1
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Patlar B. On the Role of Seminal Fluid Protein and Nucleic Acid Content in Paternal Epigenetic Inheritance. Int J Mol Sci 2022; 23:ijms232314533. [PMID: 36498858 PMCID: PMC9739459 DOI: 10.3390/ijms232314533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/10/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
The evidence supports the occurrence of environmentally-induced paternal epigenetic inheritance that shapes the offspring phenotype in the absence of direct or indirect paternal care and clearly demonstrates that sperm epigenetics is one of the major actors mediating these paternal effects. However, in most animals, while sperm makes up only a small portion of the seminal fluid, males also have a complex mixture of proteins, peptides, different types of small noncoding RNAs, and cell-free DNA fragments in their ejaculate. These seminal fluid contents (Sfcs) are in close contact with the reproductive cells, tissues, organs, and other molecules of both males and females during reproduction. Moreover, their production and use are adjusted in response to environmental conditions, making them potential markers of environmentally- and developmentally-induced paternal effects on the next generation(s). Although there is some intriguing evidence for Sfc-mediated paternal effects, the underlying molecular mechanisms remain poorly defined. In this review, the current evidence regarding the links between seminal fluid and environmental paternal effects and the potential pathways and mechanisms that seminal fluid may follow in mediating paternal epigenetic inheritance are discussed.
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Affiliation(s)
- Bahar Patlar
- Animal Ecology, Department of Zoology, Martin-Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany
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2
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Liu M, Liu P, Chang Y, Xu B, Wang N, Qin L, Zheng J, Liu Y, Wu L, Yan H. Genome-wide DNA methylation profiles and small noncoding RNA signatures in sperm with a high DNA fragmentation index. J Assist Reprod Genet 2022; 39:2255-2274. [PMID: 36190595 PMCID: PMC9596664 DOI: 10.1007/s10815-022-02618-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND A growing number of studies have reported that sperm DNA fragmentation (SDF) is associated with male infertility. However, no studies have compared genome-wide DNA methylation profiles and sncRNA signatures between sperm with high and low sperm DNA fragmentation indices (DFIs). METHODS Whole-genome bisulfite sequencing (WGBS) was performed on sperm samples from a weak group (DFI ≥ 30%, n = 6) and normal group (DFI ≤ 15%, n = 7). Small noncoding RNA (sncRNA) deep sequencing was conducted for sperm samples from the weak (DFI ≥ 30%, n = 13) and normal (DFI ≤ 15%, n = 17) groups. RESULTS A total of 4939 differentially methylated regions (DMRs) were identified in the weak group sperm samples relative to normal group sperm samples, with 2072 (41.95%) of them located in promoter regions. The percentages of hypermethylated DMRs were higher than those of hypomethylated DMRs in all seven examined gene annotation groups. Hypermethylated DMRs were significantly enriched in terms associated with neurons and microtubules. Compared with the normal group, the global DNA methylation level of the weak group sperm showed a downward trend, with lower correlation for methylation in the weak group sperm; therefore, the chromosomes of high-DFI sperm may be loose. On average, 40.5% of sncRNAs were annotated as rsRNAs, 19.3% as tsRNAs, 10.4% as yRNAs, and 7.1% as miRNAs. A total of 27 miRNAs, 151 tsRNAs, and 70 rsRNAs were differentially expressed between the two groups of sperm samples. Finally, 7 sncRNAs were identified as candidate sperm quality biomarkers, and the target genes of the differentially expressed miRNAs are involved in nervous system development. CONCLUSION Our findings suggest that genome-wide DNA methylation profiles and sncRNA signatures are significantly altered in high-DFI sperm. Our study provides potential biomarkers for sperm quality.
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Affiliation(s)
- Minghua Liu
- Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Peiru Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunjian Chang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Beiying Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Nengzhuang Wang
- Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Lina Qin
- Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Jufen Zheng
- Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China.
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
| | - Hongli Yan
- Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China.
