanisms of their action in various CSC types. We further discuss the use of CSC-related ncRNAs as putative biomarkers of high diagnostic, prognostic, and therapeutic value.
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Affiliation(s)
- Athina A. Kyriazi
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - Efstathios Papiris
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - Konstantinos Kitsos Kalyvianakis
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - George Sakellaris
- Surgery Unit, University General Hospital, 71500 Heraklion (PAGNH), Greece;
| | - Stavroula Baritaki
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
- Correspondence: ; Tel.: +30-2810394727
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Systematic analysis of long intergenic non-coding RNAs in C. elegans germline uncovers roles in somatic growth. RNA Biol 2020; 18:435-445. [PMID: 32892705 DOI: 10.1080/15476286.2020.1814549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides that are transcribed from non-coding loci yet undergo biosynthesis similar to coding mRNAs. The disproportional number of lincRNAs expressed in testes suggests that lincRNAs are important during gametogenesis, but experimental evidence has implicated very few lincRNAs in this process. We took advantage of the relatively limited number of lincRNAs in the genome of the nematode Caenorhabditis elegans to systematically analyse the functions of lincRNAs during meiosis. We deleted six lincRNA genes that are highly and dynamically expressed in the C. elegans gonad and tested the effects on central meiotic processes. Surprisingly, whereas the lincRNA deletions did not strongly impact fertility, germline apoptosis, crossovers, or synapsis, linc-4 was required for somatic growth. Slower growth was observed in linc-4-deletion mutants and in worms depleted of linc-4 using RNAi, indicating that linc-4 transcripts are required for this post-embryonic process. Unexpectedly, analysis of worms depleted of linc-4 in soma versus germline showed that the somatic role stems from linc-4 expression in germline cells. This unique feature suggests that some lincRNAs, like some small non-coding RNAs, are required for germ-soma interactions.
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Li T, Chen B, Yang P, Wang D, Du B, Kang L. Long Non-coding RNA Derived from lncRNA-mRNA Co-expression Networks Modulates the Locust Phase Change. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:664-678. [PMID: 32866667 PMCID: PMC8377017 DOI: 10.1016/j.gpb.2020.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/14/2020] [Accepted: 05/31/2020] [Indexed: 12/19/2022]
Abstract
Long non-coding RNAs (lncRNAs) regulate various biological processes ranging from gene expression to animal behavior. Although protein-coding genes, microRNAs, and neuropeptides play important roles in the regulation of phenotypic plasticity in migratory locust, empirical studies on the function of lncRNAs in this process remain limited. Here, we applied high-throughput RNA-seq to compare the expression patterns of lncRNAs and mRNAs in the time course of locust phase change. We found that lncRNAs responded more rapidly at the early stages of phase transition. Functional annotations demonstrated that early changed lncRNAs employed different pathways in isolation and crowding phases to cope with changes in the population density. Two overlapping hub lncRNA loci in the crowding and isolation networks were screened for functional verification. One of them, LNC1010057, was validated as a potential regulator of locust phase change. This work offers insights into the molecular mechanism underlying locust phase change and expands the scope of lncRNA functions in animal behavior.
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Affiliation(s)
- Ting Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Chen
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Depin Wang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baozhen Du
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; College of Life Sciences, Hebei University, Baoding 071002, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Genome-Wide Analysis Reveals Changes in Long Noncoding RNAs in the Differentiation of Canine BMSCs into Insulin-Producing Cells. Int J Mol Sci 2020; 21:ijms21155549. [PMID: 32756402 PMCID: PMC7432238 DOI: 10.3390/ijms21155549] [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: 07/01/2020] [Revised: 07/24/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been extensively explored over the past decade, including mice and humans. However, their impact on the transdifferentiation of canine bone marrow mesenchymal stem cells (cBMSCs) into insulin-producing cells (IPCs) is largely unknown. In this study, we used a three-step induction procedure to induce cBMSCs into IPCs, and samples (two biological replicates each) were obtained after each step; the samples consisted of “BMSCs” (B), “stage 1” (S1), “stage 2” (S2), “stage 3” (S3), and “islets” (I). After sequencing, 15,091 lncRNAs were identified, and we screened 110, 41, 23, and 686 differentially expressed lncRNAs (padjusted < 0.05) in B vs. S1, S1 vs. S2, S2 vs. S3, and I vs. S3 pairwise comparisons, respectively. In lncRNA target prediction, there were 166,623 colocalized targets and 2,976,362 correlated targets. Gene Ontology (GO) analysis showed that binding represented the main molecular functions of both the cis- and trans-modes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that the insulin signaling pathway, Rap1 signaling pathway, tight junctions, MAPK signaling pathway, and cell cycle were enriched for these relative genes. The expression of lncRNAs was verified using qRT-PCR. This study provides a lncRNA catalog for future research concerning the mechanism of the transdifferentiation of cBMSCs into IPCs.
