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1.
Eur J Obstet Gynecol Reprod Biol ; 294: 163-169, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38266482

ABSTRACT

OBJECTIVE: Are circulating luteinizing hormone (LH) levels predictive of ovarian response in oocyte donors triggered with gonadotropin-releasing hormone (GnRH) agonists? STUDY DESIGN: A prospective cohort study with 224 oocyte donation cycles between 2021 and 2022 at a single center, examined the relationship between circulating luteinizing hormone (LH) levels and ovarian response. Oocyte donors underwent GnRH antagonist downregulation followed by GnRH agonist trigger. LH, estradiol, and progesterone levels were measured on day one of stimulation, trigger-day and 12 h post-trigger. Oocyte retrieval and maturity rates were analyzed using univariate and multivariate analyses, and the correlation between post-trigger LH levels and outcomes was assessed by Pearson's correlation test. A significance level of p < 0.05 was used. RESULTS: Mean age was 26 ± 4.3 years, mean body mass index (BMI, kg/m2) was 22.6 ± 3.2 and mean antral follicle count (AFC) was 21.7 ± 8.2. Post-trigger LH levels averaged 51.3 IU/L (SD 34.8), and oocyte retrieval rate and maturity rates were 112,7% (+/-48,1%) and 77,8% (+/- 17,2%), respectively. No significant differences were found in these outcomes for donors with post-trigger LH values below and above 15 IU/L (Mann Whitney's p > 0.05). However, exploratory analyses revealed that post-trigger LH values < 22 IU/L and basal LH levels < 4 IU/L were associated with significantly lower oocyte retrieval rate (90 % vs 110 %, p = 0.019 and 100 % vs 110 %, p = 0.019, respectively). CONCLUSIONS: This study, a first in exclusively focusing on oocyte donors, did not support the previously reported LH value of 15 IU/L as predictive of suboptimal ovarian response. TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier: NCT05109403.


Subject(s)
Gonadotropin-Releasing Hormone , Ovulation Induction , Female , Humans , Young Adult , Adult , Prospective Studies , Oocytes , Luteinizing Hormone , Fertilization in Vitro
2.
Reprod Biomed Online ; 47(3): 103228, 2023 09.
Article in English | MEDLINE | ID: mdl-37308341

ABSTRACT

RESEARCH QUESTION: Does long-term storage of vitrified oocytes affect laboratory and reproductive outcomes after intracytoplasmic sperm injection? DESIGN: Retrospective cohort study including 41,783 vitrified-warmed oocytes from 5362 oocyte donation cycles between 2013 and 2021. Five categories of storage time were established to analyse its effect on clinical and reproductive outcomes (≤1 year [reference group], 1-2 years, 2-3 years, 3-4 years and >4 years). RESULTS: The mean number of warmed oocytes was 8.0 ± 2.5 oocytes. Oocyte storage time ranged from 3 days to 8.2 years (mean: 0.7 ± 0.9). Mean oocyte survival (90.2% ± 14.7% overall) did not significantly decrease with longer storage time after adjusting for confounders (88.9% for time >4 years, P = 0.963). A linear regression model did not show a significant effect of oocyte storage time on fertilization rate (about 70% in all time categories) (P > 0.05). Reproductive outcomes after the first embryo transfer were statistically comparable across storage times (P > 0.05 for all categories). Longer term oocyte storage (>4 years) did not affect the chances of clinical pregnancy (OR 0.700, 95% CI 0.423 to 1.158, P = 0.2214) or live birth (OR 0.716, 95% CI 0.425 to 1.208, P = 0.2670). CONCLUSIONS: Oocyte survival, fertilization rate, pregnancy and live birth rates are not affected by the time spent by vitrified oocytes in vapour-phase nitrogen tanks.