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3
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Assante G, Chandrasekaran S, Ng S, Tourna A, Chung CH, Isse KA, Banks JL, Soffientini U, Filippi C, Dhawan A, Liu M, Rozen SG, Hoare M, Campbell P, Ballard JWO, Turner N, Morris MJ, Chokshi S, Youngson NA. Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease. Genome Med 2022; 14:67. [PMID: 35739588 PMCID: PMC9219160 DOI: 10.1186/s13073-022-01071-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of non-alcoholic fatty liver disease (NAFLD)-associated hepatocellular carcinoma (HCC) is increasing worldwide, but the steps in precancerous hepatocytes which lead to HCC driver mutations are not well understood. Here we provide evidence that metabolically driven histone hyperacetylation in steatotic hepatocytes can increase DNA damage to initiate carcinogenesis. METHODS Global epigenetic state was assessed in liver samples from high-fat diet or high-fructose diet rodent models, as well as in cultured immortalized human hepatocytes (IHH cells). The mechanisms linking steatosis, histone acetylation and DNA damage were investigated by computational metabolic modelling as well as through manipulation of IHH cells with metabolic and epigenetic inhibitors. Chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) and transcriptome (RNA-seq) analyses were performed on IHH cells. Mutation locations and patterns were compared between the IHH cell model and genome sequence data from preneoplastic fatty liver samples from patients with alcohol-related liver disease and NAFLD. RESULTS Genome-wide histone acetylation was increased in steatotic livers of rodents fed high-fructose or high-fat diet. In vitro, steatosis relaxed chromatin and increased DNA damage marker γH2AX, which was reversed by inhibiting acetyl-CoA production. Steatosis-associated acetylation and γH2AX were enriched at gene clusters in telomere-proximal regions which contained HCC tumour suppressors in hepatocytes and human fatty livers. Regions of metabolically driven epigenetic change also had increased levels of DNA mutation in non-cancerous tissue from NAFLD and alcohol-related liver disease patients. Finally, genome-scale network modelling indicated that redox balance could be a key contributor to this mechanism. CONCLUSIONS Abnormal histone hyperacetylation facilitates DNA damage in steatotic hepatocytes and is a potential initiating event in hepatocellular carcinogenesis.
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Affiliation(s)
- Gabriella Assante
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Sriram Chandrasekaran
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stanley Ng
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Aikaterini Tourna
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Carolina H Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kowsar A Isse
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Jasmine L Banks
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ugo Soffientini
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Celine Filippi
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Anil Dhawan
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Mo Liu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | | | - J William O Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Nigel Turner
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | | | - Shilpa Chokshi
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Neil A Youngson
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK.
- King's College London, Faculty of Life Sciences and Medicine, London, UK.
- UNSW Sydney, Sydney, Australia.
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4
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Panera N, Mandato C, Crudele A, Bertrando S, Vajro P, Alisi A. Genetics, epigenetics and transgenerational transmission of obesity in children. Front Endocrinol (Lausanne) 2022; 13:1006008. [PMID: 36452324 PMCID: PMC9704419 DOI: 10.3389/fendo.2022.1006008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Sedentary lifestyle and consumption of high-calorie foods have caused a relentless increase of overweight and obesity prevalence at all ages. Its presently epidemic proportion is disquieting due to the tight relationship of obesity with metabolic syndrome and several other comorbidities which do call for urgent workarounds. The usual ineffectiveness of present therapies and failure of prevention campaigns triggered overtime a number of research studies which have unveiled some relevant aspects of obesity genetic and epigenetic inheritable profiles. These findings are revealing extremely precious mainly to serve as a likely extra arrow to allow the clinician's bow to achieve still hitherto unmet preventive goals. Evidence now exists that maternal obesity/overnutrition during pregnancy and lactation convincingly appears associated with several disorders in the offspring independently of the transmission of a purely genetic predisposition. Even the pre-conception direct exposure of either father or mother gametes to environmental factors can reprogram the epigenetic architecture of cells. Such phenomena lie behind the transfer of the obesity susceptibility to future generations through a mechanism of epigenetic inheritance. Moreover, a growing number of studies suggests that several environmental factors such as maternal malnutrition, hypoxia, and exposure to excess hormones and endocrine disruptors during pregnancy and the early postnatal period may play critical roles in programming childhood adipose tissue and obesity. A deeper understanding of how inherited genetics and epigenetics may generate an obesogenic environment at pediatric age might strengthen our knowledge about pathogenetic mechanisms and improve the clinical management of patients. Therefore, in this narrative review, we attempt to provide a general overview of the contribution of heritable genetic and epigenetic patterns to the obesity susceptibility in children, placing a particular emphasis on the mother-child dyad.
