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Li JW, Qian YJ, Mao SJ, Chao YQ, Qin YF, Hu CX, Li ZL, Zou CC. Clinical features associated with maternal uniparental disomy for chromosome 6. Mol Cytogenet 2024; 17:18. [PMID: 39075593 PMCID: PMC11287833 DOI: 10.1186/s13039-024-00688-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 07/20/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Maternal uniparental disomy for chromosome 6 (upd(Cajaiba MM, Witchel S, Madan-Khetarpal S, Hoover J, Hoffner L, Macpherson T, et al. Prenatal diagnosis of trisomy 6 rescue resulting in paternal UPD6 with novel placental findings. Am J Med Genet Part A. 2011;155 A(8):1996-2002.)mat) has been previously reported to cause intrauterine growth restriction (IUGR), but the specific clinical phenotype has not been defined. Based on clinical data from two new cases and patients from the literature, specific phenotypes and mechanisms will be discussed further. CASE PRESENTATION In case 1, a maternal isodisomy mixed with a heterodisomy was found on chromosome 6, including a regional absence of heterozygosity between 6q23.3 and 6q27. In case 2, a homozygous SCUBE3 mutation and upd(Cajaiba MM, Witchel S, Madan-Khetarpal S, Hoover J, Hoffner L, Macpherson T, et al. Prenatal diagnosis of trisomy 6 rescue resulting in paternal UPD6 with novel placental findings. Am J Med Genet Part A. 2011;155 A(8):1996-2002.)mat, involving the 6p21.1-25.1 region were found. Clinical data related to upd(Cajaiba MM, Witchel S, Madan-Khetarpal S, Hoover J, Hoffner L, Macpherson T, et al. Prenatal diagnosis of trisomy 6 rescue resulting in paternal UPD6 with novel placental findings. Am J Med Genet Part A. 2011;155 A(8):1996-2002.)mat were also reviewed. Of all the 21 reported cases with upd(Cajaiba MM, Witchel S, Madan-Khetarpal S, Hoover J, Hoffner L, Macpherson T, et al. Prenatal diagnosis of trisomy 6 rescue resulting in paternal UPD6 with novel placental findings. Am J Med Genet Part A. 2011;155 A(8):1996-2002.)mat (including our 2 cases), 18 (85.7%) presented IUGR. CONCLUSIONS The phenotypes of the two newly identified patients with upd(Cajaiba MM, Witchel S, Madan-Khetarpal S, Hoover J, Hoffner L, Macpherson T, et al. Prenatal diagnosis of trisomy 6 rescue resulting in paternal UPD6 with novel placental findings. Am J Med Genet Part A. 2011;155 A(8):1996-2002.)mat further suggest that IUGR is associated with upd(Cajaiba MM, Witchel S, Madan-Khetarpal S, Hoover J, Hoffner L, Macpherson T, et al. Prenatal diagnosis of trisomy 6 rescue resulting in paternal UPD6 with novel placental findings. Am J Med Genet Part A. 2011;155 A(8):1996-2002.)mat and case 2 is the first reported upd(Cajaiba MM, Witchel S, Madan-Khetarpal S, Hoover J, Hoffner L, Macpherson T, et al. Prenatal diagnosis of trisomy 6 rescue resulting in paternal UPD6 with novel placental findings. Am J Med Genet Part A. 2011;155 A(8):1996-2002.)mat patient with a homozygous SCUBE3 gene mutation. However, the specific phenotypes involved in upd(Cajaiba MM, Witchel S, Madan-Khetarpal S, Hoover J, Hoffner L, Macpherson T, et al. Prenatal diagnosis of trisomy 6 rescue resulting in paternal UPD6 with novel placental findings. Am J Med Genet Part A. 2011;155 A(8):1996-2002.)mat and the related mechanisms need to be further studied.
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Affiliation(s)
- Jing-Wen Li
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, No 3333 Binsheng Road, Hangzhou, 310052, China
| | - Yan-Jie Qian
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, No 3333 Binsheng Road, Hangzhou, 310052, China
| | - Shao-Jia Mao
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, No 3333 Binsheng Road, Hangzhou, 310052, China
| | - Yun-Qi Chao
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, No 3333 Binsheng Road, Hangzhou, 310052, China
| | - Yi-Fang Qin
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, No 3333 Binsheng Road, Hangzhou, 310052, China
| | - Chen-Xi Hu
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, No 3333 Binsheng Road, Hangzhou, 310052, China
| | - Zheng-Lan Li
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, No 3333 Binsheng Road, Hangzhou, 310052, China
- Department of Pediatrics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215008, China
| | - Chao-Chun Zou
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, No 3333 Binsheng Road, Hangzhou, 310052, China.