Subject(s)
Birth Rate , Cryopreservation , Pregnancy , Female , Male , Humans , Pregnancy Rate , Vitrification , Retrospective Studies , Oocyte Donation , Semen , Oocytes , Live Birth
3.
Reprod Biomed Online ; 46(6): 911-916, 2023 06.
Article in English | MEDLINE | ID: mdl-37045673

ABSTRACT

RESEARCH QUESTION: Do morphokinetic parameters vary between male and female preimplantation embryos? DESIGN: This was a retrospective cohort study of 175 cycles between March 2018 and June 2021 at two reproductive centres. It included time-lapse data from 92 female and 83 male preimplantation embryos exclusively issued from fresh oocyte donation and undergoing intracytoplasmic sperm injection (ICSI). Only fresh elective single-embryo transfers on day 5 were assessed, and the sex of the embryo was confirmed at birth. The morphokinetic parameters analysed were measured in hours post-insemination (hpi). A two-tailed Student's t-test was used to compare the morphokinetics between embryo sexes and a value of P < 0.05 was considered statistically significant. RESULTS: Following strict inclusion criteria to avoid poor-quality preimplantation embryos, no significant differences were found in morphokinetic parameters when comparing cycles that resulted in female versus male live births for the following: time to pronuclear fading (22.1 ± 2.4 versus 22.4 ± 2.9 hpi; P = 0.52); time to the 2-cell stage (24.6 ± 2.5 versus 25.0 ± 2.5 hpi; P = 0.34); time to the 3-cell stage (35.3 ± 3.3 versus 35.8 ± 3.1 hpi; P = 0.28); time to the 4-cell stage (36.3 ± 3.4 versus 36.9 ± 3.7 hpi; P = 0.20); time to the 5-cell stage (47.9 ± 4.6 versus 48.0 ± 4.8 hpi; P = 0.88); time to the 8-cell stage (54.0 ± 6.5 versus 54.1 ± 6.5 hpi; P = 0.91); time to the start of blastulation (86.3 ± 14.6 versus 85.7 ± 15.5 hpi; P = 0.78); and time to the full blastocyst stage (93.0 ± 16.9 versus 93.2 ± 17.2 hpi; P = 0.94). CONCLUSIONS: There are no significant differences in morphokinetics between male and female preimplantation embryos.


Subject(s)
Blastocyst , Semen , Pregnancy , Male , Female , Humans , Retrospective Studies , Sperm Injections, Intracytoplasmic , Live Birth , Time-Lapse Imaging/methods , Fertilization in Vitro/methods , Embryo Culture Techniques
4.
Fertil Steril ; 119(6): 964-973, 2023 06.
Article in English | MEDLINE | ID: mdl-36787873

ABSTRACT

OBJECTIVES: To gain insights into the technical feasibility of maternal spindle transfer (MST) applied in the context of repeated in vitro fertilization (IVF) failures for the treatment of idiopathic infertility. DESIGN: A prospective pilot study. SETTING: IVF center. PATIENT(S): Twenty-five infertile couples with multiple previous unsuccessful IVF cycles (range, 3-11), no previous pregnancy, and no history of mitochondrial DNA (mtDNA) disease participated. The study focused on women <40 years, with previous IVF attempts characterized by a pattern of low fertilization rates and/or impaired embryo development. Couples with severe male-factor infertility were not eligible. Oocyte donors with previous successful IVF outcomes were matched with patients according to standard practice. INTERVENTION(S): We performed MST by transferring metaphase II spindles from the patients' oocytes into the previously enucleated donor oocytes, followed by intracytoplasmic sperm injection, in vitro embryo culture, blastocyst biopsy, and vitrification. Only euploid blastocysts were considered for embryo transfer. MAIN OUTCOME MEASURE(S): Outcome measures included oocyte fertilization, blastocyst development, clinical pregnancy and live birth, incidence of mitochondrial carryover and potential mtDNA reversal, as well as general health of the children born. RESULT(S): Twenty-eight MST cycles produced 6 children (19 embryo transfers, 7 clinical pregnancies). Pediatric follow-up of the children, performed at intervals from birth to 12-24 months of age, revealed their development to be unremarkable. DNA fingerprinting confirmed that the nuclear DNA of MST children was inherited from both parents, without any contribution from the oocyte donor. For 5 of the children, mtDNA was derived almost exclusively (>99%) from the donor. However, 1 child, who had similarly low mtDNA carryover (0.8%) at the blastocyst stage, showed an increase in the maternal mtDNA haplotype, accounting for 30% to 60% of the total at birth. CONCLUSION(S): This pilot study provides the first insights into the feasibility of applying MST for patients with idiopathic infertility and repeated IVF failures. Reconstructed oocytes produced embryos capable of implanting, developing to term and producing apparently healthy newborns/children. However, claims concerning the efficacy of MST with respect to infertility treatment would be premature considering the limitations of this study. Importantly, mtDNA reversal was detected in one child born after MST, a finding with possible implications for mitochondrial replacement therapies. CLINICAL TRIAL REGISTRATION NUMBER: Pilot trial registry number, ISRCTN11455145. The date of registration: 20/02/2018. The date of enrolment of the first patients: 18/03/2018.