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Affiliation(s)
- Nadia Panera
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Claudia Mandato
- Pediatrics Section, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salermo, Italy
- *Correspondence: Anna Alisi, ; Claudia Mandato,
| | - Annalisa Crudele
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Sara Bertrando
- Pediatrics Clinic, San Giovanni di Dio e Ruggi d’Aragona University Hospital, Salerno, Italy
| | - Pietro Vajro
- Pediatrics Section, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salermo, Italy
| | - Anna Alisi
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- *Correspondence: Anna Alisi, ; Claudia Mandato,
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5
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Ghai M, Kader F. A Review on Epigenetic Inheritance of Experiences in Humans. Biochem Genet 2021; 60:1107-1140. [PMID: 34792705 DOI: 10.1007/s10528-021-10155-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022]
Abstract
If genetics defines the inheritance of DNA, epigenetics aims to regulate and make it adaptable. Epigenetic alterations include DNA methylation, chromatin remodelling, post-translational modifications of histone proteins and activity of non-coding RNAs. Several studies, especially in animal models, have reported transgenerational inheritance of epigenetic marks. However, evidence of transgenerational inheritance in humans via germline in the absence of any direct exposure to the driving external stimulus remains controversial. Most of the epimutations exist in relation with genetic variants. The present review looks at intergenerational and transgenerational inheritance in humans, (both father and mother) in response to diet, exposure to chemicals, stress, exercise, and disease status. If not transgenerational, at least intergenerational human studies could help to understand early processes of inheritance. In humans, female and male germline development follow separate paths of epigenetic events and both oocyte and sperm possess their own unique epigenomes. While DNA methylation alterations are reset during epigenetic reprogramming, non-coding RNAs via human sperm provide evidence of being reliable carriers for transgenerational inheritance. Human studies reveal that one mechanism of epigenetic inheritance cannot be applied to the complete human genome. Multiple factors including time, type, and tissue of exposure determine if the modified epigenetic mark could be transmissible and till which generation. Population-specific differences should also be taken into consideration while associating inheritance to an environmental exposure. A longitudinal study targeting one environmental factor, but different population groups should be conducted at a specific geographical location to pinpoint heritable epigenetic changes.
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Affiliation(s)
- Meenu Ghai
- Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, KwaZulu Natal, South Africa.