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Karabaeva RZ, Vochshenkova TA, Mussin NM, Albayev RK, Kaliyev AA, Tamadon A. Epigenetics of hypertension as a risk factor for the development of coronary artery disease in type 2 diabetes mellitus. Front Endocrinol (Lausanne) 2024; 15:1365738. [PMID: 38836231 PMCID: PMC11148232 DOI: 10.3389/fendo.2024.1365738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024] Open
Abstract
Hypertension, a multifaceted cardiovascular disorder influenced by genetic, epigenetic, and environmental factors, poses a significant risk for the development of coronary artery disease (CAD) in individuals with type 2 diabetes mellitus (T2DM). Epigenetic alterations, particularly in histone modifications, DNA methylation, and microRNAs, play a pivotal role in unraveling the complex molecular underpinnings of blood pressure regulation. This review emphasizes the crucial interplay between epigenetic attributes and hypertension, shedding light on the prominence of DNA methylation, both globally and at the gene-specific level, in essential hypertension. Additionally, histone modifications, including acetylation and methylation, emerge as essential epigenetic markers linked to hypertension. Furthermore, microRNAs exert regulatory influence on blood pressure homeostasis, targeting key genes within the aldosterone and renin-angiotensin pathways. Understanding the intricate crosstalk between genetics and epigenetics in hypertension is particularly pertinent in the context of its interaction with T2DM, where hypertension serves as a notable risk factor for the development of CAD. These findings not only contribute to the comprehensive elucidation of essential hypertension but also offer promising avenues for innovative strategies in the prevention and treatment of cardiovascular complications, especially in the context of T2DM.
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Affiliation(s)
- Raushan Zh Karabaeva
- Gerontology Center, Medical Center Hospital of the President’s Affairs Administration of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Tamara A. Vochshenkova
- Gerontology Center, Medical Center Hospital of the President’s Affairs Administration of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Nadiar M. Mussin
- General Surgery, West Kazakhstan Marat Ospanov Medical University, Aktobe, Kazakhstan
| | - Rustam K. Albayev
- Gerontology Center, Medical Center Hospital of the President’s Affairs Administration of the Republic of Kazakhstan, Astana, Kazakhstan
| | - Asset A. Kaliyev
- General Surgery, West Kazakhstan Marat Ospanov Medical University, Aktobe, Kazakhstan
| | - Amin Tamadon
- Department for Natural Sciences, West Kazakhstan Marat Ospanov Medical University, Aktobe, Kazakhstan
- Department of Research and Development, PerciaVista R&D Co., Shiraz, Iran
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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Zhang Y, Sui Z, Zhang Z, Wang C, Li X, Xing F. Cloning, tissue expression and imprinting status analysis of the NDN gene in Dolang sheep. Mol Biol Rep 2024; 51:166. [PMID: 38252343 DOI: 10.1007/s11033-023-08990-5] [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: 08/16/2023] [Accepted: 10/10/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Genomic imprinting refers to expressing parent-specific genes in mammalian diploid cells. The NDN gene is maternally imprinted in humans and mice and correlates with the timing of puberty. This study aimed to investigate its imprinting status and its relationship with the onset of puberty in Dolang sheep. METHODS AND RESULTS In this study, cloning and sequencing obtained the NDN gene cDNA sequence of 1082 bp of Dolang sheep, coding for 325 amino acids. Similarity analysis and phylogenetic tree showed that the NDN gene conformed to the law of speciation and was highly conserved among mammals. RT-qPCR results showed the highest expression of NDN mRNA was found in the hypothalamus at puberty, and the expression was significantly increased and then significantly decreased from prepuberty to postpuberty in the hypothalamus, pituitary, and ovary and oviduct. Based on expressed single nucleotide polymorphism (SNP), the NDN gene was expressed monoallelically in the tissues of adult and neonatal umbilical cords, and the expressed allele was paternally inherited. The NDN promoter region of 3400 bp was obtained by cloning and identified in monoallelic-expressing tissues (hypothalamus, ovary, spleen) as a differentially methylated region (DMR). CONCLUSION These findings will enrich the number of imprinted genes in sheep and suggest that the NDN gene could be a candidate gene for studying puberty initiation in Dolang sheep.
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Affiliation(s)
- Yongjie Zhang
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, China
| | - Zhiyuan Sui
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, China
| | - Zhishuai Zhang
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, China
| | - Chenguang Wang
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, China
| | - Xiaojun Li
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, China
| | - Feng Xing
- College of Animal Science and Technology, Tarim University, Alar, Xinjiang, China.
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar, China.
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Guo Z, Liu Y, Zhan S, Cao J, Wang L, Guo J, Li L, Zhang H, Zhong T. Expression patterns and DNA methylation profile of GTL2 gene in goats. Anim Biotechnol 2023; 34:3617-3625. [PMID: 36911908 DOI: 10.1080/10495398.2023.2184698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Gene trap locus 2 (GTL2), a long non-coding paternal imprinting gene, participates in various biological processes, including cell proliferation, differentiation, and apoptosis, by regulating the transcription of target mRNA, which is tightly related to the growth of the organic and maintenance of function. In this study, DNA methylation patterns of CpG islands (CGI) of GTL2 were explored, and its expression level was quantified in six tissues, rumen epithelium cells, and skeletal muscle cells in goats. GTL2 expression levels were measured by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), and the methylation model was confirmed by bisulfite-sequencing PCR (BSP). CGI methylation of GTL2 indicated a moderate methylation (ranging from 81.42 to 86.83%) in the brain, heart, liver, kidney, lung, and longissimus dorsi. GTL2 is most highly expressed in brain tissues, but there is no significant difference in the other five tissues. In addition, in the rumen epithelium cell proliferation, GTL2 expression was highest at 60 h, followed by 72 h, and almost unchanged at 12-48 h. In the skeletal muscle cell differentiation, GTL2 expression was highest at 0 and 24 h, significantly decreasing at 72 and 128 h. Pearson correlation analysis did not indicate a clear relationship between methylation and GTL2 expression levels, suggesting that other regulatory factors may modulate GTL2 expression. This study will provide a better understanding of the expression regulation mechanism of genes in the delta-like homolog 1 gene (DLK1)-GTL2 domain.
