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Zhang X, Li Y, Ma L, Zhang G, Liu M, Wang C, Zheng Y, Li R. A new sex-specific underlying mechanism for female schizophrenia: accelerated skewed X chromosome inactivation. Biol Sex Differ 2020; 11:39. [PMID: 32680558 PMCID: PMC7368719 DOI: 10.1186/s13293-020-00315-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND X chromosome inactivation (XCI) is the mechanism by which the X-linked gene dosage is adjusted between the sexes. Evidence shows that many sex-specific diseases have their basis in X chromosome biology. While female schizophrenia patients often have a delayed age of disease onset and clinical phenotypes that are different from those of males, it is unknown whether the sex differences in schizophrenia are associated with X-linked gene dosage and the choice of X chromosome silencing in female cells. Previous studies demonstrated that sex chromosome aneuploidies may be related to the pathogeneses of some psychiatric diseases. Here, we examined the changes in skewed XCI in patients with schizophrenia. METHODS A total of 109 female schizophrenia (SCZ) patients and 80 age- and sex-matched healthy controls (CNTLs) were included in this study. We evaluated clinical features including disease onset age, disease duration, clinical symptoms by the Positive and Negative Syndrome Scale (PANSS) and antipsychotic treatment dosages. The XCI skewing patterns were analyzed by the methylation profile of the HUMARA gene found in DNA isolated from SCZ patient and CNTL leukocytes in the three age groups. RESULTS First, we found that the frequency of skewed XCI in SCZ patients was 4 times more than that in the age- and sex-matched CNTLs (p < 0.01). Second, we found an earlier onset of severe XCI skewing in the SCZ patients than in CNTLs. Third, we demonstrated a close relationship between the severity of skewed XCI and schizophrenic symptoms (PANSS score ≥ 90) as well as the age of disease onset. Fourth, we demonstrated that the skewed XCI in SCZ patients was not transmitted from the patients' mothers. LIMITATIONS The XCI skewing pattern might differ depending on tissues or organs. Although this is the first study to explore skewed XCI in SCZ, in the future, samples from different tissues or cells in SCZ patients might be important for understanding the impact of skewed XCI in this disease. CONCLUSION Our study, for the first time, investigated skewed XCI in female SCZ patients and presented a potential mechanism for the sex differences in SCZ. Our data also suggested that XCI might be a potential target for the development of female-specific interventions for SCZ.
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Affiliation(s)
- Xinzhu Zhang
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Yuhong Li
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Lei Ma
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Guofu Zhang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Min Liu
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Chuanyue Wang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Yi Zheng
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Rena Li
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China. .,The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China.
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202
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Jusic A, Salgado-Somoza A, Paes AB, Stefanizzi FM, Martínez-Alarcón N, Pinet F, Martelli F, Devaux Y, Robinson EL, Novella S. Approaching Sex Differences in Cardiovascular Non-Coding RNA Research. Int J Mol Sci 2020; 21:E4890. [PMID: 32664454 PMCID: PMC7402336 DOI: 10.3390/ijms21144890] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular disease (CVD) is the biggest cause of sickness and mortality worldwide in both males and females. Clinical statistics demonstrate clear sex differences in risk, prevalence, mortality rates, and response to treatment for different entities of CVD. The reason for this remains poorly understood. Non-coding RNAs (ncRNAs) are emerging as key mediators and biomarkers of CVD. Similarly, current knowledge on differential regulation, expression, and pathology-associated function of ncRNAs between sexes is minimal. Here, we provide a state-of-the-art overview of what is known on sex differences in ncRNA research in CVD as well as discussing the contributing biological factors to this sex dimorphism including genetic and epigenetic factors and sex hormone regulation of transcription. We then focus on the experimental models of CVD and their use in translational ncRNA research in the cardiovascular field. In particular, we want to highlight the importance of considering sex of the cellular and pre-clinical models in clinical studies in ncRNA research and to carefully consider the appropriate experimental models most applicable to human patient populations. Moreover, we aim to identify sex-specific targets for treatment and diagnosis for the biggest socioeconomic health problem globally.
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Affiliation(s)
- Amela Jusic
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, 75000 Tuzla, Bosnia and Herzegovina;
| | - Antonio Salgado-Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Ana B. Paes
- INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain; (A.B.P.); (N.M.-A.)
| | - Francesca Maria Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Núria Martínez-Alarcón
- INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain; (A.B.P.); (N.M.-A.)
| | - Florence Pinet
- INSERM, CHU Lille, Institut Pasteur de Lille, University of Lille, U1167 F-59000 Lille, France;
| | - Fabio Martelli
- Molecular Cardiology Laboratory, Policlinico San Donato IRCCS, San Donato Milanese, 20097 Milan, Italy;
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (A.S.-S.); (F.M.S.); (Y.D.)
| | - Emma Louise Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Susana Novella
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, and INCLIVA Biomedical Research Institute, Menéndez Pelayo 4 Accesorio, 46010 Valencia, Spain
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203
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Katoh K, Aiba K, Fukushi D, Yoshimura J, Suzuki Y, Mitsui J, Morishita S, Tuji S, Yamada K, Wakamatsu N. Clinical and molecular genetic characterization of two female patients harboring the Xq27.3q28 deletion with different ratios of X chromosome inactivation. Hum Mutat 2020; 41:1447-1460. [PMID: 32485067 DOI: 10.1002/humu.24058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 11/10/2022]
Abstract
A heterozygous deletion at Xq27.3q28 including FMR1, AFF2, and IDS causing intellectual disability and characteristic facial features is very rare in females, with only 10 patients having been reported. Here, we examined two female patients with different clinical features harboring the Xq27.3q28 deletion and determined the chromosomal breakpoints. Moreover, we assessed the X chromosome inactivation (XCI) in peripheral blood from both patients. Both patients had an almost overlapping deletion at Xq27.3q28, however, the more severe patient (Patient 1) showed skewed XCI of the normal X chromosome (79:21) whereas the milder patient (Patient 2) showed random XCI. Therefore, deletion at Xq27.3q28 critically affected brain development, and the ratio of XCI of the normal X chromosome greatly affected the clinical characteristics of patients with deletion at Xq27.3q28. As the chromosomal breakpoints were determined, we analyzed a change in chromatin domains termed topologically associated domains (TADs) using published Hi-C data on the Xq27.3q28 region, and found that only patient 1 had a possibility of a drastic change in TADs. The altered chromatin topologies on the Xq27.3q28 region might affect the clinical features of patient 1 by changing the expression of genes just outside the deletion and/or the XCI establishment during embryogenesis resulting in skewed XCI.
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Affiliation(s)
- Kimiko Katoh
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | - Kaori Aiba
- Department of Pediatrics, Toyohashi Municipal Hospital, Toyohashi, Aichi, Japan
| | - Daisuke Fukushi
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyo Suzuki
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | - Jun Mitsui
- Department of Molecular Neurology, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Shoji Tuji
- Department of Molecular Neurology, The University of Tokyo, Tokyo, Japan
| | - Kenichiro Yamada
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | - Nobuaki Wakamatsu
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan.,Department of Neurology, Neurology and Stroke Center, Takamatsu Municipal Hospital, Takamatsu, Kagawa, Japan.,Department of Pathology and Host Defense, Faculty of Medicine, Kagawa University, Miki, Kagawa, Japan
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204
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Strehle M, Guttman M. Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. Curr Opin Cell Biol 2020; 64:139-147. [PMID: 32535328 DOI: 10.1016/j.ceb.2020.04.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/13/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022]
Abstract
X chromosome inactivation (XCI) is the process whereby one of the X chromosomes in female mammalian cells is silenced to equalize X-linked gene expression with males. XCI depends on the long noncoding RNA Xist, which coats the inactive X chromosome in cis and triggers a cascade of events that ultimately lead to chromosome-wide transcriptional silencing that is stable for the lifetime of an organism. In recent years, the discovery of proteins that interact with Xist have led to new insights into how the initiation of XCI occurs. Nevertheless, there are still various unknowns about the mechanisms by which Xist orchestrates and maintains stable X-linked silencing. Here, we review recent work elucidating the role of Xist and its protein partners in mediating chromosome-wide transcriptional repression, as well as discuss a model by which Xist may compartmentalize proteins across the inactive X chromosome to enable both the initiation and maintenance of XCI.
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Affiliation(s)
- Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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205
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Chen Z, Zhang Y. Maternal H3K27me3-dependent autosomal and X chromosome imprinting. Nat Rev Genet 2020; 21:555-571. [PMID: 32514155 DOI: 10.1038/s41576-020-0245-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 12/19/2022]
Abstract
Genomic imprinting and X-chromosome inactivation (XCI) are classic epigenetic phenomena that involve transcriptional silencing of one parental allele. Germline-derived differential DNA methylation is the best-studied epigenetic mark that initiates imprinting, but evidence indicates that other mechanisms exist. Recent studies have revealed that maternal trimethylation of H3 on lysine 27 (H3K27me3) mediates autosomal maternal allele-specific gene silencing and has an important role in imprinted XCI through repression of maternal Xist. Furthermore, loss of H3K27me3-mediated imprinting contributes to the developmental defects observed in cloned embryos. This novel maternal H3K27me3-mediated non-canonical imprinting mechanism further emphasizes the important role of parental chromatin in development and could provide the basis for improving the efficiency of embryo cloning.
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Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA. .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. .,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Boston, MA, USA.