| | - Farzeen Kader
- Discipline of Genetics, School of Life Sciences, Westville Campus, University of KwaZulu-Natal, Private Bag X54001, Durban, KwaZulu Natal, South Africa
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6
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Åsenius F, Gorrie-Stone TJ, Brew A, Panchbhaya Y, Williamson E, Schalkwyk LC, Rakyan VK, Holland ML, Marzi SJ, Williams DJ. The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations. PLoS Genet 2020; 16:e1009035. [PMID: 33048947 PMCID: PMC7584170 DOI: 10.1371/journal.pgen.1009035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/23/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022] Open
Abstract
Epidemiological research suggests that paternal obesity may increase the risk of fathering small for gestational age offspring. Studies in non-human mammals indicate that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. It is unclear, however, whether this differential DNA methylation is reflected in spermatozoa. We profiled genome-wide DNA methylation using the Illumina MethylationEPIC array in a cross-sectional study of matched human blood and sperm from lean (discovery n = 47; replication n = 21) and obese (n = 22) males to analyse tissue covariation of DNA methylation, and identify obesity-associated methylomic signatures. We found that DNA methylation signatures of human blood and spermatozoa are highly discordant, and methylation levels are correlated at only a minority of CpG sites (~1%). At the majority of these sites, DNA methylation appears to be influenced by genetic variation. Obesity-associated DNA methylation in blood was not generally reflected in spermatozoa, and obesity was not associated with altered covariation patterns or accelerated epigenetic ageing in the two tissues. However, one cross-tissue obesity-specific hypermethylated site (cg19357369; chr4:2429884; P = 8.95 × 10-8; 2% DNA methylation difference) was identified, warranting replication and further investigation. When compared to a wide range of human somatic tissue samples (n = 5,917), spermatozoa displayed differential DNA methylation across pathways enriched in transcriptional regulation. Overall, human sperm displays a unique DNA methylation profile that is highly discordant to, and practically uncorrelated with, that of matched peripheral blood. We observed that obesity was only nominally associated with differential DNA methylation in sperm, and therefore suggest that spermatozoal DNA methylation is an unlikely mediator of intergenerational effects of metabolic traits.
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Affiliation(s)
- Fredrika Åsenius
- UCL EGA Institute for Women’s Health, University College London, London, United Kingdom
| | | | - Ama Brew
- The Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Yasmin Panchbhaya
- UCL Genomics, Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Elizabeth Williamson
- Fertility & reproductive medicine laboratory, University College Hospital, London, United Kingdom
| | | | - Vardhman K. Rakyan
- The Blizard Institute, Queen Mary University of London, London, United Kingdom
| | - Michelle L. Holland
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - Sarah J. Marzi
- UK Dementia Research Institute, Imperial College London, London, United Kingdom
- Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - David J. Williams
- UCL EGA Institute for Women’s Health, University College London, London, United Kingdom
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7
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Thompson MD. Developmental Programming of NAFLD by Parental Obesity. Hepatol Commun 2020; 4:1392-1403. [PMID: 33024911 PMCID: PMC7527686 DOI: 10.1002/hep4.1578] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
The surge of obesity across generations has become an increasingly relevant issue, with consequences for associated comorbidities in offspring. Data from longitudinal birth cohort studies support an association between maternal obesity and offspring nonalcoholic fatty liver disease (NAFLD), suggesting that perinatal obesity or obesogenic diet exposure reprograms offspring liver and increases NAFLD susceptibility. In preclinical models, offspring exposed to maternal obesogenic diet have increased hepatic steatosis after diet-induced obesity; however, the implications for later NAFLD development and progression are still unclear. Although some models show increased NAFLD incidence and progression in offspring, development of nonalcoholic steatohepatitis with fibrosis may be model dependent. Multigenerational programming of NAFLD phenotypes occurs after maternal obesogenic diet exposure; however, the mechanisms for such programming remain poorly understood. Likewise, emerging data on the role of paternal obesity in offspring NAFLD development reveal incomplete mechanisms. This review will explore the impact of parental obesity and obesogenic diet exposure on offspring NAFLD and areas for further investigation, including the impact of parental diet on disease progression, and consider potential interventions in preclinical models.
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Affiliation(s)
- Michael D. Thompson
- Division of Endocrinology and DiabetesDepartment of PediatricsWashington University School of MedicineSt. LouisMO
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8
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Galan C, Krykbaeva M, Rando OJ. Early life lessons: The lasting effects of germline epigenetic information on organismal development. Mol Metab 2020; 38:100924. [PMID: 31974037 PMCID: PMC7300385 DOI: 10.1016/j.molmet.2019.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND An organism's metabolic phenotype is primarily affected by its genotype, its lifestyle, and the nutritional composition of its food supply. In addition, it is now clear from studies in many different species that ancestral environments can also modulate metabolism in at least one to two generations of offspring. SCOPE OF REVIEW We limit ourselves here to paternal effects in mammals, primarily focusing on studies performed in inbred rodent models. Although hundreds of studies link paternal diets and offspring metabolism, the mechanistic basis by which epigenetic information in sperm programs nutrient handling in the next generation remains mysterious. Our goal in this review is to provide a brief overview of paternal effect paradigms and the germline epigenome. We then pivot to exploring one key mystery in this literature: how do epigenetic changes in sperm, most of which are likely to act transiently in the early embryo, ultimately direct a long-lasting physiological response in offspring? MAJOR CONCLUSIONS Several potential mechanisms exist by which transient epigenetic modifications, such as small RNAs or methylation states erased shortly after fertilization, could be transferred to more durable heritable information. A detailed mechanistic understanding of this process will provide deep insights into early development, and could be of great relevance for human health and disease.