Subject(s)
Infertility, Male , Semen , Pregnancy , Humans , Male , Female , Pilot Projects , Prospective Studies , Fertilization in Vitro , DNA, Mitochondrial/genetics , Pregnancy Rate , Retrospective Studies
5.
Nat Cell Biol ; 24(10): 1528-1540, 2022 10.
Article in English | MEDLINE | ID: mdl-36202974

ABSTRACT

The biological purpose of long non-coding RNAs (lncRNAs) is poorly understood. Haploinsufficient mutations in HNF1A homeobox A (HNF1A), encoding a homeodomain transcription factor, cause diabetes mellitus. Here, we examine HASTER, the promoter of an lncRNA antisense to HNF1A. Using mouse and human models, we show that HASTER maintains cell-specific physiological HNF1A concentrations through positive and negative feedback loops. Pancreatic ß cells from Haster mutant mice consequently showed variegated HNF1A silencing or overexpression, resulting in hyperglycaemia. HASTER-dependent negative feedback was essential to prevent HNF1A binding to inappropriate genomic regions. We demonstrate that the HASTER promoter DNA, rather than the lncRNA, modulates HNF1A promoter-enhancer interactions in cis and thereby regulates HNF1A transcription. Our studies expose a cis-regulatory element that is unlike classic enhancers or silencers, it stabilizes the transcription of its target gene and ensures the fidelity of a cell-specific transcription factor program. They also show that disruption of a mammalian lncRNA promoter can cause diabetes mellitus.


Subject(s)
Hepatocyte Nuclear Factor 1-alpha , Promoter Regions, Genetic , RNA, Long Noncoding , Animals , Humans , Mice , Hepatocyte Nuclear Factor 1-alpha/genetics , Mammals , RNA, Long Noncoding/genetics , Transcription, Genetic/genetics , Transcription, Genetic/physiology
6.
Dev Cell ; 57(16): 1922-1936.e9, 2022 08 22.
Article in English | MEDLINE | ID: mdl-35998583

ABSTRACT

Sequence variants in cis-acting enhancers are important for polygenic disease, but their role in Mendelian disease is poorly understood. Redundancy between enhancers that regulate the same gene is thought to mitigate the pathogenic impact of enhancer mutations. Recent findings, however, have shown that loss-of-function mutations in a single enhancer near PTF1A cause pancreas agenesis and neonatal diabetes. Using mouse and human genetic models, we show that this enhancer activates an entire PTF1A enhancer cluster in early pancreatic multipotent progenitors. This leading role, therefore, precludes functional redundancy. We further demonstrate that transient expression of PTF1A in multipotent progenitors sets in motion an epigenetic cascade that is required for duct and endocrine differentiation. These findings shed insights into the genome regulatory mechanisms that drive pancreas differentiation. Furthermore, they reveal an enhancer that acts as a regulatory master key and is thus vulnerable to pathogenic loss-of-function mutations.


Subject(s)
Diabetes Mellitus , Transcription Factors , Animals , Cell Differentiation/genetics , Diabetes Mellitus/metabolism , Enhancer Elements, Genetic/genetics , Gene Expression Regulation, Developmental , Humans , Infant, Newborn , Mice , Mutation/genetics , Pancreas/metabolism , Regulatory Sequences, Nucleic Acid , Transcription Factors/metabolism
7.
Nat Genet ; 54(5): 560-572, 2022 05.
Article in English | MEDLINE | ID: mdl-35551307

ABSTRACT

We assembled an ancestrally diverse collection of genome-wide association studies (GWAS) of type 2 diabetes (T2D) in 180,834 affected individuals and 1,159,055 controls (48.9% non-European descent) through the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. Multi-ancestry GWAS meta-analysis identified 237 loci attaining stringent genome-wide significance (P < 5 × 10-9), which were delineated to 338 distinct association signals. Fine-mapping of these signals was enhanced by the increased sample size and expanded population diversity of the multi-ancestry meta-analysis, which localized 54.4% of T2D associations to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying the foundations for functional investigations. Multi-ancestry genetic risk scores enhanced transferability of T2D prediction across diverse populations. Our study provides a step toward more effective clinical translation of T2D GWAS to improve global health for all, irrespective of genetic background.