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206
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Jiang Q, Xing W, Cheng J, Yu Y. Knockdown of lncRNA XIST Suppresses Cell Tumorigenicity in Human Non-Small Cell Lung Cancer by Regulating miR-142-5p/PAX6 Axis. Onco Targets Ther 2020; 13:4919-4929. [PMID: 32581553 PMCID: PMC7276200 DOI: 10.2147/ott.s238808] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 05/16/2020] [Indexed: 12/17/2022] Open
Abstract
Background Long noncoding RNA X inactivate-specific transcript (lncRNA XIST) has been identified to contribute to the development and progression of non-small cell lung cancer (NSCLC). Thus, it is important to explore more specific functions and molecular mechanisms of XIST in NSCLC tumorigenesis. Materials and Methods The expression of XIST, microRNA (miR)-142-5p and paired box 6 (PAX6) was measured using quantitative real-time polymerase chain reaction or Western blot, respectively. Cell proliferation was analyzed using cell counting kit-8 (CCK-8) assay. Flow cytometry was utilized to measure apoptotic cells. Cell migration and invasion were determined by Transwell assay. The interaction between miR-142-5p and XIST or PAX6 was confirmed by the dual-luciferase reporter assay and RNA immunoprecipitation assay. In vivo experiments were performed through the murine xenograft model. Results XIST was elevated in NSCLC, and XIST knockdown suppressed cell proliferation, migration, invasion and induced apoptosis in vitro as well as repressed tumor growth in vivo. MiR-142-5p was a target of XIST, and silencing miR-142-5p reversed the anti-tumor functions mediated by XIST knockdown in NSCLC cells. PAX6 was confirmed to be a target of miR-142-5p, and the inhibitory effects caused by miR-142-5p restoration in NSCLC cell malignant phenotypes were attenuated by PAX6 overexpression. Besides that, XIST could indirectly regulate PAX6 expression by sponging miR-142-5p in vivo and in vitro. Conclusion XIST suppresses cell tumorigenicity in human NSCLC by regulating miR-142-5p/PAX6 axis, which indicates a novel insight into the pathogenesis of NSCLC and lays a foundation for the molecular therapy of NSCLC.
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Affiliation(s)
- Qingfeng Jiang
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, People's Republic of China
| | - Wenqun Xing
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, People's Republic of China
| | - Jinhua Cheng
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, People's Republic of China
| | - Yongkui Yu
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan 450008, People's Republic of China
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207
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Oertelt-Prigione S, Mariman E. The impact of sex differences on genomic research. Int J Biochem Cell Biol 2020; 124:105774. [PMID: 32470538 DOI: 10.1016/j.biocel.2020.105774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 01/23/2023]
Abstract
Sex and gender differences affect all dimensions of human health ranging from the biological basis of disease to therapeutic access, choice and response. Genomics research has long ignored the role of sex differences as potential modulators and the concept is gaining more attention only recently. In the present review we summarize the current knowledge of the impact of sex differences on genomic and epigenomic research, the potential interaction of genomics and gender and the role of these differences in disease etiopathogenesis. Sex differences can emerge from differences in the sex chromosomes themselves, from their interaction with the genome and from the influence of hormones on genomic processes. The impact of these processes on the incidence of autoimmune and oncologic disease is well documented. The growing field of systems biology, which aims at integrating information from different networks of the human body, could also greatly benefit from this approach. In the present review we summarize the current knowledge and provide recommendations for the future performance of sex-sensitive genomics research.
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Affiliation(s)
- Sabine Oertelt-Prigione
- Department of Primary and Community Care, Radboud Institute of Health Sciences, Radboudumc, Nijmegen, The Netherlands; Institute of Legal and Forensic Medicine, Charité - Universitätsmedizin, Berlin, Germany.
| | - Edwin Mariman
- Department of Human Biology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
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208
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Slack FJ, Chinnaiyan AM. The Role of Non-coding RNAs in Oncology. Cell 2020; 179:1033-1055. [PMID: 31730848 DOI: 10.1016/j.cell.2019.10.017] [Citation(s) in RCA: 922] [Impact Index Per Article: 230.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/09/2019] [Accepted: 10/18/2019] [Indexed: 02/07/2023]
Abstract
For decades, research into cancer biology focused on the involvement of protein-coding genes. Only recently was it discovered that an entire class of molecules, termed non-coding RNA (ncRNA), plays key regulatory roles in shaping cellular activity. An explosion of studies into ncRNA biology has since shown that they represent a diverse and prevalent group of RNAs, including both oncogenic molecules and those that work in a tumor suppressive manner. As a result, hundreds of cancer-focused clinical trials involving ncRNAs as novel biomarkers or therapies have begun and these are likely just the beginning.
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Affiliation(s)
- Frank J Slack
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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209
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Maguire EM, Xiao Q. Noncoding RNAs in vascular smooth muscle cell function and neointimal hyperplasia. FEBS J 2020; 287:5260-5283. [DOI: 10.1111/febs.15357] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Eithne Margaret Maguire
- Centre for Clinical Pharmacology William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London UK
| | - Qingzhong Xiao
- Centre for Clinical Pharmacology William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London UK
- Key Laboratory of Cardiovascular Diseases at The Second Affiliated Hospital Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation School of Basic Medical Sciences Guangzhou Medical University China
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210
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Yuan Q, Guo X, Ren Y, Wen X, Gao L. Cluster correlation based method for lncRNA-disease association prediction. BMC Bioinformatics 2020; 21:180. [PMID: 32393162 PMCID: PMC7216352 DOI: 10.1186/s12859-020-3496-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/15/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In recent years, increasing evidences have indicated that long non-coding RNAs (lncRNAs) are deeply involved in a wide range of human biological pathways. The mutations and disorders of lncRNAs are closely associated with many human diseases. Therefore, it is of great importance to predict potential associations between lncRNAs and complex diseases for the diagnosis and cure of complex diseases. However, the functional mechanisms of the majority of lncRNAs are still remain unclear. As a result, it remains a great challenge to predict potential associations between lncRNAs and diseases. RESULTS Here, we proposed a new method to predict potential lncRNA-disease associations. First, we constructed a bipartite network based on known associations between diseases and lncRNAs/protein coding genes. Then the cluster association scores were calculated to evaluate the strength of the inner relationships between disease clusters and gene clusters. Finally, the gene-disease association scores are defined based on disease-gene cluster association scores and used to measure the strength for potential gene-disease associations. CONCLUSIONS Leave-One Out Cross Validation (LOOCV) and 5-fold cross validation tests were implemented to evaluate the performance of our method. As a result, our method achieved reliable performance in the LOOCV (AUCs of 0.8169 and 0.8410 based on Yang's dataset and Lnc2cancer 2.0 database, respectively), and 5-fold cross validation (AUCs of 0.7573 and 0.8198 based on Yang's dataset and Lnc2cancer 2.0 database, respectively), which were significantly higher than the other three comparative methods. Furthermore, our method is simple and efficient. Only the known gene-disease associations are exploited in a graph manner and further new gene-disease associations can be easily incorporated in our model. The results for melanoma and ovarian cancer have been verified by other researches. The case studies indicated that our method can provide informative clues for further investigation.
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Affiliation(s)
- Qianqian Yuan
- School of Computer Science and Technology, XIDIAN UNIVERSITY, Xi'an, Shaanxi, China
| | - Xingli Guo
- School of Computer Science and Technology, XIDIAN UNIVERSITY, Xi'an, Shaanxi, China.
| | - Yang Ren
- School of Computer Science and Technology, XIDIAN UNIVERSITY, Xi'an, Shaanxi, China
| | - Xiao Wen
- School of Computer Science and Technology, XIDIAN UNIVERSITY, Xi'an, Shaanxi, China
| | - Lin Gao
- School of Computer Science and Technology, XIDIAN UNIVERSITY, Xi'an, Shaanxi, China.
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211
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Salvatori B, Biscarini S, Morlando M. Non-coding RNAs in Nervous System Development and Disease. Front Cell Dev Biol 2020; 8:273. [PMID: 32435641 PMCID: PMC7218086 DOI: 10.3389/fcell.2020.00273] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
The rapid advance of RNA sequencing technologies contributed to a deep understanding of transcriptome composition and has allowed the discovery of a large number of non-coding RNAs (ncRNAs). The ability of these RNA molecules to be engaged in intricate and dynamic interactions with proteins and nucleic acids led to a great expansion of gene expression regulation mechanisms. By this matter, ncRNAs contribute to the increase in regulatory complexity that becomes highly specific between tissues and cell types. Among the ncRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are especially abundant in nervous system and have been shown to be implicated in its development, plasticity and aging as well as in neurological disorders. This review provides an overview of how these two diverse classes of ncRNAs control cellular processes during nervous system development, physiology, and disease conditions with particular emphasis on neurodegenerative disorders. The use of ncRNAs as biomarkers, tools, or targets for therapeutic intervention in neurodegeneration are also discussed.
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Affiliation(s)
- Beatrice Salvatori
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Perugia, Italy
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212
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AFB1 Induced Transcriptional Regulation Related to Apoptosis and Lipid Metabolism in Liver of Chicken. Toxins (Basel) 2020; 12:toxins12050290. [PMID: 32375309 PMCID: PMC7290437 DOI: 10.3390/toxins12050290] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 01/10/2023] Open
Abstract
Aflatoxin B1 (AFB1) leads to a major risk to poultry and its residues in meat products can also pose serious threat to human health. In this study, after feeding 165-day-old Roman laying hens for 35 days, the toxic effects of aflatoxin B1 at different concentrations were evaluated. The purpose of this study was to explore the mechanism of liver toxicosis responses to AFB1. We found that highly toxic group exposure resulted in liver fat deposition, increased interstitial space, and hepatocyte apoptosis in laying hens. Furthermore, a total of 164 differentially expressed lnRNAs and 186 differentially expressed genes were found to be highly correlated (Pearson Correlation Coefficient > 0.80, p-value < 0.05) by sequencing the transcriptome of control (CB) and highly toxic group (TB3) chickens. We also identify 29 differentially expressed genes and 19 miRNAs that have targeted regulatory relationships. Based on the liver cell apoptosis and fatty liver syndrome that this research focused on, we found that the highly toxic AFB1 led to dysregulation of the expression of PPARG and BCL6. They are cis-regulated by TU10057 and TU45776, respectively. PPARG was the target gene of gga-miR-301a-3p, gga-miR-301b-3p, and BCL6 was the target gene of gga-miR-190a-3p. In summary, highly toxic AFB1 affects the expression levels of protein-coding genes and miRNAs in the liver of Roman layer hens, as well as the expression level of long non-coding RNA in the liver, which upregulates the expression of PPARG and downregulates the expression of Bcl-6. Our study provides information on possible genetic regulatory networks in AFB1-induced hepatic fat deposition and hepatocyte apoptosis.