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Affiliation(s)
- Carolina Galan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Marina Krykbaeva
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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9
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Capra E, Lazzari B, Turri F, Cremonesi P, Portela AMR, Ajmone-Marsan P, Stella A, Pizzi F. Epigenetic analysis of high and low motile sperm populations reveals methylation variation in satellite regions within the pericentromeric position and in genes functionally related to sperm DNA organization and maintenance in Bos taurus. BMC Genomics 2019; 20:940. [PMID: 31810461 PMCID: PMC6898967 DOI: 10.1186/s12864-019-6317-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 11/21/2019] [Indexed: 12/31/2022] Open
Abstract
Background Sperm epigenetics is an emerging area of study supported by observations reporting that abnormal sperm DNA methylation patterns are associated with infertility. Here, we explore cytosine-guanine dinucleotides (CpGs) methylation in high (HM) and low motile (LM) Bos taurus sperm populations separated by Percoll gradient. HM and LM methylation patterns were investigated by bisulfite sequencing. Results Comparison between HM and LM sperm populations revealed that methylation variation affects genes involved in chromatin organization. CpG Islands (CGIs), were highly remodelled. A high proportion of CGIs was found to be methylated at low/intermediate level (20–60%) and associated to the repetitive element BTSAT4 satellite. The low/intermediate level of methylation in BTSAT4 was stably maintained in pericentric regions of chromosomes. BTSAT4 was hypomethylated in HM sperm populations. Conclusions The characterization of the epigenome in HM and LM Bos taurus sperm populations provides a first step towards the understanding of the effect of methylation on sperm fertility. Methylation variation observed in HM and LM populations in genes associated to DNA structure remodelling as well as in a repetitive element in pericentric regions suggests that maintenance of chromosome structure through epigenetic regulation is probably crucial for correct sperm functionality.
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Affiliation(s)
- Emanuele Capra
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein, 26900, Lodi, Italy
| | - Barbara Lazzari
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein, 26900, Lodi, Italy
| | - Federica Turri
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein, 26900, Lodi, Italy
| | - Paola Cremonesi
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein, 26900, Lodi, Italy
| | | | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition - DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italy.,Proteomics and Nutrigenomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein, 26900, Lodi, Italy
| | - Flavia Pizzi
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein, 26900, Lodi, Italy.
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10
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Estill MS, Hauser R, Krawetz SA. RNA element discovery from germ cell to blastocyst. Nucleic Acids Res 2019; 47:2263-2275. [PMID: 30576549 PMCID: PMC6411832 DOI: 10.1093/nar/gky1223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/31/2018] [Accepted: 11/24/2018] [Indexed: 12/19/2022] Open
Abstract
Recent studies have shown that tissue-specific transcriptomes contain multiple types of RNAs that are transcribed from intronic and intergenic sequences. The current study presents a tool for the discovery of transcribed, unannotated sequence elements from RNA-seq libraries. This RNA Element (RE) discovery algorithm (REDa) was applied to a spectrum of tissues and cells representing germline, embryonic, and somatic tissues and examined as a function of differentiation through the first set of cell divisions of human development. This highlighted extensive transcription throughout the genome, yielding previously unidentified human spermatogenic RNAs. Both exonic and novel X-chromosome REs were subject to robust meiotic sex chromosome inactivation, although an extensive de-repression occurred in the post-meiotic stages of spermatogenesis. Surprisingly, 2.4% of the 10,395 X chromosome exonic REs were present in mature sperm. Transcribed genomic repetitive sequences, including simple centromeric repeats, HERVE and HSAT1, were also shown to be associated with RE expression during spermatogenesis. These results suggest that pervasive intergenic repetitive sequence expression during human spermatogenesis may play a role in regulating chromatin dynamics. Repetitive REs switching repeat classes during differentiation upon fertilization and embryonic genome activation was evident.