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Chu Q, Xu T, Zheng W, Chang R, Zhang L. Long noncoding RNA MARL regulates antiviral responses through suppression miR-122-dependent MAVS downregulation in lower vertebrates. PLoS Pathog 2020; 16:e1008670. [PMID: 32678830 PMCID: PMC7390449 DOI: 10.1371/journal.ppat.1008670] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/29/2020] [Accepted: 05/31/2020] [Indexed: 12/19/2022] Open
Abstract
Increasing evidence suggests important roles for long noncoding RNAs (lncRNAs) as new gene modulators involved in various biological processes. However, the function roles of lncRNAs in lower vertebrates are still unknown. Here, we firstly identify a lncRNA, named MAVS antiviral-related lncRNA (MARL), as a key regulator for antiviral immunity in teleost fish. The results indicate that fish MAVS play essential roles in host antiviral responses and inhibition of Siniperca chuatsi rhabdovirus (SCRV) replication. miR-122 reduces MAVS expression and suppress MAVS-mediated antiviral responses, which may help viruses evade host antiviral responses. Further, MARL functions as a competing endogenous RNA (ceRNA) for miR-122 to control protein abundance of MAVS, thereby inhibiting SCRV replication and promoting antiviral responses. Our data not only shed new light on understanding the function role of lncRNA in biological processes in lower vertebrates, but confirmed the hypothesis that ceRNA regulatory networks exist widely in vertebrates. Increasing evidence indicates that lncRNAs participate in the regulation of various biological processes, especially innate and adaptive immunity. However, the relationship between lncRNAs and host antiviral responses remains largely unknown, particularly in lower vertebrates. Our results provided the first direct evidence that a lncRNA, termed MAVS antiviral-related lncRNA (MARL), acts as a key regulator for antiviral immunity in lower vertebrates. lncRNAs have been identified to function as competing endogenous RNAs (ceRNAs) and cross-talk with mRNAs by competing shared for miRNAs. Such ceRNAs regulate the distribution of miRNA molecules on their targets and thereby apply an additional level of post-transcriptional regulation. In our study, MARL functions as a ceRNA for miR-122 to control protein abundance of fish MAVS, thereby inhibiting virus replication and promoting antiviral responses. This is the first study to demonstrate ceRNA regulatory networks existing in lower vertebrates, which can provide new insights into understanding the effects of lncRNAs on host-virus interactions.
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Affiliation(s)
- Qing Chu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
- * E-mail:
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai, China
| | - Renjie Chang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Lei Zhang
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
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Wang F, Luo L, Gu Z, Yang N, Wang L, Gao C. Integrative Analysis of Long Noncoding RNAs in Patients with Graft-versus-Host Disease. Acta Haematol 2020; 143:533-551. [PMID: 32289782 DOI: 10.1159/000505255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/04/2019] [Indexed: 01/17/2023]
Abstract
BACKGROUND Chronic graft-versus-host disease (cGVHD) remains a major cause of late non-recurrence mortality despite remarkable improvements in the field of allogeneic hematopoietic stem cell transplantation. Although recent studies have found that B-cell receptor (BCR)-activated B cells contribute to pathogenesis in cGVHD, the specific molecular mechanisms of B cells in this process remain unclear. METHODS In our study, human long noncoding RNA (lncRNA) microarrays and bioinformatic analysis were performed to identify different expressions of lncRNAs in peripheral blood B cells from cGVHD patients compared with healthy ones. The differential expression of lncRNA was confirmed in additional samples by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS The microarray analysis revealed that 106 of 198 differentially expressed lncRNAs were upregulated and 92 were downregulated in cGVHD patients compared with healthy controls. Intergenic lncRNAs accounted for the majority of differentially expressed lncRNAs. A KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis showed that the differentially expressed mRNAs, which were coexpressed with lncRNA, between the cGVHD group and the healthy group were significantly enriched in the BCR signaling pathway. Further analysis of the BCR signaling pathway and its coexpression network identified three lncRNAs with the strongest correlation with BCR signaling and cGVHD, as well as a series of protein-coding genes and transcription factors associated with them. The three candidate lncRNAs were further validated in another group of cGVHD patients by qRT-PCR. CONCLUSIONS This is the first study on the correlation between lncRNA and cGVHD using lncRNA microarray analysis. Our study provides novel enlightenment in exploring the molecular pathogenesis of cGVHD.