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213
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Li Y, Liu YD, Chen SL, Chen X, Ye DS, Zhou XY, Zhe J, Zhang J. Down-regulation of long non-coding RNA MALAT1 inhibits granulosa cell proliferation in endometriosis by up-regulating P21 via activation of the ERK/MAPK pathway. Mol Hum Reprod 2020; 25:17-29. [PMID: 30371869 DOI: 10.1093/molehr/gay045] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 10/25/2018] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Is there a specific mechanism underlying the association between lung adenocarcinoma transcript 1 (MALAT1) and endometriosis-related infertility? SUMMARY ANSWER The down-regulation of MALAT1 in endometriosis granulosa cells (GCs) may have an adverse effect on the growth and development of oocytes by inhibiting GC proliferation, due to cell cycle-dependent mechanisms that enhance P21 expression through activation of the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) pathway. WHAT IS KNOWN ALREADY The association between endometriosis and infertility is well supported throughout the literature, and endometriosis per se and its surgical treatment have an adverse effect on the ovarian reserve and on oocyte development. MALAT1, one of the most extensively expressed and evolutionarily conserved transcripts, has been implicated to play a role in human development and many diseases. However, little is known about the role of MALAT1 long non-coding RNA (lncRNA) in endometriosis and its associated infertility. STUDY DESIGN, SIZE, DURATION We measured MALAT1 lncRNA expression levels in GCs from 52 endometriosis patients and 52 controls. Also, MALAT1 was knocked down in a human GC tumor-derived cell line, KGN, to investigate the role of MALAT1 and its molecular mechanism in cell proliferation. PARTICIPANTS/MATERIALS, SETTING, METHODS GCs were collected from women with or without endometriosis undergoing IVF or ICSI treatment. All endometriosis patients were diagnosed by laparoscopy or laparotomy, and control patients were limited to male factor or tubal disease and had a normal ovarian reserve. Quantitative real-time PCR (qRT-PCR) was used to measure the differential expression levels of MALAT1 lncRNA between endometriosis patients and controls. The receiver operating characteristic (ROC) curve was drawn to evaluate the diagnostic values of MALAT1 in endometriosis. In the KGN cell line, MALAT1 was knocked down with locked nucleic acid GapmeRs. Cell counting kit-8 assays, ethynyl-2-deoxyuridine assays and flow cytometry were used to study the role of MALAT1 in cell proliferation and cell-cycle progression, and western blotting was performed to detect the potential underlying mechanism. MAIN RESULTS AND THE ROLE OF CHANCE We first found that MALAT1 lncRNA was significantly down-regulated in endometriosis GCs and was associated with the antral follicle count (R = 0.376, P < 0.001 versus control). In addition, MALAT1 lncRNA levels were significantly lower in the GCs of infertile women with advanced stages of endometriosis (P = 0.01 versus control). The ROC curves illustrated strong separation between all the endometriosis patients and the control group (AUC: 0.705; 95% CI: 0.606-0.804; P < 0.001), Stage I-II and control group (AUC: 0.651; 95% CI: 0.536-0.767; P = 0.016), and Stage III-IV and control group (AUC: 0.827; 95% CI: 0.718-0.936; P < 0.001). MALAT1 lncRNA was primarily localized in the nuclei of GCs. We found a negative correlation between MALAT1 lncRNA and P21 mRNA in the GCs from patients (R = -0.628; P < 0.001). MALAT1 knockdown in KGN cells inhibited cell proliferation and cell-cycle progression. In addition, MALAT1 knockdown induced an increase in both the mRNA and protein levels of P21, and of P53, phosphorylated ERK1/2 (p-ERK1/2) and phosphorylated c-Jun N-terminal protein kinase (p-JNK) protein levels, as well as causing a decrease in cyclin dependent kinase 2 (CDK2), cyclin D1 and p-P38 MAPK protein levels. Furthermore, inhibition of the ERK/MAPK pathway with U0126, the up-regulation of p-ERK1/2, P21 and P53, and the down-regulation of CDK2 and cyclin D1 by the knockdown of MALAT1 were all attenuated by MALAT1 knockdown. Therefore, MALAT1 may regulate GC proliferation through P21/P53-dependent control of the cell cycle, and the ERK/MAPK pathway participates in this process. LARGE SCALE DATA None. LIMITATIONS, REASONS FOR CAUTION The hormonal treatment used in IVF and surgical removal of endometriotic lesions may have altered MALAT1 expression in GCs. The ovarian granulosa-like tumor cell line, KGN, was used for further functional and mechanistic studies due to the difficulties in obtaining human GCs in sizable amounts and maintaining primary cultures. WIDER IMPLICATIONS OF THE FINDINGS Our finding represents the first example of an lncRNA-based mechanism in endometriosis GCs. Women with endometriosis show altered MALAT1 expression levels in GCs that may impair fertility by regulating the function of GCs. Therefore, analysis of MALAT1 and its molecular mechanisms of action provide new insights into the pathogenesis of endometriosis and its associated infertility. STUDY FUNDING/COMPETING INTEREST(s) This work was supported by the National Natural Science Foundation of China (grant number: 81671524) and the National key research and development program of China (grant number: 2017YFC1001100). The authors declare there is no conflict of interest.
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Affiliation(s)
- Ying Li
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yu-Dong Liu
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Shi-Ling Chen
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xin Chen
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - De-Sheng Ye
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xing-Yu Zhou
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jing Zhe
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jun Zhang
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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Sexually dimorphic DNA-methylation in cardiometabolic health: A systematic review. Maturitas 2020; 135:6-26. [DOI: 10.1016/j.maturitas.2020.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
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Tang B, Li W, Ji T, Li X, Qu X, Feng L, Zhu Y, Qi Y, Zhu C, Bai S. Downregulation of XIST ameliorates acute kidney injury by sponging miR-142-5p and targeting PDCD4. J Cell Physiol 2020; 235:8852-8863. [PMID: 32347551 DOI: 10.1002/jcp.29729] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
Acute kidney injury (AKI) is a common kidney disease that markedly affects public health. To date, the roles of long noncoding RNA XIST in AKI are poorly understood. Here, we investigated the biological functions of XIST in AKI. We observed that XIST expression increased in patients with AKI and HK-2 cells stimulated by CoCl2 . In addition, a rat AKI model induced by ischemia-reperfusion was established. Tumor necrosis factor-α, interleukin-6, and cyclooxygenase-2 messenger RNA expression were induced in vivo; moreover, XIST expression was upregulated. Knockdown of XIST significantly repressed CoCl2 -triggered injury in HK-2 cells. However, microRNA (miR)-142-5p, a downstream target of XIST, was downregulated in AKI. miR-142-5p was repressed by XIST and miR-142-5p could inhibit CoCl2 -induced injury in HK-2 cells. Moreover, PDCD4 expression was significantly increased in AKI. PDCD4 was predicted to be the target of miR-142-5p. Subsequently, loss of PDCD4 was able to retard injury in HK-2 cells exposed to CoCl2. Thus, we suggest that XIST regulates miR-142-5p and PDCD4, and it has the potential to function as a biomarker in therapeutic strategies for AKI.
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Affiliation(s)
- Bo Tang
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Weiliang Li
- Department of Urology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Tingting Ji
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Xiaoying Li
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Xiaolei Qu
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Linhong Feng
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Yingchun Zhu
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Yinghui Qi
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Chun Zhu
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Shoujun Bai
- Department of Nephrology, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, Shanghai, China
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Bekric D, Neureiter D, Ritter M, Jakab M, Gaisberger M, Pichler M, Kiesslich T, Mayr C. Long Non-Coding RNAs in Biliary Tract Cancer-An Up-to-Date Review. J Clin Med 2020; 9:jcm9041200. [PMID: 32331331 PMCID: PMC7231154 DOI: 10.3390/jcm9041200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
The term long non-coding RNA (lncRNA) describes non protein-coding transcripts with a length greater than 200 base pairs. The ongoing discovery, characterization and functional categorization of lncRNAs has led to a better understanding of the involvement of lncRNAs in diverse biological and pathological processes including cancer. Aberrant expression of specific lncRNA species was demonstrated in various cancer types and associated with unfavorable clinical characteristics. Recent studies suggest that lncRNAs are also involved in the development and progression of biliary tract cancer, a rare disease with high mortality and limited therapeutic options. In this review, we summarize current findings regarding the manifold roles of lncRNAs in biliary tract cancer and give an overview of the clinical and molecular consequences of aberrant lncRNA expression as well as of underlying regulatory functions of selected lncRNA species in the context of biliary tract cancer.
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Affiliation(s)
- Dino Bekric
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria;
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Markus Ritter
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Paracelsus Medical University, 5020 Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Martin Jakab
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
| | - Martin Gaisberger
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Paracelsus Medical University, 5020 Salzburg, Austria
- Gastein Research Institute, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Clinical Oncology, Department of Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria;
| | - Tobias Kiesslich
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria
| | - Christian Mayr
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria; (D.B.); (M.R.); (M.J.); (M.G.); (T.K.)