Subject(s)
Diabetes Mellitus, Type 2 , Genome-Wide Association Study , Diabetes Mellitus, Type 2/epidemiology , Ethnicity , Genetic Predisposition to Disease , Humans , Polymorphism, Single Nucleotide/genetics , Risk Factors
8.
Cell Rep ; 37(2): 109807, 2021 10 12.
Article in English | MEDLINE | ID: mdl-34644572

ABSTRACT

Genome-wide association studies (GWASs) identified hundreds of signals associated with type 2 diabetes (T2D). To gain insight into their underlying molecular mechanisms, we have created the translational human pancreatic islet genotype tissue-expression resource (TIGER), aggregating >500 human islet genomic datasets from five cohorts in the Horizon 2020 consortium T2DSystems. We impute genotypes using four reference panels and meta-analyze cohorts to improve the coverage of expression quantitative trait loci (eQTL) and develop a method to combine allele-specific expression across samples (cASE). We identify >1 million islet eQTLs, 53 of which colocalize with T2D signals. Among them, a low-frequency allele that reduces T2D risk by half increases CCND2 expression. We identify eight cASE colocalizations, among which we found a T2D-associated SLC30A8 variant. We make all data available through the TIGER portal (http://tiger.bsc.es), which represents a comprehensive human islet genomic data resource to elucidate how genetic variation affects islet function and translates into therapeutic insight and precision medicine for T2D.


Subject(s)
Diabetes Mellitus, Type 2/genetics , Genetic Variation , Genomics , Islets of Langerhans/metabolism , Cyclin D2/genetics , Cyclin D2/metabolism , Databases, Genetic , Diabetes Mellitus, Type 2/metabolism , Epigenome , Europe , Gene Frequency , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Phenotype , Quantitative Trait Loci , Transcriptome , Zinc Transporter 8/genetics , Zinc Transporter 8/metabolism
9.
Nat Commun ; 12(1): 2397, 2021 04 23.
Article in English | MEDLINE | ID: mdl-33893274

ABSTRACT

Gene targeting studies in primary human islets could advance our understanding of mechanisms driving diabetes pathogenesis. Here, we demonstrate successful genome editing in primary human islets using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9). CRISPR-based targeting efficiently mutated protein-coding exons, resulting in acute loss of islet ß-cell regulators, like the transcription factor PDX1 and the KATP channel subunit KIR6.2, accompanied by impaired ß-cell regulation and function. CRISPR targeting of non-coding DNA harboring type 2 diabetes (T2D) risk variants revealed changes in ABCC8, SIX2 and SIX3 expression, and impaired ß-cell function, thereby linking regulatory elements in these target genes to T2D genetic susceptibility. Advances here establish a paradigm for genetic studies in human islet cells, and reveal regulatory and genetic mechanisms linking non-coding variants to human diabetes risk.


Subject(s)
CRISPR-Cas Systems , Gene Editing/methods , Insulin-Secreting Cells/metabolism , Islets of Langerhans/metabolism , Models, Genetic , Base Sequence , Diabetes Mellitus, Type 2/genetics , Gene Expression Regulation , Homeodomain Proteins/genetics , Humans , Insulin-Secreting Cells/cytology , Islets of Langerhans/cytology , Potassium Channels, Inwardly Rectifying/genetics , Trans-Activators/genetics
10.
Nat Commun ; 12(1): 2436, 2021 04 23.
Article in English | MEDLINE | ID: mdl-33893285

ABSTRACT

Genome-wide association studies (GWAS) are not fully comprehensive, as current strategies typically test only the additive model, exclude the X chromosome, and use only one reference panel for genotype imputation. We implement an extensive GWAS strategy, GUIDANCE, which improves genotype imputation by using multiple reference panels and includes the analysis of the X chromosome and non-additive models to test for association. We apply this methodology to 62,281 subjects across 22 age-related diseases and identify 94 genome-wide associated loci, including 26 previously unreported. Moreover, we observe that 27.7% of the 94 loci are missed if we use standard imputation strategies with a single reference panel, such as HRC, and only test the additive model. Among the new findings, we identify three novel low-frequency recessive variants with odds ratios larger than 4, which need at least a three-fold larger sample size to be detected under the additive model. This study highlights the benefits of applying innovative strategies to better uncover the genetic architecture of complex diseases.