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MESH Headings
- Algorithms
- Blastocyst/cytology
- Blastocyst/metabolism
- Cell Differentiation
- Cell Line
- Chromatin/genetics
- Chromatin/metabolism
- Chromosomes, Human, X/genetics
- Embryonic Development/genetics
- Exons/genetics
- Female
- Fertilization
- Gene Expression Regulation, Developmental
- Genomics
- Humans
- Liver/cytology
- Liver/metabolism
- Male
- Meiosis/genetics
- Oocytes/cytology
- Oocytes/metabolism
- Poly A/analysis
- Poly A/genetics
- Poly A/isolation & purification
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- Regulatory Sequences, Ribonucleic Acid/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, RNA
- Spermatogenesis/genetics
- Spermatozoa/cytology
- Spermatozoa/metabolism
- Transcription, Genetic
- X Chromosome Inactivation
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Affiliation(s)
- Molly S Estill
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
| | - Russ Hauser
- Vincent Memorial Obstetrics and Gynecology Service, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
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An T, Zhang T, Teng F, Zuo JC, Pan YY, Liu YF, Miao JN, Gu YJ, Yu N, Zhao DD, Mo FF, Gao SH, Jiang G. Long non-coding RNAs could act as vectors for paternal heredity of high fat diet-induced obesity. Oncotarget 2018; 8:47876-47889. [PMID: 28599310 PMCID: PMC5564612 DOI: 10.18632/oncotarget.18138] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/24/2017] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in epigenetic regulation, and abnormalities may lead to male infertility. To investigate whether lncRNAs are involved in intergenerational inheritance of obesity and obesity-induced decline in fertility, we divided mice into obesity (F0 mice fed a high-fat diet, F0-HFD) and non-obese (F0 mice fed normal chow, F0-NC) model groups and their male offspring (F1-HFD and F1-NC, respectively). We examined the differences in the expression levels of lncRNAs and mRNAs in the F0-HFD/F0-NC and F1-HFD/F1-NC groups. The results revealed similar expression patterns in the F1-HFD/F0-HFD groups at both the lncRNA and mRNA levels. The maximum difference in the lncRNA expression was observed between the F0-HFD and F0-NC groups. The differentially expressed lncRNA targets and mRNAs identified in our study are mainly involved in GnRH signalling pathway, metabolic process, and Hippo signalling pathway; similarly expressed lncRNAs and mRNAs in F1-HFD/F0-HFD are closely linked with G-protein coupled receptor signalling pathway, pancreatic polypeptide receptor activity, and lysine biosynthesis, which may play an important role in the molecular mechanism of intergenerational inheritance of obesity. Furthermore, potential genes that might play important roles in the pathogenesis of obesity-related low fertility were revealed by lncRNA-and mRNA-interaction studies based on the microarray expression profiles. In conclusion, we found that lncRNA could be involved in obesity-induced infertility by expressing abnormalities, which could act as genetic vectors of paternal inheritance of obesity.