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria
- Correspondence:
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217
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Lin B, Xu J, Wang F, Wang J, Zhao H, Feng D. LncRNA XIST promotes myocardial infarction by regulating FOS through targeting miR-101a-3p. Aging (Albany NY) 2020; 12:7232-7247. [PMID: 32315985 PMCID: PMC7202499 DOI: 10.18632/aging.103072] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
The purpose of this study was to reveal the hypothesis that lncRNA X inactive specific transcript (XIST) can participate in the regulation of cardiomyocyte apoptosis in neonatal mice cardiomyocytes (NMCMs) and myocardial infarction (MI) through targeting miR-101a-3p. NMCMs were isolated from neonatal C57BL/6 mice and anoxia was induced in hypoxic chamber. MTT assay and flow cytometry were used to determine proliferation and apoptosis respectively. The target relationship among XIST, miR-101a-3p and FOS was revealed by bioinformatic analysis, luciferase reporter assay, pull-down assay and RNA immunoprecipitation assay. The expression of XIST, miR-101a-3p, FOS and apoptosis-related proteins was determined by qRT-PCR or western blot. MI model was constructed to reveal the role of XIST. We found that XIST was up-regulated in NMCMs under anoxia condition. Moreover, XIST increased FOS expression by sponging miR-101a-3p in anoxia cells. Silencing XIST expression improved cell viability and suppressed apoptosis in vitro and inhibited myocardial infarction by reducing the level of c-FOS and apoptosis-related proteins in vivo. Our findings suggest that XIST is involved in MI, modulation of its level can be used as a new strategy or potential target in the treatment of myocardial infarction.
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Affiliation(s)
- Bin Lin
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Jing Xu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Feng Wang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Jiaxiang Wang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Hui Zhao
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Deguang Feng
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
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218
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Sharma S, Munger K. The Role of Long Noncoding RNAs in Human Papillomavirus-associated Pathogenesis. Pathogens 2020; 9:pathogens9040289. [PMID: 32326624 PMCID: PMC7238103 DOI: 10.3390/pathogens9040289] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/15/2022] Open
Abstract
Infections with high-risk human papillomaviruses cause ~5% of all human cancers. E6 and E7 are the only viral genes that are consistently expressed in cancers, and they are necessary for tumor initiation, progression, and maintenance. E6 and E7 encode small proteins that lack intrinsic enzymatic activities and they function by binding to cellular regulatory molecules, thereby subverting normal cellular homeostasis. Much effort has focused on identifying protein targets of the E6 and E7 proteins, but it has been estimated that ~98% of the human transcriptome does not encode proteins. There is a growing interest in studying noncoding RNAs as biochemical targets and biological mediators of human papillomavirus (HPV) E6/E7 oncogenic activities. This review focuses on HPV E6/E7 targeting cellular long noncoding RNAs, a class of biologically versatile molecules that regulate almost every known biological process and how this may contribute to viral oncogenesis.
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219
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Jiang Y, Giase G, Grennan K, Shieh AW, Xia Y, Han L, Wang Q, Wei Q, Chen R, Liu S, White KP, Chen C, Li B, Liu C. DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data. PLoS Comput Biol 2020; 16:e1007522. [PMID: 32282793 PMCID: PMC7179940 DOI: 10.1371/journal.pcbi.1007522] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/23/2020] [Accepted: 02/28/2020] [Indexed: 11/28/2022] Open
Abstract
Studies of complex disorders benefit from integrative analyses of multiple omics data. Yet, sample mix-ups frequently occur in multi-omics studies, weakening statistical power and risking false findings. Accurately aligning sample information, genotype, and corresponding omics data is critical for integrative analyses. We developed DRAMS (https://github.com/Yi-Jiang/DRAMS) to Detect and Re-Align Mixed-up Samples to address the sample mix-up problem. It uses a logistic regression model followed by a modified topological sorting algorithm to identify the potential true IDs based on data relationships of multi-omics. According to tests using simulated data, the more types of omics data used or the smaller the proportion of mix-ups, the better that DRAMS performs. Applying DRAMS to real data from the PsychENCODE BrainGVEX project, we detected and corrected 201 (12.5% of total data generated) mix-ups. Of the 21 mix-ups involving errors of racial identity, DRAMS re-assigned all data to the correct racial group in the 1000 Genomes project. In doing so, quantitative trait loci (QTL) (FDR<0.01) increased by an average of 1.62-fold. The use of DRAMS in multi-omics studies will strengthen statistical power of the study and improve quality of the results. Even though very limited studies have multi-omics data in place, we expect such data will increase quickly with the needs of DRAMS.
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Affiliation(s)
- Yi Jiang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Gina Giase
- School of Public Health, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kay Grennan
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Annie W. Shieh
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Yan Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Lide Han
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Quan Wang
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Qiang Wei
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Rui Chen
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Sihan Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kevin P. White
- Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Tempus Labs Inc, Chicago, Illinois, United States of America
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, New York, United States of America
- School of Psychology, Shaanxi Normal University, Xi’an, Shaanxi, China
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220
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Robinson EK, Covarrubias S, Carpenter S. The how and why of lncRNA function: An innate immune perspective. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194419. [PMID: 31487549 PMCID: PMC7185634 DOI: 10.1016/j.bbagrm.2019.194419] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the "blueprint" is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen.
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Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America.
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221
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Tsagakis I, Douka K, Birds I, Aspden JL. Long non-coding RNAs in development and disease: conservation to mechanisms. J Pathol 2020; 250:480-495. [PMID: 32100288 PMCID: PMC8638664 DOI: 10.1002/path.5405] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/05/2020] [Accepted: 02/18/2020] [Indexed: 12/22/2022]
Abstract
Our genomes contain the blueprint of what makes us human and many indications as to why we develop disease. Until the last 10 years, most studies had focussed on protein-coding genes, more specifically DNA sequences coding for proteins. However, this represents less than 5% of our genomes. The other 95% is referred to as the 'dark matter' of our genomes, our understanding of which is extremely limited. Part of this 'dark matter' includes regions that give rise to RNAs that do not code for proteins. A subset of these non-coding RNAs are long non-coding RNAs (lncRNAs), which in particular are beginning to be dissected and their importance to human health revealed. To improve our understanding and treatment of disease it is vital that we understand the molecular and cellular function of lncRNAs, and how their misregulation can contribute to disease. It is not yet clear what proportion of lncRNAs is actually functional; conservation during evolution is being used to understand the biological importance of lncRNA. Here, we present key themes within the field of lncRNAs, emphasising the importance of their roles in both the nucleus and the cytoplasm of cells, as well as patterns in their modes of action. We discuss their potential functions in development and disease using examples where we have the greatest understanding. Finally, we emphasise why lncRNAs can serve as biomarkers and discuss their emerging potential for therapy. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Ioannis Tsagakis
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- LeedsOmicsUniversity of LeedsLeedsUK
| | - Katerina Douka
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- LeedsOmicsUniversity of LeedsLeedsUK
| | - Isabel Birds
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- LeedsOmicsUniversity of LeedsLeedsUK
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological SciencesUniversity of LeedsLeedsUK
- LeedsOmicsUniversity of LeedsLeedsUK
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Xu X, Zhou X, Chen Z, Gao C, Zhao L, Cui Y. Silencing of lncRNA XIST inhibits non-small cell lung cancer growth and promotes chemosensitivity to cisplatin. Aging (Albany NY) 2020; 12:4711-4726. [PMID: 32209729 PMCID: PMC7138551 DOI: 10.18632/aging.102673] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/25/2019] [Indexed: 01/05/2023]
Abstract
Long noncoding RNAs (lncRNAs) play critical roles in tumour progression and metastasis. Emerging evidence indicates that the lncRNA X inactive-specific transcript (XIST) is dysregulated in several tumor types, including non-small cell lung cancer (NSCLC). However, in NSCLC and other cancers the oncogenic mechanism of XIST remains incompletely understood. Here, we confirmed that XIST is upregulated in human NSCLC specimens, and is especially overexpressed in tumors previously treated with cisplatin (cis-diamminedichloroplatinum(II); DDP). In vitro, XIST knockdown inhibited NSCLC cell growth and promoted DDP chemosensitivity by stimulating apoptosis and pyroptosis. Moreover, XIST's oncogenic effects and ability to promote DDP chemoresistance were largely related to its binding to the TGF-β effector SMAD2, which inhibited its translocation to the nucleus and prevented the transcription of p53 and NLRP3, crucial regulators of apoptosis and pyroptosis, respectively. Using DDP-resistant NSCLC cells, mouse xenograft studies verified the oncogenic function of XIST and its ability to inhibit programmed cell death, thereby mediating DDP chemoresistance. These findings suggest that XIST expression may serve as a novel biomarker to predict DDP treatment efficacy, and may help in the design of new therapies to circumvent DDP chemoresistance in NSCLC and other tumor types.
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Affiliation(s)
- Xiaohui Xu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Wangfujing, Dongcheng, Beijing 100730, P.R. China
| | - Xiaoyun Zhou
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Wangfujing, Dongcheng, Beijing 100730, P.R. China
| | - Zhenju Chen
- Beijing 100biotech Co., Ltd., Beijing 100006, China
| | - Chao Gao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Wangfujing, Dongcheng, Beijing 100730, P.R. China
| | - Luo Zhao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Wangfujing, Dongcheng, Beijing 100730, P.R. China
| | - Yushang Cui
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Wangfujing, Dongcheng, Beijing 100730, P.R. China
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223
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Liu X, Xie S, Zhang J, Kang Y. Long Noncoding RNA XIST Contributes to Cervical Cancer Development Through Targeting miR-889-3p/SIX1 Axis. Cancer Biother Radiopharm 2020; 35:640-649. [PMID: 32191528 DOI: 10.1089/cbr.2019.3318] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background: Cervical cancer (CC) is one of the most common cancers among women in the world. Long noncoding RNAs and microRNAs were identified as important regulators in many physiological processes. The objective of this study was to illuminate the mechanism of X-inactive-specific transcript (XIST)/miR-889-3p/Sine oculis homeobox 1 (SIX1) axis in CC. Methods: The expression levels of XIST, miR-889-3p, and SIX1 were detected by quantitative real-time polymerase chain reaction. Cell proliferation was assessed by cell counting Kit 8 assay. Cell migration and invasion were evaluated by transwell assay. Cell apoptosis was detected by flow cytometry assay. Murine model was established using transfected Me180 cell. The interaction among XIST, miR-889-3p, and SIX1 was tested by dual-luciferase reporter and RNA immunoprecipitation assays. Protein level of SIX1 was measured by Western blot. Results: XIST was highly expressed in CC tissues and cells. Silenced XIST inhibited proliferation, migration, and invasion and induced apoptosis. Moreover, XIST silencing blocked tumor growth in vivo. XIST directly bound to miR-889-3p, and XIST promoted proliferation, migration, and invasion and hindered apoptosis by suppressing miR-889-3p expression. MiR-889-3p targeted SIX1 and negatively regulated SIX1 expression. Furthermore, miR-889-3p had a low expression and SIX1 had a high expression in CC tissues and cells. XIST knockdown reduced SIX1 level by targeting miR-889-3p. In addition, miR-889-3p inhibition abolished the effects of SIX silencing on proliferation, migration, invasion, and apoptosis. Conclusion: XIST knockdown restrained cell proliferation, migration, and invasion and promoted apoptosis by regulating miR-889-3p/SIX1 axis.