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Affiliation(s)
- Feiyan Wang
- Medical School, Nankai University, Tianjin, China
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Lan Luo
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Zhenyang Gu
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Nan Yang
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Li Wang
- Department of Hematology and Oncology, Laoshan Branch, Chinese PLA 401 Hospital, Qingdao, China
| | - Chunji Gao
- Medical School, Nankai University, Tianjin, China,
- Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China,
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Yang CX, Wang PC, Liu S, Miao JK, Liu XM, Miao YL, Du ZQ. Long noncoding RNA 2193 regulates meiosis through global epigenetic modification and cytoskeleton organization in pig oocytes. J Cell Physiol 2020; 235:8304-8318. [PMID: 32239703 DOI: 10.1002/jcp.29675] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/10/2020] [Indexed: 12/13/2022]
Abstract
Long noncoding RNAs (lncRNAs) regulate a variety of physiological and pathological processes. However, the biological function of lncRNAs in mammalian germ cells remains largely unexplored. Here we identified one novel lncRNA (lncRNA2193) from single-cell RNA sequencing performed on porcine oocytes and investigated its function in oocyte meiosis. During in vitro maturation (IVM), from germinal vesicle (GV, 0 hr), GV breakdown (GVBD, 24 hr), to metaphase II stage (MII, 44 hr), the transcriptional abundance of lncRNA2193 remained stable and high. LncRNA2193 interference by small interfering RNA microinjection into porcine GV oocytes could significantly inhibit rates of GVBD and the first polar body extrusion, but enhance the rates of oocytes with a nuclear abnormality. Moreover, lncRNA2193 knockdown disturbed cytoskeletal organization (F-actin and spindle), and decreased DNA 5-methylcytosine (5mC) and histone trimethylation (H3K4me3, H3K9me3, H3K27me3, and H3K36me3) levels. The lncRNA2193 downregulation induced a decrease of 5mC level could be partially due to the reduction of DNA methyltransferase 3A and 3B, and the elevation of 5mC-hydroxylase ten-11 translocation 2 (TET2). After parthenogenetic activation of MII oocytes, parthenotes exhibited higher fragmentation but lower cleavage rates in the lncRNA2193 downregulated group. However, lncRNA2193 interference performed on mature MII oocytes and parthenotes at 1-cell stage did not affect the cleavage and blasctocyst rates of pathenotes. Taken together, lncRNA2193 plays an important role in porcine oocyte maturation, providing more insights for relevant investigations on mammalian germ cells.
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Affiliation(s)
- Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Pei-Chao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Shuai Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Jia-Kun Miao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiao-Man Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang, China
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38
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Zheng Z, Xiong X, Zhang J, Lv S, Jiao Y, Deng Y. The global effects of PmRunt co-located and co-expressed with a lincRNA lncRunt in pearl oyster Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2019; 91:209-215. [PMID: 31112790 DOI: 10.1016/j.fsi.2019.05.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Runt related transcription factors as trans-acting elements play critical roles in the developmental control of cell fate, hematopoiesis, bone formation and cancers. In previous study, the homologue of runt related transcription factor PmRunt has been identified from pearl oyster Pinctada fucata martensii and considered to play an important role in nacre formation. In this study, we used the same samples to perform RNA-seq to detect the global effects after the decrease of PmRunt expression. The transcription levels of several nacre shell matrix protein (NSMP) genes were significantly changed and the potential compensatory effect could happen internal gene families. Downregulation of PmRunt could also influence the biosynthesis of NSMPs through affecting amino acid metabolism, translation, protein processing and export. The inhibition of PmRunt also possibly affected the expression of caspases, IAPs and C1qs that related to apoptosis and immune. In addition, PmRunt highly expressed at 12 h and 12 d after transplantation in hemolymph, which was corresponded to transplantation immunity immune response and the morphology of pearl sac, suggested the cross-talk of biomineralization-immune regulation in hemocytes. Furthermore, a lincRNA (LncRunt) that co-located with PmRunt was identified and showed a significantly relative expression with PmRunt, which suggested the potential regulation. Therefore, these findings provided new idea to find the regulation targets of runt-related transcription factors and offers evidence of lncRNAs in potential biomineralization-immune regulation.