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Affiliation(s)
- Ziwei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yue Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Siyuan Zhan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiaxue Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linjie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiazhong Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Tao Zhong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Sciorio R, Campos G, Tramontano L, Bulletti FM, Baldini GM, Vinciguerra M. Exploring the effect of cryopreservation in assisted reproductive technology and potential epigenetic risk. ZYGOTE 2023; 31:420-432. [PMID: 37409505 DOI: 10.1017/s0967199423000345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Since the birth of the first baby by in vitro fertilization in 1978, more than 9 million children have been born worldwide using medically assisted reproductive treatments. Fertilization naturally takes place in the maternal oviduct where unique physiological conditions enable the early healthy development of the embryo. During this dynamic period of early development major waves of epigenetic reprogramming, crucial for the normal fate of the embryo, take place. Increasingly, over the past 20 years concerns relating to the increased incidence of epigenetic anomalies in general, and genomic-imprinting disorders in particular, have been raised following assisted reproduction technology (ART) treatments. Epigenetic reprogramming is particularly susceptible to environmental conditions during the periconceptional period and non-physiological conditions such as ovarian stimulation, in vitro fertilization and embryo culture, as well as cryopreservation procedure, might have the potential to independently or collectively contribute to epigenetic dysregulation. Therefore, this narrative review offers a critical reappraisal of the evidence relating to the association between embryo cryopreservation and potential epigenetic regulation and the consequences on gene expression together with long-term consequences for offspring health and wellbeing. Current literature suggests that epigenetic and transcriptomic profiles are sensitive to the stress induced by vitrification, in terms of osmotic shock, temperature and pH changes, and toxicity of cryoprotectants, it is therefore, critical to have a more comprehensive understanding and recognition of potential unanticipated iatrogenic-induced perturbations of epigenetic modifications that may or may not be a consequence of vitrification.
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Affiliation(s)
- Romualdo Sciorio
- Edinburgh Assisted Conception Programme, EFREC, Royal Infirmary of Edinburgh, UK
| | | | - Luca Tramontano
- Department of Women, Infants and Adolescents, Division of Obstetrics, Geneve University Hospitals, Boulevard de la Cluse 30, Geneve 14, Switzerland
| | - Francesco M Bulletti
- Department Obstetrics and Gynecology, University Hospital of Vaud, Lausanne, Switzerland
| | | | - Marina Vinciguerra
- Department of Biomedical Sciences and Human Oncology, Obstetrics and Gynaecology Section, University of Bari, Italy
- Clinic of Obstetrics and Gynecology 'Santa Caterina Novella', Galatina Hospital, Italy
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Rodriguez-Caro F, Moore EC, Good JM. Evolution of parent-of-origin effects on placental gene expression in house mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554674. [PMID: 37662315 PMCID: PMC10473692 DOI: 10.1101/2023.08.24.554674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The mammalian placenta is a hotspot for the evolution of genomic imprinting, a form of gene regulation that involves the parent-specific epigenetic silencing of one allele. Imprinted genes are central to placental development and are thought to contribute to the evolution of reproductive barriers between species. However, it is unclear how rapidly imprinting evolves or how functional specialization among placental tissues influences the evolution of imprinted expression. We compared parent-of-origin expression bias across functionally distinct placental layers sampled from reciprocal crosses within three closely related lineages of mice ( Mus ). Using genome-wide gene expression and DNA methylation data from fetal and maternal tissues, we developed an analytical strategy to minimize pervasive bias introduced by maternal contamination of placenta samples. We corroborated imprinted expression at 42 known imprinted genes and identified five candidate imprinted genes showing parent-of-origin specific expression and DNA methylation. Paternally-biased expression was enriched in the labyrinth zone, a layer specialized in nutrient transfer, and maternally-biased genes were enriched in the junctional zone, which specializes in modulation of maternal physiology. Differentially methylated regions were predominantly determined through epigenetic modification of the maternal genome and were associated with both maternally- and paternally-biased gene expression. Lastly, comparisons between lineages revealed a small set of co-regulated genes showing rapid divergence in expression levels and imprinted status in the M. m. domesticus lineage. Together, our results reveal important links between core functional elements of placental biology and the evolution of imprinted gene expression among closely related rodent species.
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Sciorio R, Manna C, Fauque P, Rinaudo P. Can Cryopreservation in Assisted Reproductive Technology (ART) Induce Epigenetic Changes to Gametes and Embryos? J Clin Med 2023; 12:4444. [PMID: 37445479 DOI: 10.3390/jcm12134444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/05/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Since the birth of Louise Brown in 1978, more than nine million children have been conceived using assisted reproductive technologies (ARTs). While the great majority of children are healthy, there are concerns about the potential epigenetic consequences of gametes and embryo manipulation. In fact, during the preimplantation period, major waves of epigenetic reprogramming occur. Epigenetic reprogramming is susceptible to environmental changes induced by ovarian stimulation, in-vitro fertilization, and embryo culture, as well as cryopreservation procedures. This review summarizes the evidence relating to oocytes and embryo cryopreservation and potential epigenetic regulation. Overall, it appears that the stress induced by vitrification, including osmotic shock, temperature and pH changes, and toxicity of cryoprotectants, might induce epigenetic and transcriptomic changes in oocytes and embryos. It is currently unclear if these changes will have potential consequences for the health of future offspring.