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Affiliation(s)
- Xiaojuan Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Shuangshuang Xie
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Jing Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Yanhua Kang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
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224
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He RZ, Jiang J, Luo DX. The functions of N6-methyladenosine modification in lncRNAs. Genes Dis 2020; 7:598-605. [PMID: 33335959 PMCID: PMC7729116 DOI: 10.1016/j.gendis.2020.03.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/05/2020] [Accepted: 03/08/2020] [Indexed: 01/08/2023] Open
Abstract
Increasing evidence indicates that mRNAs are often subject to posttranscriptional modifications. Among them, N6-methyladenosine (m6A), which has been shown to play key roles in RNA splicing, stability, nuclear export, and translation, is the most abundant modification of RNA. Extensive studies of m6A modification of mRNAs have been carried out, while little is known about m6A modification of long non-coding RNAs (lncRNAs). Recently, several studies reported m6A modification of lncRNAs. In this review, we focus on these m6A-modified lncRNAs and discuss possible functions of m6A modification.
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Affiliation(s)
- Rong-Zhang He
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China.,Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China
| | - Jing Jiang
- Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China.,Center for Clinical Pathology, The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, People's Republic of China
| | - Di-Xian Luo
- Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China.,Center for Clinical Pathology, The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, People's Republic of China
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225
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Akkipeddi SMK, Velleca AJ, Carone DM. Probing the function of long noncoding RNAs in the nucleus. Chromosome Res 2020; 28:87-110. [PMID: 32026224 PMCID: PMC7131881 DOI: 10.1007/s10577-019-09625-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 12/29/2019] [Indexed: 12/26/2022]
Abstract
The nucleus is a highly organized and dynamic environment where regulation and coordination of processes such as gene expression and DNA replication are paramount. In recent years, noncoding RNAs have emerged as key participants in the regulation of nuclear processes. There are a multitude of functional roles for long noncoding RNA (lncRNA), mediated through their ability to act as molecular scaffolds bridging interactions with proteins, chromatin, and other RNA molecules within the nuclear environment. In this review, we discuss the diversity of techniques that have been developed to probe the function of nuclear lncRNAs, along with the ways in which those techniques have revealed insights into their mechanisms of action. Foundational observations into lncRNA function have been gleaned from molecular cytology-based, single-cell approaches to illuminate both the localization and abundance of lncRNAs in addition to their potential binding partners. Biochemical, extraction-based approaches have revealed the molecular contacts between lncRNAs and other molecules within the nuclear environment and how those interactions may contribute to nuclear organization and regulation. Using examples of well-studied nuclear lncRNAs, we demonstrate that the emerging functions of individual lncRNAs have been most clearly deduced from combined cytology and biochemical approaches tailored to study specific lncRNAs. As more functional nuclear lncRNAs continue to emerge, the development of additional technologies to study their interactions and mechanisms of action promise to continually expand our understanding of nuclear organization, chromosome architecture, genome regulation, and disease states.
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Affiliation(s)
| | - Anthony J Velleca
- Department of Molecular Phamacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dawn M Carone
- Department of Biology, Swarthmore College, Swarthmore, PA, USA.
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226
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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227
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Yao B, Liang M, Liu H, Sui T, Song Y, Zhang Y, Deng J, Xu Y, Lai L, Li Z. The minimal promoter (P1) of Xist is non-essential for X chromosome inactivation. RNA Biol 2020; 17:623-629. [PMID: 32036747 DOI: 10.1080/15476286.2020.1725725] [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: 10/25/2022] Open
Abstract
The previous report shows the minimal promoter (P1) contributes to the Xist RNA activation in cells, while the role of the Xist P1 has not yet been investigated in animal individuals. Here, female Xist P1 knockout rabbits (Xist P1-/-) were generated for the studies. The results showed that there is no significant difference in transmission ratio, Xist and X-linked genes expression, and Xist RNA localization between the female wild type (WT) and Xist P1-/- rabbits, suggesting that P1 is non-essential for Xist expression and XCI in rabbits. Our study has explored the function of Xist P1 in animal level for the first time, and the results provide new ideas for future studies of XCI mechanisms.
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Affiliation(s)
- Bing Yao
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
| | - Mingming Liang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
| | - Hongmei Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
| | - Tingting Sui
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
| | - Yuning Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
| | - Yuxin Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
| | - Jichao Deng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
| | - Yuxin Xu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
| | - Liangxue Lai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China.,CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guang Dong Laboratory (GRMH-GDL), Guangzhou, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun, China
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228
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Darbellay F, Necsulea A. Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs. Mol Biol Evol 2020; 37:240-259. [PMID: 31539080 PMCID: PMC6984365 DOI: 10.1093/molbev/msz212] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for individual lncRNAs. Most lncRNAs with proven functions were implicated in gene expression regulation, in pathways related to cellular pluripotency, differentiation, and organ morphogenesis, suggesting that functional lncRNAs may be more abundant in embryonic development, rather than in adult organs. To test this hypothesis, we perform a multidimensional comparative transcriptomics analysis, across five developmental time points (two embryonic stages, newborn, adult, and aged individuals), four organs (brain, kidney, liver, and testes), and three species (mouse, rat, and chicken). We find that, overwhelmingly, lncRNAs are preferentially expressed in adult and aged testes, consistent with the presence of permissive transcription during spermatogenesis. LncRNAs are often differentially expressed among developmental stages and are less abundant in embryos and newborns compared with adult individuals, in agreement with a requirement for tighter expression control and less tolerance for noisy transcription early in development. For differentially expressed lncRNAs, we find that the patterns of expression variation among developmental stages are generally conserved between mouse and rat. Moreover, lncRNAs expressed above noise levels in somatic organs and during development show higher evolutionary conservation, in particular, at their promoter regions. Thus, we show that functionally constrained lncRNA loci are enriched in developing organs, and we suggest that many of these loci may function in an RNA-independent manner.
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Affiliation(s)
- Fabrice Darbellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anamaria Necsulea
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
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229
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Luo Y, Yang J, Yu J, Liu X, Yu C, Hu J, Shi H, Ma X. Long Non-coding RNAs: Emerging Roles in the Immunosuppressive Tumor Microenvironment. Front Oncol 2020; 10:48. [PMID: 32083005 PMCID: PMC7005925 DOI: 10.3389/fonc.2020.00048] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/13/2020] [Indexed: 02/05/2023] Open
Abstract
Tumor immunosuppression may assist the immune escape of cancer cells, which promotes tumor metastasis and resistance to chemo-radiotherapy. The therapeutic strategies against tumor immunosuppression mainly focus on blocking immune checkpoint receptors, enhancing T-cell recognition and neutralizing inhibitory molecules. Although immunotherapies based on these strategies have improved the clinical outcomes, immunological nonresponse and resistance are two barriers to tumor eradication. Therefore, there is an urgent need to identify new biomarkers for patient selection and therapeutic targets for the development of combination regimen with immunotherapy. Recent studies have reported that non-protein-coding modulators exhibit important functions in post-transcriptional gene regulation, which subsequently modulates multiple pathophysiological processes, including neoplastic transformation. Differentiated from microRNAs, long non-coding RNAs (lncRNAs) are reported to be involved in various processes of the immune response in the tumor microenvironment (TME) to promote tumor immunosuppression. Currently, studies on tumor immunity regulated by lncRNAs are mainly confined to certain types of cancer cells or stromal cells. Additionally, the majority of studies are focused on the events involved in T cells and myeloid-derived suppressor cells (MDSCs). Although the reported studies have indicated the significance of lncRNAs in immunotherapy, the lack of comprehensive studies prevents us from exploring useful lncRNAs. In the current review, we have summarized the roles of lncRNAs in tumor immune response, and highlighted major lncRNAs as potential biomarkers or therapeutic targets for clinical application of immunotherapy.
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Affiliation(s)
- Ya Luo
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jiqiao Yang
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.,Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Yu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xiaowei Liu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chune Yu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xuelei Ma
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.,State Key Laboratory of Biotherapy, Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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230
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Yu D, Ruan X, Huang J, Hu W, Chen C, Xu Y, Hou J, Li S. Comprehensive Analysis of Competitive Endogenous RNAs Network, Being Associated With Esophageal Squamous Cell Carcinoma and Its Emerging Role in Head and Neck Squamous Cell Carcinoma. Front Oncol 2020; 9:1474. [PMID: 32038997 PMCID: PMC6985543 DOI: 10.3389/fonc.2019.01474] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 12/09/2019] [Indexed: 12/24/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignancy with poor prognosis and survival rate. To identify meaningful long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) modules related to the ESCC prognosis, The Cancer Genome Atlas-ESCC was downloaded and processed, and then, a weighted gene co-expression network analysis was applied to construct lncRNA co-expression networks, miRNA co-expression networks, and mRNA co-expression networks. Twenty-one hub lncRNAs, seven hub miRNAs, and eight hub mRNAs were clarified. Additionally, a competitive endogenous RNAs network was constructed, and the emerging role of the network involved in head and neck squamous cell carcinoma (HNSCC) was also analyzed using several webtools. The expression levels of eight hub genes (TBC1D2, ATP6V0E1, SPI1, RNASE6, C1QB, C1QC, CSF1R, and C1QA) were different between normal esophageal tissues and HNSCC tissues. The expression levels of TBC1D2 and ATP6V0E1 were related to the survival time of HNSCC. The competitive endogenous RNAs network might provide common mechanisms involving in ESCC and HNSCC. More importantly, useful clues were provided for clinical treatments of both diseases based on novel molecular advances.