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Affiliation(s)
- Zhe Zheng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Technology Research Center for Pearl Aquaculture and Process, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Xinwei Xiong
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Technology Research Center for Pearl Aquaculture and Process, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Jinghong Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Shijin Lv
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Technology Research Center for Pearl Aquaculture and Process, Guangdong Ocean University, Zhanjiang, 524025, China.
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Guangdong Technology Research Center for Pearl Aquaculture and Process, Guangdong Ocean University, Zhanjiang, 524025, China.
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Antonov IV, Mazurov E, Borodovsky M, Medvedeva YA. Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools. Brief Bioinform 2019; 20:551-564. [PMID: 29697742 DOI: 10.1093/bib/bby032] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/26/2018] [Indexed: 01/22/2023] Open
Abstract
The genomes of mammalian species are pervasively transcribed producing as many noncoding as protein-coding RNAs. There is a growing body of evidence supporting their functional role. Long noncoding RNA (lncRNA) can bind both nucleic acids and proteins through several mechanisms. A reliable computational prediction of the most probable mechanism of lncRNA interaction can facilitate experimental validation of its function. In this study, we benchmarked computational tools capable to discriminate lncRNA from mRNA and predict lncRNA interactions with other nucleic acids. We assessed the performance of 9 tools for distinguishing protein-coding from noncoding RNAs, as well as 19 tools for prediction of RNA-RNA and RNA-DNA interactions. Our conclusions about the considered tools were based on their performances on the entire genome/transcriptome level, as it is the most common task nowadays. We found that FEELnc and CPAT distinguish between coding and noncoding mammalian transcripts in the most accurate manner. ASSA, RIBlast and LASTAL, as well as Triplexator, turned out to be the best predictors of RNA-RNA and RNA-DNA interactions, respectively. We showed that the normalization of the predicted interaction strength to the transcript length and GC content may improve the accuracy of inferring RNA interactions. Yet, all the current tools have difficulties to make accurate predictions of short-trans RNA-RNA interactions-stretches of sparse contacts. All over, there is still room for improvement in each category, especially for predictions of RNA interactions.
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Affiliation(s)
- Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Moscow, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | | | - Mark Borodovsky
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Moscow, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation.,Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russian Federation
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40
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Guo N, Sun Q, Fu D, Zhang Y. Long non-coding RNA UCA1 promoted the growth of adrenocortical cancer cells via modulating the miR-298-CDK6 axis. Gene 2019; 703:26-34. [DOI: 10.1016/j.gene.2019.03.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 12/21/2022]
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Hu Y, Li S, Zou Y. Knockdown of LncRNA H19 Relieves LPS-Induced Damage by Modulating miR-130a in Osteoarthritis. Yonsei Med J 2019; 60:381-388. [PMID: 30900425 PMCID: PMC6433564 DOI: 10.3349/ymj.2019.60.4.381] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/21/2018] [Accepted: 12/29/2018] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Osteoarthritis (OA) is a commonly occurring illness without a definitive cure, at present. Long non-coding RNAs (lncRNAs) have been widely confirmed to be involved in the modulation of OA progression. This study aimed to investigate the role and mechanism of lncRNA H19 in OA. MATERIALS AND METHODS Abundances of H19 and microRNA-130a (miR-130a) in lipopolysaccharide (LPS)-treated C28/I2 cells were measured by reverse-transcription quantitative PCR (RT-qPCR). CCK-8 and flow cytometry analyses were carried out to assess cell viability and apoptosis. Starbase online software was used to predict the putative binding sites between H19 and miR-130a. Luciferase reporter, RNA pull down, and RT-qPCR were performed to analyze the true interaction between H19 and miR-130a. RESULTS A notably dose-dependent elevation of H19 levels was observed in LPS-treated C28/I2 cells. Knockdown of H19 ameliorated the injury of LPS-induced C28/I2 cells, reflected by induced viability, decreased apoptosis, and reduced inflammatory factor secretions. Moreover, H19 negatively regulated the expression of miR-130a via acting as a molecular sponge for miR-130a. The stimulatory effects of H19 on cell damage were abolished following the restoration of miR-130a. CONCLUSION LncRNA H19 aggravated the injury of LPS-induced C28/I2 cells by sponging miR-130a, hinting a novel regulatory mechanism and a potential therapeutic target for OA.