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Affiliation(s)
- Romualdo Sciorio
- Edinburgh Assisted Conception Programme, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Claudio Manna
- Biofertility IVF and Infertility Center, 00198 Rome, Italy
| | - Patricia Fauque
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Development (GAD) INSERM UMR1231, F-21000 Dijon, France
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, F-21000 Dijon, France
| | - Paolo Rinaudo
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 92037, USA
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Shi Q, Qi K. Developmental origins of health and disease: Impact of paternal nutrition and lifestyle. Pediatr Investig 2023; 7:111-131. [PMID: 37324600 PMCID: PMC10262906 DOI: 10.1002/ped4.12367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/29/2023] [Indexed: 09/20/2023] Open
Abstract
Most epidemiological and experimental studies have focused on maternal influences on offspring's health. The impact of maternal undernutrition, overnutrition, hypoxia, and stress is linked to adverse offspring outcomes across a range of systems including cardiometabolic, respiratory, endocrine, and reproduction among others. During the past decade, it has become evident that paternal environmental factors are also linked to the development of diseases in offspring. In this article, we aim to outline the current understanding of the impact of male health and environmental exposure on offspring development, health, and disease and explore the mechanisms underlying the paternal programming of offspring health. The available evidence suggests that poor paternal pre-conceptional nutrition and lifestyle, and advanced age can increase the risk of negative outcomes in offspring, via both direct (genetic/epigenetic) and indirect (maternal uterine environment) effects. Beginning at preconception, and during utero and the early life after birth, cells acquire an epigenetic memory of the early exposure which can be influential across the entire lifespan and program a child's health. Potentially not only mothers but also fathers should be advised that maintaining a healthy diet and lifestyle is important to improve offspring health as well as the parental health status. However, the evidence is mostly based on animal studies, and well-designed human studies are urgently needed to verify findings from animal data.
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Affiliation(s)
- Qiaoyu Shi
- Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's HospitalCapital Medical University, National Center for Children's HealthBeijingChina
| | - Kemin Qi
- Laboratory of Nutrition and Development, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's HospitalCapital Medical University, National Center for Children's HealthBeijingChina
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Srihi H, López-Carbonell D, Ibáñez-Escriche N, Casellas J, Hernández P, Negro S, Varona L. A Bayesian Multivariate Gametic Model in a Reciprocal Cross with Genomic Information: An Example with Two Iberian Varieties. Animals (Basel) 2023; 13:ani13101648. [PMID: 37238078 DOI: 10.3390/ani13101648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
INGA FOOD, S.A. initiated a crossbreeding program between two Iberian pig varieties, Retinto (R) and Entrepelado (E), with the goal of producing a hybrid sow (F1). Several studies have been conducted to evaluate its productive performance, and these studies have revealed differences in litter size between the two reciprocal crosses, suggesting the presence of genomic imprinting effects. To further investigate these effects, this study introduces a multivariate gametic model designed to estimate gametic correlations between paternal and maternal effects originating from both genetic backgrounds involved in the reciprocal crosses. The dataset consisted of 1258 records (the total number born-TNB and the number born alive-NBA) from 203 crossbred dams for the Entrepelado (sire) × Retinto (dam) cross and 700 records from 125 crossbred dams for the Retinto (sire) × Entrepelado (dam) cross. All animals were genotyped using the GeneSeek® GPP Porcine 70 K HDchip (Illumina Inc., San Diego, CA, USA). The results indicated that the posterior distribution of the gametic correlation between paternal and maternal effects was distinctly different between the two populations. Specifically, in the Retinto population, the gametic correlation showed a positive skew with posterior probabilities of 0.78 for the TNB and 0.80 for the NBA. On the other hand, the Entrepelado population showed a posterior probability of a positive gametic correlation between paternal and maternal effects of approximately 0.50. The differences in the shape of the posterior distribution of the gametic correlations between paternal and maternal effects observed in the two varieties may account for the distinct performance outcomes observed in the reciprocal crosses.
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Affiliation(s)
- Houssemeddine Srihi
- Facultad de Veterinaria, Instituto Agrolimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - David López-Carbonell
- Facultad de Veterinaria, Instituto Agrolimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Joaquim Casellas
- Department of Animal and Food Science, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Pilar Hernández
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Sara Negro
- Programa de Mejora Genética "Castúa", INGA FOOD S.A. (Nutreco), 06200 Almendralejo, Spain
| | - Luis Varona
- Facultad de Veterinaria, Instituto Agrolimentario de Aragón (IA2), Universidad de Zaragoza, 50013 Zaragoza, Spain
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Wu Z, Hu G, Zhang Y, Ao Z. IGF2 May Enhance Placental Fatty Acid Metabolism by Regulating Expression of Fatty Acid Carriers in the Growth of Fetus and Placenta during Late Pregnancy in Pigs. Genes (Basel) 2023; 14:genes14040872. [PMID: 37107630 PMCID: PMC10137774 DOI: 10.3390/genes14040872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Fatty acids (FAs) are essential substances for the growth and development of the fetus and placenta. The growing fetus and placenta must obtain adequate FAs received from the maternal circulation and facilitated by various placental FA carriers, including FA transport proteins (FATPs), FA translocase (FAT/CD36), and cytoplasmic FA binding proteins (FABPs). Placental nutrition transport was regulated by imprinted genes H19 and insulin-like growth factor 2 (IGF2). Nevertheless, the relationship between the expression patterns of H19/IGF2 and placental fatty acid metabolism throughout pig pregnancy remains poorly studied and unclear. We investigated the placental fatty acid profile, expression patterns of FA carriers, and H19/IGF2 in the placentae on Days 40 (D40), 65 (D65), and 95 (D95) of pregnancy. The results showed that the width of the placental folds and the number of trophoblast cells of D65 placentae were significantly increased than those of D40 placentae. Several important long-chain FAs (LCFAs), including oleic acid, linoleic acid, arachidonatic acid, eicosapentaenoic acid, and docosatetraenoic acid, in the pig placenta showed dramatically increased levels throughout pregnancy. The pig placenta possessed higher expression levels of CD36, FATP4, and FABP5 compared with other FA carriers, and their expression levels had significantly upregulated 2.8-, 5.6-, and 12.0-fold from D40 to D95, respectively. The transcription level of IGF2 was dramatically upregulated and there were corresponding lower DNA methylation levels in the IGF2 DMR2 in D95 placentae relative to D65 placentae. Moreover, in vitro experimentation revealed that the overexpression of IGF2 resulted in a significant increase in fatty acid uptake and expression levels of CD36, FATP4, and FABP5 in PTr2 cells. In conclusion, our results indicate that CD36, FATP4, and FABP5 may be important regulators that enhance the transport of LCFAs in the pig placenta and that IGF2 may be involved in FA metabolism by affecting the FA carriers expression to support the growth of the fetus and placenta during late pregnancy in pigs.