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Affiliation(s)
- Tian An
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Teng Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fei Teng
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Jia-Cheng Zuo
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Yan-Yun Pan
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Yu-Fei Liu
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jia-Nan Miao
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Yu-Jie Gu
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Na Yu
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Dan-Dan Zhao
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Fang-Fang Mo
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Si-Hua Gao
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Guangjian Jiang
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
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12
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McCarrey JR, Lehle JD, Raju SS, Wang Y, Nilsson EE, Skinner MK. Tertiary Epimutations - A Novel Aspect of Epigenetic Transgenerational Inheritance Promoting Genome Instability. PLoS One 2016; 11:e0168038. [PMID: 27992467 PMCID: PMC5167269 DOI: 10.1371/journal.pone.0168038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 11/23/2016] [Indexed: 11/29/2022] Open
Abstract
Exposure to environmental factors can induce the epigenetic transgenerational inheritance of disease. Alterations to the epigenome termed “epimutations” include “primary epimutations” which are epigenetic alterations in the absence of genetic change and “secondary epimutations” which form following an initial genetic change. To determine if secondary epimutations contribute to transgenerational transmission of disease following in utero exposure to the endocrine disruptor vinclozolin, we exposed pregnant female rats carrying the lacI mutation-reporter transgene to vinclozolin and assessed the frequency of mutations in kidney tissue and sperm recovered from F1 and F3 generation progeny. Our results confirm that vinclozolin induces primary epimutations rather than secondary epimutations, but also suggest that some primary epimutations can predispose a subsequent accelerated accumulation of genetic mutations in F3 generation descendants that have the potential to contribute to transgenerational phenotypes. We therefore propose the existence of “tertiary epimutations” which are initial primary epimutations that promote genome instability leading to an accelerated accumulation of genetic mutations.
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Affiliation(s)
- John R. McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
- * E-mail:
| | - Jake D. Lehle
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Seetha S. Raju
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX United States of America
| | - Eric E. Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA United States of America
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13
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Chowdhury SS, Lecomte V, Erlich JH, Maloney CA, Morris MJ. Paternal High Fat Diet in Rats Leads to Renal Accumulation of Lipid and Tubular Changes in Adult Offspring. Nutrients 2016; 8:E521. [PMID: 27563922 PMCID: PMC5037508 DOI: 10.3390/nu8090521] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 12/28/2022] Open
Abstract
Along with diabetes and obesity, chronic kidney disease (CKD) is increasing across the globe. Although some data support an effect of maternal obesity on offspring kidney, the impact of paternal obesity is unknown; thus, we have studied the effect of paternal obesity prior to conception. Male Sprague Dawley rats were fed chow diet or high fat diet (HFD) for 13-14 weeks before mating with chow-fed females. Male offspring were weaned onto chow and killed at 27 weeks for renal gene expression and histology. Fathers on HFD were 30% heavier than Controls at mating. At 27 weeks of age offspring of obese fathers weighed 10% less; kidney triglyceride content was significantly increased (5.35 ± 0.84 vs. 2.99 ± 0.47 μg/mg, p < 0.05, n = 8 litters per group. Histological analysis of the kidney demonstrated signs of tubule damage, with significantly greater loss of brush border, and increased cell sloughing in offspring of obese compared to Control fathers. Acat1, involved in entry of fatty acid for beta-oxidation, was significantly upregulated, possibly to counteract increased triglyceride storage. However other genes involved in lipid metabolism, inflammation and kidney injury showed no changes. Paternal obesity was associated with renal triglyceride accumulation and histological changes in tubules, suggesting a mild renal insult in offspring, who may be at risk of developing CKD.
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Affiliation(s)
- Sabiha S Chowdhury
- School of Medical Sciences, University of New South Wales, Sydney 2052, NSW, Australia.
| | - Virginie Lecomte
- School of Medical Sciences, University of New South Wales, Sydney 2052, NSW, Australia.
| | - Jonathan H Erlich
- Prince of Wales Clinical School, University of New South Wales, Sydney 2052, NSW, Australia.
- Department of Nephrology, Prince of Wales Hospital, Randwick 2031, NSW, Australia.
| | - Christopher A Maloney
- School of Medical Sciences, University of New South Wales, Sydney 2052, NSW, Australia.
| | - Margaret J Morris
- School of Medical Sciences, University of New South Wales, Sydney 2052, NSW, Australia.