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Affiliation(s)
- Yi Hu
- Department of Orthopedics, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
- Department of Orthopedics, Chongqing Dongnan Hospital, Chongqing, China
| | - Sukai Li
- Department One of Orthopedics, Dianjiang People's Hospital of Chongqing, Dianjiang County, Chongqing, China
| | - Yonggen Zou
- Department of Orthopedics, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.
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Zhang L, Fang WJ, Zhang KM, Jiang WW, Chen M, Liao WQ, Pan WH. Long noncoding RNA expression profile from cryptococcal meningitis patients identifies DPY19L1p1 as a new disease marker. CNS Neurosci Ther 2019; 25:772-782. [PMID: 30767376 PMCID: PMC6515894 DOI: 10.1111/cns.13109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 12/14/2022] Open
Abstract
AIMS LncRNAs play a vital role in the pathological and physiological process. This study aimed to explore the involvement of lncRNAs in cryptococcal meningitis. METHODS Microarray was performed in cryptococcal meningitis patients, and then, GO and KEGG pathways were analyzed. Coexpression relationship between lncRNA and mRNA was explored. The expressions of the lncRNAs and mRNAs, and their changes after treatment were detected by PCR. RESULTS A total of 325 mRNAs (201 upregulated and 124 downregulated) and 497 lncRNAs (263 upregulated and 234 downregulated) were identified. The top three enriched GO terms for the mRNAs were arachidonic acid binding, activin receptor binding, and replication fork protection complex. The top three pathways in KEGG were asthma, one carbon pool by folate, and allograft rejection. A total of 305 coexpression relationships were found between 108 lncRNAs and 87 mRNAs. LncRNA-DPY19L1p1 was significantly increased in patients and decreased after treatment. ROC analysis revealed DPY19L1p1 was a potential diagnostic marker (AUCROC = 0.9389). Furthermore, the target genes of DPY19L1p1 in cis or trans regulation were mainly involved in immune-related pathways like the interleukin signaling pathway. CONCLUSIONS This study analyzed the differential lncRNA profile in cryptococcal meningitis patients and revealed DPY19L1p1 could be used for treatment evaluation and disease diagnosis.
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Affiliation(s)
- Lei Zhang
- Department of Dermatology and Venereology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wen-Jie Fang
- Department of Dermatology and Venereology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ke-Ming Zhang
- Department of Dermatology and Venereology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wei-Wei Jiang
- Department of Dermatology and Venereology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Min Chen
- Department of Dermatology and Venereology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wan-Qing Liao
- Department of Dermatology and Venereology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wei-Hua Pan
- Department of Dermatology and Venereology, Changzheng Hospital, Second Military Medical University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
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Baskozos G, Dawes JM, Austin JS, Antunes-Martins A, McDermott L, Clark AJ, Trendafilova T, Lees JG, McMahon SB, Mogil JS, Orengo C, Bennett DL. Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury. Pain 2019; 160:463-485. [PMID: 30335683 PMCID: PMC6343954 DOI: 10.1097/j.pain.0000000000001416] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/26/2016] [Accepted: 10/09/2018] [Indexed: 12/19/2022]
Abstract
Dorsal root ganglion (DRG) neurons provide connectivity between peripheral tissues and the spinal cord. Transcriptional plasticity within DRG sensory neurons after peripheral nerve injury contributes to nerve repair but also leads to maladaptive plasticity, including the development of neuropathic pain. This study presents tissue and neuron-specific expression profiling of both known and novel long noncoding RNAs (LncRNAs) in the rodent DRG after nerve injury. We have identified a large number of novel LncRNAs expressed within the rodent DRG, a minority of which were syntenically conserved between the mouse, rat, and human, and including, both intergenic and antisense LncRNAs. We have also identified neuron type-specific LncRNAs in the mouse DRG and LncRNAs that are expressed in human IPS cell-derived sensory neurons. We show significant plasticity in LncRNA expression after nerve injury, which in mice is strain and gender dependent. This resource is publicly available and will aid future studies of DRG neuron identity and the transcriptional landscape in both the naive and injured DRG. We present our work regarding novel antisense and intergenic LncRNAs as an online searchable database, accessible from PainNetworks (http://www.painnetworks.org/). We have also integrated all annotated gene expression data in PainNetworks, so they can be examined in the context of their protein interactions.