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Affiliation(s)
- Donghu Yu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Xiaolan Ruan
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jingyu Huang
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Weidong Hu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chen Chen
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
| | - Yu Xu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jinxuan Hou
- Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Sheng Li
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan, China
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231
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Chen X, Sun YZ, Guan NN, Qu J, Huang ZA, Zhu ZX, Li JQ. Computational models for lncRNA function prediction and functional similarity calculation. Brief Funct Genomics 2020; 18:58-82. [PMID: 30247501 DOI: 10.1093/bfgp/ely031] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/17/2018] [Accepted: 08/30/2018] [Indexed: 02/01/2023] Open
Abstract
From transcriptional noise to dark matter of biology, the rapidly changing view of long non-coding RNA (lncRNA) leads to deep understanding of human complex diseases induced by abnormal expression of lncRNAs. There is urgent need to discern potential functional roles of lncRNAs for further study of pathology, diagnosis, therapy, prognosis, prevention of human complex disease and disease biomarker detection at lncRNA level. Computational models are anticipated to be an effective way to combine current related databases for predicting most potential lncRNA functions and calculating lncRNA functional similarity on the large scale. In this review, we firstly illustrated the biological function of lncRNAs from five biological processes and briefly depicted the relationship between mutations or dysfunctions of lncRNAs and human complex diseases involving cancers, nervous system disorders and others. Then, 17 publicly available lncRNA function-related databases containing four types of functional information content were introduced. Based on these databases, dozens of developed computational models are emerging to help characterize the functional roles of lncRNAs. We therefore systematically described and classified both 16 lncRNA function prediction models and 9 lncRNA functional similarity calculation models into 8 types for highlighting their core algorithm and process. Finally, we concluded with discussions about the advantages and limitations of these computational models and future directions of lncRNA function prediction and functional similarity calculation. We believe that constructing systematic functional annotation systems is essential to strengthen the prediction accuracy of computational models, which will accelerate the identification process of novel lncRNA functions in the future.
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Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Ya-Zhou Sun
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Na-Na Guan
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jia Qu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China
| | - Zhi-An Huang
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Ze-Xuan Zhu
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
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232
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Patrat C, Ouimette JF, Rougeulle C. X chromosome inactivation in human development. Development 2020; 147:147/1/dev183095. [PMID: 31900287 DOI: 10.1242/dev.183095] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
X chromosome inactivation (XCI) is a key developmental process taking place in female mammals to compensate for the imbalance in the dosage of X-chromosomal genes between sexes. It is a formidable example of concerted gene regulation and a paradigm for epigenetic processes. Although XCI has been substantially deciphered in the mouse model, how this process is initiated in humans has long remained unexplored. However, recent advances in the experimental capacity to access human embryonic-derived material and in the laws governing ethical considerations of human embryonic research have allowed us to enlighten this black box. Here, we will summarize the current knowledge of human XCI, mainly based on the analyses of embryos derived from in vitro fertilization and of pluripotent stem cells, and highlight any unanswered questions.
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Affiliation(s)
- Catherine Patrat
- Université de Paris, UMR 1016, Institut Cochin, 75014 Paris, France .,Service de Biologie de la Reproduction - CECOS, Paris Centre Hospital, APHP.centre, 75014 Paris, France
| | | | - Claire Rougeulle
- Université de Paris, Epigenetics and Cell Fate, CNRS, F-75013 Paris, France
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233
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Yoshino Y, Dwivedi Y. Non-Coding RNAs in Psychiatric Disorders and Suicidal Behavior. Front Psychiatry 2020; 11:543893. [PMID: 33101077 PMCID: PMC7522197 DOI: 10.3389/fpsyt.2020.543893] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/14/2020] [Indexed: 12/18/2022] Open
Abstract
It is well known that only a small proportion of the human genome code for proteins; the rest belong to the family of RNAs that do not code for protein and are known as non-coding RNAs (ncRNAs). ncRNAs are further divided into two subclasses based on size: 1) long non-coding RNAs (lncRNAs; >200 nucleotides) and 2) small RNAs (<200 nucleotides). Small RNAs contain various family members that include microRNAs (miRNAs), small interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and small nuclear RNAs (snRNAs). The roles of ncRNAs, especially lncRNAs and miRNAs, are well documented in brain development, homeostasis, stress responses, and neural plasticity. It has also been reported that ncRNAs can influence the development of psychiatric disorders including schizophrenia, major depressive disorder, and bipolar disorder. More recently, their roles are being investigated in suicidal behavior. In this article, we have comprehensively reviewed the findings of lncRNA and miRNA expression changes and their functions in various psychiatric disorders including suicidal behavior. We primarily focused on studies that have been done in postmortem human brain. In addition, we have briefly reviewed the role of other small RNAs (e.g. piwiRNA, siRNA, snRNA, and snoRNAs) and their expression changes in psychiatric illnesses.
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Affiliation(s)
- Yuta Yoshino
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yogesh Dwivedi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
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234
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Jansz N, Nesterova T, Keniry A, Iminitoff M, Hickey PF, Pintacuda G, Masui O, Kobelke S, Geoghegan N, Breslin KA, Willson TA, Rogers K, Kay GF, Fox AH, Koseki H, Brockdorff N, Murphy JM, Blewitt ME. Smchd1 Targeting to the Inactive X Is Dependent on the Xist-HnrnpK-PRC1 Pathway. Cell Rep 2019; 25:1912-1923.e9. [PMID: 30428357 DOI: 10.1016/j.celrep.2018.10.044] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/06/2018] [Accepted: 10/11/2018] [Indexed: 01/08/2023] Open
Abstract
We and others have recently reported that the SMC protein Smchd1 is a regulator of chromosome conformation. Smchd1 is critical for the structure of the inactive X chromosome and at autosomal targets such as the Hox genes. However, it is unknown how Smchd1 is recruited to these sites. Here, we report that Smchd1 localizes to the inactive X via the Xist-HnrnpK-PRC1 (polycomb repressive complex 1) pathway. Contrary to previous reports, Smchd1 does not bind Xist or other RNA molecules with any specificity. Rather, the localization of Smchd1 to the inactive X is H2AK119ub dependent. Following perturbation of this interaction, Smchd1 is destabilized, which has consequences for gene silencing genome-wide. Our work adds Smchd1 to the PRC1 silencing pathway for X chromosome inactivation.
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Affiliation(s)
- Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tatyana Nesterova
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Greta Pintacuda
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Osamu Masui
- Centre for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Simon Kobelke
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Niall Geoghegan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kelsey A Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Tracy A Willson
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia
| | - Kelly Rogers
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Graham F Kay
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Archa H Fox
- School of Human Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Haruhiko Koseki
- Centre for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia; Department of Genetics, University of Melbourne, Melbourne, VIC 3010, Australia.
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235
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Statistical methods for testing X chromosome variant associations: application to sex-specific characteristics of bipolar disorder. Biol Sex Differ 2019; 10:57. [PMID: 31818333 PMCID: PMC6902568 DOI: 10.1186/s13293-019-0272-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/21/2019] [Indexed: 11/17/2022] Open
Abstract
Background Bipolar disorder (BD) affects both sexes, but important sex differences exist with respect to its symptoms and comorbidities. For example, rapid cycling (RC) is more prevalent in females, and alcohol use disorder (AUD) is more prevalent in males. We hypothesize that X chromosome variants may be associated with sex-specific characteristics of BD. Few studies have explored the role of the X chromosome in BD, which is complicated by X chromosome inactivation (XCI). This process achieves “dosage compensation” for many X chromosome genes by silencing one of the two copies in females, and most statistical methods either ignore that XCI occurs or falsely assume that one copy is inactivated at all loci. We introduce new statistical methods that do not make these assumptions. Methods We investigated this hypothesis in 1001 BD patients from the Genetic Association Information Network (GAIN) and 957 BD patients from the Mayo Clinic Bipolar Disorder Biobank. We examined the association of over 14,000 X chromosome single nucleotide polymorphisms (SNPs) with sex-associated BD traits using two statistical approaches that account for whether a SNP may be undergoing or escaping XCI. In the “XCI-informed approach,” we fit a sex-adjusted logistic regression model assuming additive genetic effects where we coded the SNP either assuming one copy is expressed or two copies are expressed based on prior knowledge about which regions are inactivated. In the “XCI-robust approach,” we fit a logistic regression model with sex, SNP, and SNP-sex interaction effects that is flexible to whether the region is inactivated or escaping XCI. Results Using the “XCI-informed approach,” which considers only the main effect of SNP and does not allow the SNP effect to differ by sex, no significant associations were identified for any of the phenotypes. Using the “XCI-robust approach,” intergenic SNP rs5932307 was associated with BD (P = 8.3 × 10−8), with a stronger effect in females (odds ratio in males (ORM) = 1.13, odds ratio in females for a change of two allele copies (ORW2) = 3.86). Conclusion X chromosome association studies should employ methods which account for its unique biology. Future work is needed to validate the identified associations with BD, to formally assess the performance of both approaches under different true genetic architectures, and to apply these approaches to study sex differences in other conditions.