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Affiliation(s)
- Zhimin Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Guangling Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Yiyu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Zheng Ao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
- Guizhou Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang 550025, China
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12
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Shi Q, Liu X, Fan X, Wang R, Qi K. Paternal dietary ratio of n-6: n-3 polyunsaturated fatty acids programs offspring leptin expression and gene imprinting in mice. Front Nutr 2022; 9:1043876. [PMID: 36618698 PMCID: PMC9816484 DOI: 10.3389/fnut.2022.1043876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/08/2022] [Indexed: 12/25/2022] Open
Abstract
Background This study determined the effects of the paternal dietary ratio of n-6: n-3 polyunsaturated fatty acids (PUFAs) on leptin expression in the offspring and associated gene imprinting in a mouse model. Methods Three- to four-week-old male C57BL/6J mice (F0) were fed an n-3 PUFA-deficient (n-3 D) diet, a diet with normal n-3 PUFA content (n-3 N; n-6: n-3 = 4.3:1), or a diet with a high n-3 PUFA content (n-3 H; n-6: n-3 = 1.5:1) for 8 weeks. Two subsequent generations were generated by mating F0 and F1 male mice with 10-week-old virgin female C57 BL/6J mice, to produce F1 and F2 offspring. Results Compared to the paternal n-3 D diet, paternal n-3 N and n-3 H diets reduced adipose mRNA expression of leptin (Lep) and its plasma concentrations in juvenile F1 male and female offspring, and adult F1 male and F2 female offspring, with upregulated Lep receptor mRNA expression in the hypothalamus. Meanwhile, paternal n-3 N and n-3 H diets altered the expression of the imprinted genes H19, Igf2, Igf2r, Plagl1, Cdkn1c, Kcnq1ot1, Peg3, and Grb10 in the adipose tissue of juvenile and adult F1 males, with almost no effects on F1 females, while more effects were observed in the adult F2 females than F2 males. Principal component analysis verified that Plagl1, Cdkn1c, and Kcnq1ot1 contributed the most to variation in adipose tissue expression in all offspring. Some of these genes (Plagl1, Cdkn1c, Kcnq1ot1, Peg3, and Grb10) were altered by the paternal n-3 N and n-3 H diets in the F1 and F2 generation testes as well. Furthermore, adipose Lep expression was positively correlated with expressions of H19, Igf2r, Plagl1, and Kcnq1ot1 in juvenile F1 males and females, negatively correlated with the Kcnq1ot1 expression in adult F1 males, and positively correlated with the Plagl1 expression in adult F2 females. Conclusion These data imply that paternal Plagl1, Cdkn1c, and Kcnq1ot1 might be part of the pathways involved in offspring leptin programming. Therefore, a lower ratio of n-6: n-3 PUFAs, with higher intake of n-3 PUFAs in paternal pre-conception, may help maintain the offspring's optimal leptin pattern in a sex-specific manner through multiple generations, and thereby, be beneficial for the offspring's long-term health.
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Schroeder M, Badini G, Sferruzzi-Perri AN, Albrecht C. The Consequences of Assisted Reproduction Technologies on the Offspring Health Throughout Life: A Placental Contribution. Front Cell Dev Biol 2022; 10:906240. [PMID: 35747691 PMCID: PMC9210138 DOI: 10.3389/fcell.2022.906240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
The use of assisted reproductive technologies (ART) worldwide has led to the conception and birth of over eight million babies since being implemented in 1978. ART use is currently on the rise, given growing infertility and the increase in conception age among men and women in industrialized countries. Though obstetric and perinatal outcomes have improved over the years, pregnancies achieved by ART still bear increased risks for the mother and the unborn child. Moreover, given that the first generation of ART offspring is now only reaching their forties, the long-term effects of ART are currently unknown. This is important, as there is a wealth of data showing that life-long health can be predetermined by poor conditions during intrauterine development, including irregularities in the structure and functioning of the placenta. In the current review, we aim to summarize the latest available findings examining the effects of ART on the cardiometabolic, cognitive/neurodevelopmental, and behavioral outcomes in the perinatal period, childhood and adolescence/adulthood; and to examine placental intrinsic factors that may contribute to the developmental outcomes of ART offspring. Altogether, the latest knowledge about life outcomes beyond adolescence for those conceived by ART appears to suggest a better long-term outcome than previously predicted. There are also changes in placenta structure and functional capacity with ART. However, more work in this area is critically required, since the potential consequences of ART may still emerge as the offspring gets older. In addition, knowledge of the placenta may help to foresee and mitigate any adverse outcomes in the offspring.