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Affiliation(s)
- Georgios Baskozos
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - John M. Dawes
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Jean S. Austin
- Departments of Psychology and
- Anesthesia, Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Ana Antunes-Martins
- Neurorestoration Group, Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Lucy McDermott
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alex J. Clark
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Teodora Trendafilova
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Jon G. Lees
- Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Stephen B. McMahon
- Neurorestoration Group, Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, United Kingdom
| | - Jeffrey S. Mogil
- Departments of Psychology and
- Anesthesia, Alan Edwards Centre for Research on Pain, McGill University, Montreal, QC, Canada
| | - Christine Orengo
- Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - David L. Bennett
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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44
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Zhao X, Bhattacharyya A. Human Models Are Needed for Studying Human Neurodevelopmental Disorders. Am J Hum Genet 2018; 103:829-857. [PMID: 30526865 DOI: 10.1016/j.ajhg.2018.10.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/09/2018] [Indexed: 12/19/2022] Open
Abstract
The analysis of animal models of neurological disease has been instrumental in furthering our understanding of neurodevelopment and brain diseases. However, animal models are limited in revealing some of the most fundamental aspects of development, genetics, pathology, and disease mechanisms that are unique to humans. These shortcomings are exaggerated in disorders that affect the brain, where the most significant differences between humans and animal models exist, and could underscore failures in targeted therapeutic interventions in affected individuals. Human pluripotent stem cells have emerged as a much-needed model system for investigating human-specific biology and disease mechanisms. However, questions remain regarding whether these cell-culture-based models are sufficient or even necessary. In this review, we summarize human-specific features of neurodevelopment and the most common neurodevelopmental disorders, present discrepancies between animal models and human diseases, demonstrate how human stem cell models can provide meaningful information, and discuss the challenges that exist in our pursuit to understand distinctively human aspects of neurodevelopment and brain disease. This information argues for a more thoughtful approach to disease modeling through consideration of the valuable features and limitations of each model system, be they human or animal, to mimic disease characteristics.
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Affiliation(s)
- Xinyu Zhao
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA.
| | - Anita Bhattacharyya
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison WI 53705, USA.
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45
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Wang Y, Ye W, Wang Y. Genome-wide identification of long non-coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae. MOLECULAR PLANT PATHOLOGY 2018; 19:2177-2186. [PMID: 29665235 PMCID: PMC6638102 DOI: 10.1111/mpp.12692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/14/2018] [Accepted: 04/12/2018] [Indexed: 05/08/2023]
Abstract
Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in oomycete plant pathogens, which cause devastating damage to the economy and ecosystems. We used strand-specific RNA sequencing (RNA-seq) to generate a computational pipeline to identify lncRNAs in Phytophthora sojae, a model oomycete plant pathogen. In total, 940 lncRNAs with 1010 isoforms were identified from RNA-seq data obtained from four representative stages of P. sojae. The lncRNAs had shorter transcript lengths, longer exon lengths, fewer numbers of exons, lower GC content and higher minimum free energy values compared with protein-coding genes. lncRNAs in P. sojae exhibited low sequence conservation amongst oomycetes and P. sojae isolates. Transcriptional data indicated that P. sojae lncRNAs tended to be transcribed in a stage-specific manner; representative lncRNAs were validated by semi-quantitative reverse transcription-polymerase chain reaction. Phytophthora sojae lncRNAs were concentrated in gene-sparse regions, and lncRNAs were associated with secreted protein and effector coding genes. The neighbouring genes of lncRNAs encoded various effector family members, and RNA-seq data revealed a correlation between the transcription level of lncRNAs and their neighbouring genes. Our results provide the first comprehensive identification of lncRNAs in oomycetes and suggest a potential association between lncRNAs and effector genes.