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236
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Abstract
The non-coding RNA Xist regulates the process of X chromosome inactivation, in which one of the two X chromosomes present in cells of early female mammalian embryos is selectively and coordinately shut down. Remarkably Xist RNA functions in cis, affecting only the chromosome from which it is transcribed. This feature is attributable to the unique propensity of Xist RNA to accumulate over the territory of the chromosome on which it is synthesized, contrasting with the majority of RNAs that are rapidly exported out of the cell nucleus. In this review I provide an overview of the progress that has been made towards understanding localized accumulation of Xist RNA, drawing attention to evidence that some other non-coding RNAs probably function in a highly analogous manner. I describe a simple model for localized accumulation of Xist RNA and discuss key unresolved questions that need to be addressed in future studies.
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Affiliation(s)
- Neil Brockdorff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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237
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McDonel P, Guttman M. Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression. Cold Spring Harb Perspect Biol 2019; 11:11/12/a032151. [PMID: 31791999 DOI: 10.1101/cshperspect.a032151] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mammalian genomes encode tens of thousands of long noncoding RNAs (lncRNAs) that have been implicated in a diverse array of biological processes and human diseases. In recent years, the development of new tools for studying lncRNAs has enabled important progress in defining the mechanisms by which Xist and other lncRNAs function. This collective work provides a framework for how to define the mechanisms by which lncRNAs act. This includes defining lncRNA function, identifying and characterizing lncRNA-protein interactions, and lncRNA localization in the cell. In this review, we discuss various experimental approaches for deciphering lncRNA mechanisms and discuss issues and limitations in interpreting these results. We explore what these data can reveal about lncRNA function and mechanism as well as emerging insights into lncRNA biology that have been derived from these studies.
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Affiliation(s)
- Patrick McDonel
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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238
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Smith KN, Miller SC, Varani G, Calabrese JM, Magnuson T. Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification. Genetics 2019; 213:1093-1110. [PMID: 31796550 PMCID: PMC6893379 DOI: 10.1534/genetics.119.302661] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Lineage specification in early development is the basis for the exquisitely precise body plan of multicellular organisms. It is therefore critical to understand cell fate decisions in early development. Moreover, for regenerative medicine, the accurate specification of cell types to replace damaged/diseased tissue is strongly dependent on identifying determinants of cell identity. Long noncoding RNAs (lncRNAs) have been shown to regulate cellular plasticity, including pluripotency establishment and maintenance, differentiation and development, yet broad phenotypic analysis and the mechanistic basis of their function remains lacking. As components of molecular condensates, lncRNAs interact with almost all classes of cellular biomolecules, including proteins, DNA, mRNAs, and microRNAs. With functions ranging from controlling alternative splicing of mRNAs, to providing scaffolding upon which chromatin modifiers are assembled, it is clear that at least a subset of lncRNAs are far from the transcriptional noise they were once deemed. This review highlights the diversity of lncRNA interactions in the context of cell fate specification, and provides examples of each type of interaction in relevant developmental contexts. Also highlighted are experimental and computational approaches to study lncRNAs.
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Affiliation(s)
- Keriayn N Smith
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sarah C Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
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239
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Heritability of skewed X-inactivation in female twins is tissue-specific and associated with age. Nat Commun 2019; 10:5339. [PMID: 31767861 PMCID: PMC6877649 DOI: 10.1038/s41467-019-13340-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 11/04/2019] [Indexed: 12/16/2022] Open
Abstract
Female somatic X-chromosome inactivation (XCI) balances the X-linked transcriptional dosages between the sexes. Skewed XCI toward one parental X has been observed in several complex human traits, but the extent to which genetics and environment influence skewed XCI is largely unexplored. To address this, we quantify XCI-skew in multiple tissues and immune cell types in a twin cohort. Within an individual, XCI-skew differs between blood, fat and skin tissue, but is shared across immune cell types. XCI skew increases with age in blood, but not other tissues, and is associated with smoking. XCI-skew is increased in twins with Rheumatoid Arthritis compared to unaffected identical co-twins. XCI-skew is heritable in blood of females >55 years old (h2 = 0.34), but not in younger individuals or other tissues. This results in a Gene x Age interaction that shifts the functional dosage of all X-linked heterozygous loci in a tissue-restricted manner. Skewing of X chromosome inactivation (XCI) occurs when the silencing of one parental X chromosome is non-random. Here, Zito et al. report XCI patterns in lymphoblastoid cell lines, blood, subcutaneous adipose tissue samples and skin samples of monozygotic and dizygotic twins and find XCI skew to associate with tissue and age.
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240
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In-cell identification and measurement of RNA-protein interactions. Nat Commun 2019; 10:5317. [PMID: 31757954 PMCID: PMC6876571 DOI: 10.1038/s41467-019-13235-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/29/2019] [Indexed: 12/18/2022] Open
Abstract
Regulatory RNAs exert their cellular functions through RNA-binding proteins (RBPs). Identifying RNA-protein interactions is therefore key for a molecular understanding of regulatory RNAs. To date, RNA-bound proteins have been identified primarily through RNA purification followed by mass spectrometry. Here, we develop incPRINT (in cell protein-RNA interaction), a high-throughput method to identify in-cell RNA-protein interactions revealed by quantifiable luminescence. Applying incPRINT to long noncoding RNAs (lncRNAs), we identify RBPs specifically interacting with the lncRNA Firre and three functionally distinct regions of the lncRNA Xist. incPRINT confirms previously known lncRNA-protein interactions and identifies additional interactions that had evaded detection with other approaches. Importantly, the majority of the incPRINT-defined interactions are specific to individual functional regions of the large Xist transcript. Thus, we present an RNA-centric method that enables reliable identification of RNA-region-specific RBPs and is applicable to any RNA of interest. RNA-interacting proteome can be identified by RNA affinity purification followed by mass spectrometry. Here the authors developed a different RNA-centric technology that combines high-throughput immunoprecipitation of RNA binding proteins and luciferase-based detection of their interaction with the RNA.
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241
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Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat Methods 2019; 16:1297-1305. [PMID: 31740818 PMCID: PMC7768885 DOI: 10.1038/s41592-019-0617-2] [Citation(s) in RCA: 328] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 09/19/2019] [Indexed: 12/11/2022]
Abstract
High throughput cDNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and because modifications are not retained. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions. These native RNA reads had a median length of 771 bases, and a maximum aligned length of over 21,000 bases. Mitochondrial poly(A) reads provided an internal measure of read length quality. We combined these long nanopore reads with higher accuracy short-reads and annotated GM12878 promoter regions, to identify 33,984 plausible RNA isoforms. We describe strategies for assessing 3′ poly(A) tail length, base modifications, and transcript haplotypes.
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242
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Vishnubalaji R, Shaath H, Elango R, Alajez NM. Noncoding RNAs as potential mediators of resistance to cancer immunotherapy. Semin Cancer Biol 2019; 65:65-79. [PMID: 31733291 DOI: 10.1016/j.semcancer.2019.11.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/31/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]
Abstract
Substantial evolution in cancer therapy has been witnessed lately, steering mainly towards immunotherapeutic approaches, replacing or in combination with classical therapies. Whereas the use of various immunotherapy approaches, such as adoptive T cell therapy, genetically-modified T cells, or immune checkpoint inhibitors, has been a triumph for cancer immunotherapy, the great challenge is the ability of the immune system to sustain long lasting anti-tumor response. Additionally, epigenetic changes in a suppressive tumor microenvironment can pertain to T cell exhaustion, limiting their functionality. Noncoding RNAs (ncRNAs) have emerged over the last years as key players in epigenetic regulation. Among those, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have been studied extensively for their potential role in regulating tumor immunity through direct regulation of genes involved in immune activation or suppression. In this review, we will provide an overview of contemporary approaches for cancer immunotherapy and will present the current state of knowledge implicating miRNAs and lncRNAs in regulating immune response against human cancer and their potential implications in resistance to cancer immunotherapy, with main emphasis on immune checkpoints regulation.
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Affiliation(s)
- Radhakrishnan Vishnubalaji
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Hibah Shaath
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Ramesh Elango
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
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243
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Choudhari R, Sedano MJ, Harrison AL, Subramani R, Lin KY, Ramos EI, Lakshmanaswamy R, Gadad SS. Long noncoding RNAs in cancer: From discovery to therapeutic targets. Adv Clin Chem 2019; 95:105-147. [PMID: 32122521 DOI: 10.1016/bs.acc.2019.08.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently gained considerable attention as key players in biological regulation; however, the mechanisms by which lncRNAs govern various disease processes remain mysterious and are just beginning to be understood. The ease of next-generation sequencing technologies has led to an explosion of genomic information, especially for the lncRNA class of noncoding RNAs. LncRNAs exhibit the characteristics of mRNAs, such as polyadenylation, 5' methyl capping, RNA polymerase II-dependent transcription, and splicing. These transcripts comprise more than 200 nucleotides (nt) and are not translated into proteins. Directed interrogation of annotated lncRNAs from RNA-Seq datasets has revealed dramatic differences in their expression, largely driven by alterations in transcription, the cell cycle, and RNA metabolism. The fact that lncRNAs are expressed cell- and tissue-specifically makes them excellent biomarkers for ongoing biological events. Notably, lncRNAs are differentially expressed in several cancers and show a distinct association with clinical outcomes. Novel methods and strategies are being developed to study lncRNA function and will provide researchers with the tools and opportunities to develop lncRNA-based therapeutics for cancer.