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Affiliation(s)
- Mariana Schroeder
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Gina Badini
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Amanda N Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Christiane Albrecht
- Faculty of Medicine, Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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14
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Nikitina TV, Lebedev IN. Stem Cell-Based Trophoblast Models to Unravel the Genetic Causes of Human Miscarriages. Cells 2022; 11:1923. [PMID: 35741051 PMCID: PMC9221414 DOI: 10.3390/cells11121923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 02/01/2023] Open
Abstract
Miscarriage affects approximately 15% of clinically recognized pregnancies, and 1-3% of couples experience pregnancy loss recurrently. Approximately 50-60% of miscarriages result from chromosomal abnormalities, whereas up to 60% of euploid recurrent abortions harbor variants in candidate genes. The growing number of detected genetic variants requires an investigation into their role in adverse pregnancy outcomes. Since placental defects are the main cause of first-trimester miscarriages, the purpose of this review is to provide a survey of state-of-the-art human in vitro trophoblast models that can be used for the functional assessment of specific abnormalities/variants implicated in pregnancy loss. Since 2018, when primary human trophoblast stem cells were first derived, there has been rapid growth in models of trophoblast lineage. It has been found that a proper balance between self-renewal and differentiation in trophoblast progenitors is crucial for the maintenance of pregnancy. Different responses to aneuploidy have been shown in human embryonic and extra-embryonic lineages. Stem cell-based models provide a powerful tool to explore the effect of a specific aneuploidy/variant on the fetus through placental development, which is important, from a clinical point of view, for deciding on the suitability of embryos for transfer after preimplantation genetic testing for aneuploidy.
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Affiliation(s)
- Tatiana V. Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, 634050 Tomsk, Russia;
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15
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Mishra A, Prabha PK, Singla R, Kaur G, Sharma AR, Joshi R, Suroy B, Medhi B. Epigenetic Interface of Autism Spectrum Disorders (ASDs): Implications of Chromosome 15q11-q13 Segment. ACS Chem Neurosci 2022; 13:1684-1696. [PMID: 35635007 DOI: 10.1021/acschemneuro.2c00060] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Autism spectrum disorders (ASDs) are multifactorial in nature and include both genetic and environmental factors. The increasing evidence advocates an important role of epigenetics in ASD etiology. One of the most common forms of epigenetic changes observed in the case of neurodevelopmental disorders is imprinting which is tightly regulated by developmental and tissue-specific mechanisms. Interestingly, many of these disorders that demonstrate autism-like phenotypes at varying degrees have found involvement of chromosome 15q11-q13 segment. Numerous studies demonstrate occurrence of ASD in the presence of chromosomal abnormalities located mainly in Chr15q11-q13 region. Several plausible candidate genes associated with ASD are in this chromosomal segment, including gamma aminobutyric acid A (GABAA) receptor genes GABRB3, GABRA5 and GABRG3, UBE3A, ATP 10A, MKRN3, ZNF, MAGEL2, Necdin (NDN), and SNRPN. The main objective of this review is to highlight the contribution of epigenetic modulations in chromosome 15q11-q13 segment toward the genetic etiology and pathophysiology of ASD. The present review reports the abnormalities in epigenetic regulation on genes and genomic regions located on chromosome 15 in relation to either syndromic (15q11-q13 maternal duplication) or nonsyndromic forms of ASD. Furthermore, studies reviewed in this article demonstrate conditions in which epigenetic dysregulation has been found to be a pathological factor for ASD development, thereby supporting a role for epigenetics in the multifactorial etiologies of ASD. Also, on the basis of the evidence found so far, we strongly emphasize the need to develop future therapeutic strategies as well as screening procedures for ASD that target mechanisms involving genes located on the chromosomal 15q11-q13 segment.
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Affiliation(s)
- Abhishek Mishra
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Praisy K Prabha
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Rubal Singla
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Gurjeet Kaur
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Amit Raj Sharma
- Dept. of Neurology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Rupa Joshi
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Benjamin Suroy
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Bikash Medhi
- Dept. of Pharmacology, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
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16
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Li C, Su F, Liang Z, Zhang L, Liu F, Fan W, Li Z. Macrophage M1 regulatory diabetic nephropathy is mediated by m6A methylation modification of lncRNA expression. Mol Immunol 2022; 144:16-25. [DOI: 10.1016/j.molimm.2022.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/07/2021] [Accepted: 02/07/2022] [Indexed: 12/24/2022]
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17
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Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021. [PMID: 34728591 PMCID: PMC8550911 DOI: 10.1007/s12038-021-00215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
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18
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Epigenetic processes during preeclampsia and effects on fetal development and chronic health. Clin Sci (Lond) 2021; 135:2307-2327. [PMID: 34643675 DOI: 10.1042/cs20190070] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/08/2021] [Accepted: 09/29/2021] [Indexed: 01/12/2023]
Abstract
Preeclampsia (PE), the leading cause of maternal and fetal morbidity and mortality, is associated with poor fetal growth, intrauterine growth restriction (IUGR) and low birth weight (LBW). Offspring of women who had PE are at increased risk for cardiovascular (CV) disease later in life. However, the exact etiology of PE is unknown. Moreover, there are no effective interventions to treat PE or alleviate IUGR and the developmental origins of chronic disease in the offspring. The placenta is critical to fetal growth and development. Epigenetic regulatory processes such as histone modifications, microRNAs and DNA methylation play an important role in placental development including contributions to the regulation of trophoblast invasion and remodeling of the spiral arteries. Epigenetic processes that lead to changes in placental gene expression in PE mediate downstream effects that contribute to the development of placenta dysfunction, a critical mediator in the onset of PE, impaired fetal growth and IUGR. Therefore, this review will focus on epigenetic processes that contribute to the pathogenesis of PE and IUGR. Understanding the epigenetic mechanisms that contribute to normal placental development and the initiating events in PE may lead to novel therapeutic targets in PE that improve fetal growth and mitigate increased CV risk in the offspring.