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Affiliation(s)
- Yang Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsu 210095China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjingJiangsu 210095China
| | - Wenwu Ye
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsu 210095China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjingJiangsu 210095China
| | - Yuanchao Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsu 210095China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjingJiangsu 210095China
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46
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Role of Pseudogenes in Tumorigenesis. Cancers (Basel) 2018; 10:cancers10080256. [PMID: 30071685 PMCID: PMC6115995 DOI: 10.3390/cancers10080256] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/28/2018] [Accepted: 07/30/2018] [Indexed: 12/20/2022] Open
Abstract
Functional genomics has provided evidence that the human genome transcribes a large number of non-coding genes in addition to protein-coding genes, including microRNAs and long non-coding RNAs (lncRNAs). Among the group of lncRNAs are pseudogenes that have not been paid attention in the past, compared to other members of lncRNAs. However, increasing evidence points the important role of pseudogenes in diverse cellular functions, and dysregulation of pseudogenes are often associated with various human diseases including cancer. Like other types of lncRNAs, pseudogenes can also function as master regulators for gene expression and thus, they can play a critical role in various aspects of tumorigenesis. In this review we discuss the latest developments in pseudogene research, focusing on how pseudogenes impact tumorigenesis through different gene regulation mechanisms. Given the high sequence homology with the corresponding parent genes, we also discuss challenges for pseudogene research.
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47
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Genome-wide identification and characterization of lncRNAs and miRNAs in cluster bean (Cyamopsis tetragonoloba). Gene 2018; 667:112-121. [DOI: 10.1016/j.gene.2018.05.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/24/2018] [Accepted: 05/08/2018] [Indexed: 01/26/2023]
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48
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Li H, Yang J, Jiang R, Wei X, Song C, Huang Y, Lan X, Lei C, Ma Y, Hu L, Chen H. Long Non-coding RNA Profiling Reveals an Abundant MDNCR that Promotes Differentiation of Myoblasts by Sponging miR-133a. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:610-625. [PMID: 30195797 PMCID: PMC6078111 DOI: 10.1016/j.omtn.2018.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 12/31/2022]
Abstract
Muscle development is regulated by a series of complicate processes, and non-coding RNAs (ncRNAs) such as lncRNA have been reported to play important roles in regulating skeletal myogenesis and diseases. Here we profile the expression of lncRNA in cattle skeletal muscle tissue from fetus and adult developmental stages and detect 13,580 lncRNA candidates. Many of these lncRNAs are differentially expressed between two developmental stages. We further characterize one abundant lncRNA with the highest expression level of all downregulated lncRNAs, which we named muscle differentiation-associated lncRNA (MDNCR). Via luciferase screening, RNA binding protein immunoprecipitation (RIP), and RNA pull-down assays, MDNCR was observed to directly bind to miR-133a with 32 potential binding sites. GosB was identified as a target of miR-133a by luciferase activity, quantitative real-time qPCR, and western blotting assays. Overexpression of MDNCR increased the expression of GosB, whereas this effect was abolished by miR-133a. We found that MDNCR promotes myoblast differentiation and inhibits cell proliferation by sponging miR-133a. These results demonstrate that MDNCR binding miR-133a promotes cell differentiation by targeting GosB in cattle primary myoblasts.
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Affiliation(s)
- Hui Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Jiameng Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Rui Jiang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan 464000, China
| | - Chengchuang Song
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan 464000, China
| | - Linyong Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China
| | - Hong Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Shaanxi 712100, China.