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Affiliation(s)
- Ramesh Choudhari
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Melina J Sedano
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Alana L Harrison
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Ramadevi Subramani
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Ken Y Lin
- The Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Enrique I Ramos
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Rajkumar Lakshmanaswamy
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Shrikanth S Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States; Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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244
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Chen S, Yang J, Wei Y, Wei X. Epigenetic regulation of macrophages: from homeostasis maintenance to host defense. Cell Mol Immunol 2019; 17:36-49. [PMID: 31664225 PMCID: PMC6952359 DOI: 10.1038/s41423-019-0315-0] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 09/28/2019] [Indexed: 02/05/2023] Open
Abstract
Macrophages are crucial members of the innate immune response and important regulators. The differentiation and activation of macrophages require the timely regulation of gene expression, which depends on the interaction of a variety of factors, including transcription factors and epigenetic modifications. Epigenetic changes also give macrophages the ability to switch rapidly between cellular programs, indicating the ability of epigenetic mechanisms to affect phenotype plasticity. In this review, we focus on key epigenetic events associated with macrophage fate, highlighting events related to the maintenance of tissue homeostasis, responses to different stimuli and the formation of innate immune memory. Further understanding of the epigenetic regulation of macrophages will be helpful for maintaining tissue integrity, preventing chronic inflammatory diseases and developing therapies to enhance host defense.
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Affiliation(s)
- Siyuan Chen
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China
| | - Jing Yang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China.
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245
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Posynick BJ, Brown CJ. Escape From X-Chromosome Inactivation: An Evolutionary Perspective. Front Cell Dev Biol 2019; 7:241. [PMID: 31696116 PMCID: PMC6817483 DOI: 10.3389/fcell.2019.00241] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022] Open
Abstract
Sex chromosomes originate as a pair of homologus autosomes that then follow a general pattern of divergence. This is evident in mammalian sex chromosomes, which have undergone stepwise recombination suppression events that left footprints of evolutionary strata on the X chromosome. The loss of genes on the Y chromosome led to Ohno’s hypothesis of dosage equivalence between XY males and XX females, which is achieved through X-chromosome inactivation (XCI). This process transcriptionally silences all but one X chromosome in each female cell, although 15–30% of human X-linked genes still escape inactivation. There are multiple evolutionary pathways that may lead to a gene escaping XCI, including remaining Y chromosome homology, or female advantage to escape. The conservation of some escape genes across multiple species and the ability of the mouse inactive X to recapitulate human escape status both suggest that escape from XCI is controlled by conserved processes. Evolutionary pressures to minimize dosage imbalances have led to the accumulation of genetic elements that favor either silencing or escape; lack of dosage sensitivity might also allow for the escape of flanking genes near another escapee, if a boundary element is not present between them. Delineation of the elements involved in escape is progressing, but mechanistic understanding of how they interact to allow escape from XCI is still lacking. Although increasingly well-studied in humans and mice, non-trivial challenges to studying escape have impeded progress in other species. Mouse models that can dissect the role of the sex chromosomes distinct from sex of the organism reveal an important contribution for escape genes to multiple diseases. In humans, with their elevated number of escape genes, the phenotypic consequences of sex chromosome aneuplodies and sexual dimorphism in disease both highlight the importance of escape genes.
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Affiliation(s)
- Bronwyn J Posynick
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
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246
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Yo K, Rünger TM. The long non-coding RNA FLJ46906 binds to the transcription factors NF-κB and AP-1 and regulates expression of aging-associated genes. Aging (Albany NY) 2019; 10:2037-2050. [PMID: 30125263 PMCID: PMC6128423 DOI: 10.18632/aging.101528] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/13/2018] [Indexed: 01/06/2023]
Abstract
Several features differentiate aged cells from young cells, many of which are due to changes in gene expression during the aging process. The mechanisms of altered gene expression in aging cells remain incompletely understood, and we hypothesized that long non-coding (lnc) RNAs mediate at least some of these changes. We screened for alterations in lncRNA expression with aging in skin fibroblasts and identified the lncRNA FLJ46906 to be consistently upregulated with aging in-vivo and in-vitro. The function of this lncRNA has not been known. Here we show that FLJ46906 regulates several aging-associated genes, including IL1B, IL6, CXCL8, TGFB1, and ELN. We suggest that these effects are mediated through NF-κB and AP-1, because these aging-associated genes are regulated by NF-κB and AP-1, and because we found that FLJ46906 directly binds to these two transcription factors. This data supports a role of the lncRNA FLJ46906 in the aging process.
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Affiliation(s)
- Kazuyuki Yo
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA.,Current address: Dermatological R & D, POLA Chemical Industries Inc., Yokohama, Japan
| | - Thomas M Rünger
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA
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247
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Wang CY, Brand H, Shaw ND, Talkowski ME, Lee JT. Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans. Genetics 2019; 213:685-703. [PMID: 31420322 PMCID: PMC6781896 DOI: 10.1534/genetics.119.302600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an architectural factor critical for X-chromosome inactivation (XCI) and the repression of select autosomal gene clusters. In mice, homozygous nonsense mutations in Smchd1 cause female-specific embryonic lethality due to an XCI defect. However, although human mutations in SMCHD1 are associated with congenital arhinia and facioscapulohumeral muscular dystrophy type 2 (FSHD2), the diseases do not show a sex-specific bias, despite the essential nature of XCI in humans. To investigate whether there is a dosage imbalance for the sex chromosomes, we here analyze transcriptomic data from arhinia and FSHD2 patient blood and muscle cells. We find that X-linked dosage compensation is maintained in these patients. In mice, SMCHD1 controls not only protocadherin (Pcdh) gene clusters, but also Hox genes critical for craniofacial development. Ablating Smchd1 results in aberrant expression of these genes, coinciding with altered chromatin states and three-dimensional (3D) topological organization. In a subset of FSHD2 and arhinia patients, we also found dysregulation of clustered PCDH, but not HOX genes. Overall, our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters.
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Affiliation(s)
- Chen-Yu Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Natalie D Shaw
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael E Talkowski
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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Duran RCD, Wei H, Kim DH, Wu JQ. Invited Review: Long non-coding RNAs: important regulators in the development, function and disorders of the central nervous system. Neuropathol Appl Neurobiol 2019; 45:538-556. [PMID: 30636336 PMCID: PMC6626588 DOI: 10.1111/nan.12541] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Genome-wide transcriptional studies have demonstrated that tens of thousands of long non-coding RNAs (lncRNA) genes are expressed in the central nervous system (CNS) and that they exhibit tissue- and cell-type specificity. Their regulated and dynamic expression and their co-expression with protein-coding gene neighbours have led to the study of the functions of lncRNAs in CNS development and disorders. In this review, we describe the general characteristics, localization and classification of lncRNAs. We also elucidate the examples of the molecular mechanisms of nuclear and cytoplasmic lncRNA actions in the CNS and discuss common experimental approaches used to identify and unveil the functions of lncRNAs. Additionally, we provide examples of lncRNA studies of cell differentiation and CNS disorders including CNS injuries and neurodegenerative diseases. Finally, we review novel lncRNA-based therapies. Overall, this review highlights the important biological roles of lncRNAs in CNS functions and disorders.
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Affiliation(s)
- Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey, N.L., 64710, Mexico
| | - Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Dong H. Kim
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
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249
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Syrett CM, Anguera MC. When the balance is broken: X-linked gene dosage from two X chromosomes and female-biased autoimmunity. J Leukoc Biol 2019; 106:919-932. [PMID: 31125996 PMCID: PMC7206452 DOI: 10.1002/jlb.6ri0319-094r] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/17/2019] [Accepted: 04/21/2019] [Indexed: 12/21/2022] Open
Abstract
Women and men exhibit differences in innate and adaptive immunity, and women are more susceptible to numerous autoimmune disorders. Two or more X chromosomes increases the risk for some autoimmune diseases, and increased expression of some X-linked immune genes is frequently observed in female lymphocytes from autoimmune patients. Evidence from mouse models of autoimmunity also supports the idea that increased expression of X-linked genes is a feature of female-biased autoimmunity. Recent studies have begun to elucidate the correlation between abnormal X-chromosome inactivation (XCI), an essential mechanism female somatic cells use to equalize X-linked gene dosage between the sexes, and autoimmunity in lymphocytes. In this review, we highlight research describing overexpression of X-linked immunity-related genes and female-biased autoimmunity in both humans and mouse models, and make connections with our recent work elucidating lymphocyte-specific mechanisms of XCI maintenance that become altered in lupus patients.
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Affiliation(s)
- Camille M Syrett
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Montserrat C Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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250
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Murillo-Maldonado JM, Riesgo-Escovar JR. The various and shared roles of lncRNAs during development. Dev Dyn 2019; 248:1059-1069. [PMID: 31454122 DOI: 10.1002/dvdy.108] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 01/03/2023] Open
Abstract
lncRNAs, genes transcribed but not translated, longer than 200 nucleotides, are classified as a separate class of nonprotein coding genes. Since their discovery, largely from RNAseq data, a number of pioneer studies have begun to unravel its myriad functions, centered on gene expression regulation, suggesting developmental and evolutionary conservation. Since they do not code for proteins and have no open reading frames, their functional constraints likely differ from that of protein coding genes, or of genes where the majority of the nucleotide sequence is required for function, like tRNAs. This has complicated assessment of both developmental and evolutionary conservation, and the identification of homologs in different species. Here we argue that other characteristics: general synteny and particular chromosomal placement regardless of sequence, sequence micro-motifs, and secondary structure allow for "homologs" to be identified and compared, confirming developmental and evolutionary conservation of lncRNAs. We conclude exemplifying a case in point: that of the evolutionarily conserved lncRNA acal, characterized and required for embryogenesis in Drosophila.
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Affiliation(s)
- Juan M Murillo-Maldonado
- Developmental Neurobiology and Neurophysiology, Instituto de Neurobología, Campus UNAM Juriquilla, Universidad Nacional Autónoma de Mexico, Santiago de Querétaro, Querétaro, Mexico
| | - Juan R Riesgo-Escovar
- Developmental Neurobiology and Neurophysiology, Instituto de Neurobología, Campus UNAM Juriquilla, Universidad Nacional Autónoma de Mexico, Santiago de Querétaro, Querétaro, Mexico
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