Subject(s)
Aging , Disease/genetics , Genetic Predisposition to Disease/genetics , Genome, Human/genetics , Genome-Wide Association Study/methods , Age Factors , Gene Frequency , Genome-Wide Association Study/statistics & numerical data , Genotype , Haplotypes , Humans , Phenotype , Polymorphism, Single Nucleotide
11.
Signal Transduct Target Ther ; 5(1): 14, 2020 02 28.
Article in English | MEDLINE | ID: mdl-32296036

ABSTRACT

Sirtuin 3 (SIRT3) is a deacetylase that modulates proteins that control metabolism and protects against oxidative stress. Modulation of SIRT3 activity has been proposed as a promising therapeutic target for ameliorating metabolic diseases and associated cardiac disturbances. In this study, we investigated the role of SIRT3 in inflammation and fibrosis in the heart using male mice with constitutive and systemic deletion of SIRT3 and human cardiac AC16 cells. SIRT3 knockout mice showed cardiac fibrosis and inflammation that was characterized by augmented transcriptional activity of AP-1. Consistent with this, SIRT3 overexpression in human and neonatal rat cardiomyocytes partially prevented the inflammatory and profibrotic response induced by TNF-α. Notably, these effects were associated with a decrease in the mRNA and protein levels of FOS and the DNA-binding activity of AP-1. Finally, we demonstrated that SIRT3 inhibits FOS transcription through specific histone H3 lysine K27 deacetylation at its promoter. These findings highlight an important function of SIRT3 in mediating the often intricate profibrotic and proinflammatory responses of cardiac cells through the modulation of the FOS/AP-1 pathway. Since fibrosis and inflammation are crucial in the progression of cardiac hypertrophy, heart failure, and diabetic cardiomyopathy, our results point to SIRT3 as a potential target for treating these diseases.


Subject(s)
Fibrosis/genetics , Heart Failure/genetics , Proto-Oncogene Proteins c-fos/genetics , Sirtuin 3/genetics , Transcription Factor AP-1/genetics , Animals , Fibrosis/pathology , Heart , Heart Failure/pathology , Histones/genetics , Humans , Inflammation/genetics , Inflammation/pathology , Mice , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/pathology , Oxidative Stress/genetics , Protein Processing, Post-Translational/genetics , Rats
12.
Elife ; 92020 04 29.
Article in English | MEDLINE | ID: mdl-32347793

ABSTRACT

The developmental potential of early embryos is mainly dictated by the quality of the oocyte. Here, we explore the utility of the maternal spindle transfer (MST) technique as a reproductive approach to enhance oocyte developmental competence. Our proof-of-concept experiments show that replacement of the entire cytoplasm of oocytes from a sensitive mouse strain overcomes massive embryo developmental arrest characteristic of non-manipulated oocytes. Genetic analysis confirmed minimal carryover of mtDNA following MST. Resulting mice showed low heteroplasmy levels in multiple organs at adult age, normal histology and fertility. Mice were followed for five generations (F5), revealing that heteroplasmy was reduced in F2 mice and was undetectable in the subsequent generations. This pre-clinical model demonstrates the high efficiency and potential of the MST technique, not only to prevent the transmission of mtDNA mutations, but also as a new potential treatment for patients with certain forms of infertility refractory to current clinical strategies.