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49
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Zheng H, Xu J, Hao S, Liu X, Ning J, Song X, Jiang L, Liu Z. Expression of BANCR promotes papillary thyroid cancer by targeting thyroid stimulating hormone receptor. Oncol Lett 2018; 16:2009-2015. [PMID: 30034553 DOI: 10.3892/ol.2018.8810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/23/2017] [Indexed: 12/28/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common form of non-medullary thyroid cancer, accounting for ~80% of all cases of thyroid cancer. The aim of the present study was to explore the role of BRAF-activated long noncoding RNA (BANCR) in the development of PTC. Using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), the mRNA expression levels of BANCR, thyroid-stimulating hormone receptor (TSHR) and cyclin D1 between PTC and benign control thyroid nodule tissue samples from 60 patients were determined. Using RT-qPCR and western blot analysis, the expression levels of TSHR and cyclin D1 mRNA and protein were determined in cells transfected with BANCR-small interfering (si)RNA. An MTT assay and flow cytometry were used to analyze the effect of BANCR knockdown on the proliferation and cell cycle distribution of IHH-4 PTC cells. The expression of BANCR, TSHR and cyclin D1 was increased in the PTC group compared with the control group based on the RT-qPCR data. The transfection of IHH-4 cells with BANCR-siRNA induced the inhibition of TSHR and cyclin D1 expression compared with a transfection control. In addition, the proliferation of the IHH-4 cells transfected with BANCR-siRNA was suppressed, relative to the transfection control, and cells arrested in the G0/G1 phase, potentially due to the inhibition of the expression of cyclin D1. The data suggested that the expression of BANCR may promote the development of malignant thyroid nodules via the modulation of TSHR expression and its downstream effector, cyclin D1.
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Affiliation(s)
- Haitao Zheng
- Department of Thyroid Surgery, Yantai Yuhuangding Hospital, Yantai, Shangdong 264099, P.R. China
| | - Jie Xu
- Department of Thyroid Surgery, Yantai Yuhuangding Hospital, Yantai, Shangdong 264099, P.R. China
| | - Shaolong Hao
- Department of Thyroid Surgery, Yantai Yuhuangding Hospital, Yantai, Shangdong 264099, P.R. China
| | - Xincheng Liu
- Department of Thyroid Surgery, Yantai Yuhuangding Hospital, Yantai, Shangdong 264099, P.R. China
| | - Jinrao Ning
- Department of Thyroid Surgery, Yantai Yuhuangding Hospital, Yantai, Shangdong 264099, P.R. China
| | - Xicheng Song
- Department of Ear, Nose and Throat & Head and Neck Surgery, Yantai Yuhuangding Hospital, Yantai, Shangdong 264099, P.R. China
| | - Lixin Jiang
- Department of Thyroid Surgery, Yantai Yuhuangding Hospital, Yantai, Shangdong 264099, P.R. China
| | - Zongying Liu
- Department of Laboratory, People's Hospital of Pingyi County, Pingyi, Shangdong 273399, P.R. China
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50
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Karlic R, Ganesh S, Franke V, Svobodova E, Urbanova J, Suzuki Y, Aoki F, Vlahovicek K, Svoboda P. Long non-coding RNA exchange during the oocyte-to-embryo transition in mice. DNA Res 2018; 24:129-141. [PMID: 28087610 PMCID: PMC5397607 DOI: 10.1093/dnares/dsw058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/28/2016] [Indexed: 01/02/2023] Open
Abstract
The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5′ terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence. Except for a small group of ubiquitous lncRNAs, maternal and zygotic lncRNAs formed two distinct populations. The bulk of maternal lncRNAs was degraded before the zygotic genome activation. Interestingly, maternal lncRNAs seemed to undergo cytoplasmic polyadenylation observed for dormant mRNAs. We also identified lncRNAs giving rise to trans-acting short interfering RNAs, which represent a novel lncRNA category. Altogether, we defined the core OET lncRNA transcriptome and characterized its remodeling during early development. Our results are consistent with the notion that rapidly evolving lncRNAs constitute signatures of cells-of-origin while a minority plays an active role in control of gene expression across OET. Our data presented here provide an excellent source for further OET lncRNA studies.
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Affiliation(s)
- Rosa Karlic
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Sravya Ganesh
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Vedran Franke
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Eliska Svobodova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Jana Urbanova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic
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