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19
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Wu W, Lovett JL, Shedden K, Strassmann BI, Vincenz C. Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas. G3 (BETHESDA, MD.) 2021; 11:jkab176. [PMID: 34009305 PMCID: PMC8496276 DOI: 10.1093/g3journal/jkab176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/12/2021] [Indexed: 12/30/2022]
Abstract
Genomic imprinting is an epigenetic mechanism that results in allele-specific expression (ASE) based on the parent of origin. It is known to play a role in the prenatal and postnatal allocation of maternal resources in mammals. ASE detected by whole transcriptome RNA-seq (wht-RNAseq) has been widely used to analyze imprinted genes using reciprocal crosses in mice to generate large numbers of informative SNPs. Studies in humans are more challenging due to the paucity of SNPs and the poor preservation of RNA in term placentas and other tissues. Targeted RNA-seq (tar-RNAseq) can potentially mitigate these challenges by focusing sequencing resources on the regions of interest in the transcriptome. Here, we compared tar-RNAseq and wht-RNAseq in a study of ASE in known imprinted genes in placental tissue collected from a healthy human cohort in Mali, West Africa. As expected, tar-RNAseq substantially improved the coverage of SNPs. Compared to wht-RNAseq, tar-RNAseq produced on average four times more SNPs in twice as many genes per sample and read depth at the SNPs increased fourfold. In previous research on humans, discordant ASE values for SNPs of the same gene have limited the ability to accurately quantify ASE. We show that tar-RNAseq reduces this limitation as it unexpectedly increased the concordance of ASE between SNPs of the same gene, even in cases of degraded RNA. Studies aimed at discovering associations between individual variation in ASE and phenotypes in mammals and flowering plants will benefit from the improved power and accuracy of tar-RNAseq.
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Affiliation(s)
- Weisheng Wu
- BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennie L Lovett
- Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kerby Shedden
- Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beverly I Strassmann
- Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA
- Research Center for Group Dynamics, Institute for Social Research, University of Michigan, Ann Arbor, MI 48106, USA
| | - Claudius Vincenz
- Research Center for Group Dynamics, Institute for Social Research, University of Michigan, Ann Arbor, MI 48106, USA
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20
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Epigenetic Changes Induced by Maternal Factors during Fetal Life: Implication for Type 1 Diabetes. Genes (Basel) 2021; 12:genes12060887. [PMID: 34201206 PMCID: PMC8227197 DOI: 10.3390/genes12060887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023] Open
Abstract
Organ-specific autoimmune diseases, such as type 1 diabetes, are believed to result from T-cell-mediated damage of the target tissue. The immune-mediated tissue injury, in turn, is known to depend on complex interactions between genetic and environmental factors. Nevertheless, the mechanisms whereby environmental factors contribute to the pathogenesis of autoimmune diseases remain elusive and represent a major untapped target to develop novel strategies for disease prevention. Given the impact of the early environment on the developing immune system, epigenetic changes induced by maternal factors during fetal life have been linked to a likelihood of developing an autoimmune disease later in life. In humans, DNA methylation is the epigenetic mechanism most extensively investigated. This review provides an overview of the critical role of DNA methylation changes induced by prenatal maternal conditions contributing to the increased risk of immune-mediated diseases on the offspring, with a particular focus on T1D. A deeper understanding of epigenetic alterations induced by environmental stressors during fetal life may be pivotal for developing targeted prevention strategies of type 1 diabetes by modifying the maternal environment.
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21
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Migliore L, Nicolì V, Stoccoro A. Gender Specific Differences in Disease Susceptibility: The Role of Epigenetics. Biomedicines 2021; 9:652. [PMID: 34200989 PMCID: PMC8228628 DOI: 10.3390/biomedicines9060652] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 01/08/2023] Open
Abstract
Many complex traits or diseases, such as infectious and autoimmune diseases, cancer, xenobiotics exposure, neurodevelopmental and neurodegenerative diseases, as well as the outcome of vaccination, show a differential susceptibility between males and females. In general, the female immune system responds more efficiently to pathogens. However, this can lead to over-reactive immune responses, which may explain the higher presence of autoimmune diseases in women, but also potentially the more adverse effects of vaccination in females compared with in males. Many clinical and epidemiological studies reported, for the SARS-CoV-2 infection, a gender-biased differential response; however, the majority of reports dealt with a comparable morbidity, with males, however, showing higher COVID-19 adverse outcomes. Although gender differences in immune responses have been studied predominantly within the context of sex hormone effects, some other mechanisms have been invoked: cellular mosaicism, skewed X chromosome inactivation, genes escaping X chromosome inactivation, and miRNAs encoded on the X chromosome. The hormonal hypothesis as well as other mechanisms will be examined and discussed in the light of the most recent epigenetic findings in the field, as the concept that epigenetics is the unifying mechanism in explaining gender-specific differences is increasingly emerging.