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14
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Prader-Willi Syndrome: The Disease that Opened up Epigenomic-Based Preemptive Medicine. Diseases 2016; 4:diseases4010015. [PMID: 28933395 PMCID: PMC5456307 DOI: 10.3390/diseases4010015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 01/20/2023] Open
Abstract
Prader-Willi syndrome (PWS) is a congenital neurodevelopmental disorder caused by loss of function of paternally expressed genes on chromosome 15 due to paternal deletion of 15q11–q13, maternal uniparental disomy for chromosome 15, or an imprinting mutation. We previously developed a DNA methylation-based PCR assay to identify each of these three genetic causes of PWS. The assay enables straightforward and rapid diagnosis during infancy and therefore allows early intervention such as nutritional management, physical therapy, or growth hormone treatment to prevent PWS patients from complications such as obesity and type 2 diabetes. It is known that various environmental factors induce epigenomic changes during the perinatal period, which increase the risk of adult diseases such as type 2 diabetes and intellectual disabilities. Therefore, a similar preemptive approach as used in PWS would also be applicable to acquired disorders and would make use of environmentally-introduced “epigenomic signatures” to aid development of early intervention strategies that take advantage of “epigenomic reversibility”.
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15
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Maniam J, Antoniadis CP, Youngson NA, Sinha JK, Morris MJ. Sugar Consumption Produces Effects Similar to Early Life Stress Exposure on Hippocampal Markers of Neurogenesis and Stress Response. Front Mol Neurosci 2016; 8:86. [PMID: 26834554 PMCID: PMC4717325 DOI: 10.3389/fnmol.2015.00086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/18/2015] [Indexed: 12/11/2022] Open
Abstract
Adverse early life experience is a known risk factor for psychiatric disorders. It is also known that stress influences food preference. We were interested in exploring whether the choice of diet following early life stress exerts long-lasting molecular changes in the brain, particularly the hippocampus, a region critically involved in stress regulation and behavioral outcomes. Here, we examined the impact of early life stress induced by limited nesting material (LN) and chronic sucrose availability post-weaning on an array of hippocampal genes related to plasticity, neurogenesis, stress and inflammatory responses and mitochondrial biogenesis. To examine mechanisms underlying the impact of LN and sugar intake on hippocampal gene expression, we investigated the role of DNA methylation. As females are more likely to experience adverse life events, we studied female Sprague-Dawley rats. After mating LN was imposed from days 2 to 9 postpartum. From 3 to 15 weeks of age, female Control and LN siblings had unlimited to access to either chow and water, or chow, water and 25% sucrose solution. LN markedly reduced glucocorticoid receptor (GR) and neurogenic differentiation 1 (Neurod1) mRNA, markers involved in stress and hippocampal plasticity respectively, by more than 40%, with a similar effect of sugar intake in control rats. However, no further impact was observed in LN rats consuming sugar. Hippocampal Akt3 mRNA expression was similarly affected by LN and sucrose consumption. Interestingly, DNA methylation across 4 CpG sites of the GR and Neurod1 promoters was similar in LN and control rats. In summary, early life stress and post-weaning sugar intake produced long-term effects on hippocampal GR and Neurod1 expression. Moreover we found no evidence of altered promoter DNA methylation. We demonstrate for the first time that chronic sucrose consumption alone produces similar detrimental effects on the expression of hippocampal genes as LN exposure.
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Affiliation(s)
- Jayanthi Maniam
- Department of Pharmacology, School of Medical Sciences, University of New South Wales Australia Sydney, NSW, Australia
| | - Christopher P Antoniadis
- Department of Pharmacology, School of Medical Sciences, University of New South Wales Australia Sydney, NSW, Australia
| | - Neil A Youngson
- Department of Pharmacology, School of Medical Sciences, University of New South Wales Australia Sydney, NSW, Australia
| | - Jitendra K Sinha
- Endocrinology and Metabolism Division, National Institute of Nutrition, Indian Council of Medical Research Hyderabad, India
| | - Margaret J Morris
- Department of Pharmacology, School of Medical Sciences, University of New South Wales Australia Sydney, NSW, Australia
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