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Affiliation(s)
- Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
- Department of Laboratory Medicine, Azienda Ospedaliero Universitaria Pisana, 56124 Pisa, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy; (V.N.); (A.S.)
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22
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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23
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Pegoraro M, Weedall GD. Malaria in the 'Omics Era'. Genes (Basel) 2021; 12:genes12060843. [PMID: 34070769 PMCID: PMC8228830 DOI: 10.3390/genes12060843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
Genomics has revolutionised the study of the biology of parasitic diseases. The first Eukaryotic parasite to have its genome sequenced was the malaria parasite Plasmodium falciparum. Since then, Plasmodium genomics has continued to lead the way in the study of the genome biology of parasites, both in breadth—the number of Plasmodium species’ genomes sequenced—and in depth—massive-scale genome re-sequencing of several key species. Here, we review some of the insights into the biology, evolution and population genetics of Plasmodium gained from genome sequencing, and look at potential new avenues in the future genome-scale study of its biology.
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Rajeev R, Dwivedi AP, Sinha A, Agarwaal V, Dev RR, Kar A, Khosla S. Epigenetic interaction of microbes with their mammalian hosts. J Biosci 2021; 46:94. [PMID: 34728591 PMCID: PMC8550911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The interaction of microbiota with its host has the ability to alter the cellular functions of both, through several mechanisms. Recent work, from many laboratories including our own, has shown that epigenetic mechanisms play an important role in the alteration of these cellular functions. Epigenetics broadly refers to change in the phenotype without a corresponding change in the DNA sequence. This change is usually brought by epigenetic modifications of the DNA itself, the histone proteins associated with the DNA in the chromatin, non-coding RNA or the modifications of the transcribed RNA. These modifications, also known as epigenetic code, do not change the DNA sequence but alter the expression level of specific genes. Microorganisms seem to have learned how to modify the host epigenetic code and modulate the host transcriptome in their favour. In this review, we explore the literature that describes the epigenetic interaction of bacteria, fungi and viruses, with their mammalian hosts.
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Affiliation(s)
- Ramisetti Rajeev
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.411639.80000 0001 0571 5193Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Ambey Prasad Dwivedi
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.411639.80000 0001 0571 5193Graduate Studies, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Anunay Sinha
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.502122.60000 0004 1774 5631Graduate Studies, Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Viplove Agarwaal
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Rachana Roshan Dev
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Anjana Kar
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Sanjeev Khosla
- grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India ,grid.417641.10000 0004 0504 3165Institute of Microbial Technology (IMTech), Chandigarh, India
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25
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Chen H, Shan G. The physiological function of long-noncoding RNAs. Noncoding RNA Res 2020; 5:178-184. [PMID: 32959025 PMCID: PMC7494506 DOI: 10.1016/j.ncrna.2020.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
The physiological processes of cells and organisms are regulated by various biological macromolecules, including long-noncoding RNAs (lncRNAs), which cannot be translated into protein and are different from small-noncoding RNAs on their length. In animals, lncRNAs are involved in development, metabolism, reproduction, aging and other life events by cis or trans effects. For many functional lncRNAs, there is growing evidence that they play different roles on cellular level and organismal level. On the other hand, many annotated lncRNAs are not essential and could be transcription noises. In this minireview, we investigate the physiological function of lncRNAs in cells and focus on their functions and functional mechanisms on the organismal level. The studies on lncRNAs using different classic animal models such as worms and flies are summarized and discussed in this article.
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Affiliation(s)
- He Chen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China
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26
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Chan WY, Chung J, Peplow LM, Hoffmann AA, van Oppen MJH. Maternal effects in gene expression of interspecific coral hybrids. Mol Ecol 2020; 30:517-527. [PMID: 33179328 DOI: 10.1111/mec.15727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022]
Abstract
Maternal effects have been well documented for offspring morphology and life history traits in plants and terrestrial animals, yet little is known about maternal effects in corals. Further, few studies have explored maternal effects in gene expression. In a previous study, F1 interspecific hybrid and purebred larvae of the coral species Acropora tenuis and Acropora loripes were settled and exposed to ambient or elevated temperature and pCO2 conditions for 7 months. At this stage, the hybrid coral recruits from both ocean conditions exhibited strong maternal effects in several fitness traits. We conducted RNA-sequencing on these corals and showed that gene expression of the hybrid Acropora also exhibited clear maternal effects. Only 40 genes were differentially expressed between hybrids and their maternal progenitor. In contrast, ~2000 differentially expressed genes were observed between hybrids and their paternal progenitors, and between the reciprocal F1 hybrids. These results indicate that maternal effects in coral gene expression can be long-lasting. Unlike findings from most short-term stress experiments in corals, no genes were differentially expressed in the hybrid nor purebred offspring after seven months of exposure to elevated temperature and pCO2 conditions.
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Affiliation(s)
- Wing Yan Chan
- Australian Institute of Marine Science, Townsville, QLD, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Jessica Chung
- Bio21 Institute, University of Melbourne, Parkville, VIC, Australia.,Melbourne Bioinformatics, University of Melbourne, Parkville, VIC, Australia
| | - Lesa M Peplow
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Ary A Hoffmann
- Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, QLD, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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