Infertility is a growing problem that affects millions of people worldwide. Medical procedures known as in vitro fertilization (IVF) help many individuals experiencing infertility to have children. Typically in IVF, a woman's egg cells are collected, fertilized with sperm from a chosen male and grown for a few days in a laboratory, before returning them to the woman's body to continue to develop. However, there are some women whose egg cells cannot develop into a healthy baby after they have been fertilized. Many of these patients use egg cells from donors, instead. This greatly improves the chances of the IVF treatment being successful, but the resultant children are not genetically related to the intended mothers. Previous studies suggested that a cell compartment known as the cytoplasm plays a crucial role in allowing fertilized egg cells to develop normally. A new technique known as maternal spindle transfer, often shortened to MST, makes it possible to replace the entire cytoplasm of a compromised egg cell. This is achieved by transplanting the genetic material of the compromised egg cell into a donor egg cell with healthier cytoplasm that has previously had its own genetic material removed. Using this technique, it is possible to generate human egg cells for IVF that have the genetic material from the intended mother without the defects in the cytoplasm that may be responsible for infertility. However, it is not clear whether this approach would be a safe and effective way to treat infertility in humans. Costa-Borges et al. applied MST to infertile female mice and found that the technique could permanently correct deficiencies in the cytoplasms of poor quality egg cells, allowing the mice to give birth to healthy offspring. Further experiments studied the offspring and their descendants over several generations and found that they also had higher quality egg cells and normal levels of fertility. These findings open up the possibility of developing new treatments for infertility caused by problems with egg cells, so experiments involving human egg cells are now being performed to evaluate the safety and effectiveness of the technique.


Subject(s)
Embryonic Development/physiology , Mitochondrial Replacement Therapy/methods , Animals , DNA, Mitochondrial/genetics , Female , Mice , Mutation , Oocytes/physiology , Pregnancy
13.
F1000Res ; 9: 1336, 2020.
Article in English | MEDLINE | ID: mdl-34745570

ABSTRACT

The COVID-19 pandemic has posed and is continuously posing enormous societal and health challenges worldwide. The research community has mobilized to develop novel projects to find a cure or a vaccine, as well as to contribute to mass testing, which has been a critical measure to contain the infection in several countries. Through this article, we share our experiences and learnings as a group of volunteers at the Centre for Genomic Regulation (CRG) in Barcelona, Spain. As members of the ORFEU project, an initiative by the Government of Catalonia to achieve mass testing of people at risk and contain the epidemic in Spain, we share our motivations, challenges and the key lessons learnt, which we feel will help better prepare the global society to address similar situations in the future.


Subject(s)
COVID-19 , COVID-19 Testing , Genomics , Humans , Pandemics , SARS-CoV-2 , Volunteers
14.
Nat Genet ; 51(7): 1137-1148, 2019 07.
Article in English | MEDLINE | ID: mdl-31253982

ABSTRACT

Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer clusters or super-enhancers. So far, such domains have been defined through clustering of enhancers in linear genome maps rather than in three-dimensional (3D) space. Furthermore, their target genes are often unknown. We have created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated enhancers to their target genes, often located hundreds of kilobases away. It also revealed >1,300 groups of islet enhancers, super-enhancers and active promoters that form 3D hubs, some of which show coordinated glucose-dependent activity. We demonstrate that genetic variation in hubs impacts insulin secretion heritability, and show that hub annotations can be used for polygenic scores that predict T2D risk driven by islet regulatory variants. Human islet 3D chromatin architecture, therefore, provides a framework for interpretation of T2D genome-wide association study (GWAS) signals.


Subject(s)
Chromatin/chemistry , Diabetes Mellitus, Type 2/genetics , Enhancer Elements, Genetic , Gene Expression Regulation , Gene Regulatory Networks , Insulin Secretion/genetics , Islets of Langerhans/metabolism , Chromatin/genetics , Cohort Studies , Diabetes Mellitus, Type 2/metabolism , Diabetes Mellitus, Type 2/pathology , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Molecular Conformation , Promoter Regions, Genetic
15.
Nat Commun ; 9(1): 2162, 2018 05 30.
Article in English | MEDLINE | ID: mdl-29849136

ABSTRACT

In the originally published version of this Article, the affiliation details for Santi González, Jian'an Luan and Claudia Langenberg were inadvertently omitted. Santi González should have been affiliated with 'Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, 08034 Barcelona, Spain', and Jian'an Luan and Claudia Langenberg should have been affiliated with 'MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK'. Furthermore, the abstract contained an error in the SNP ID for the rare variant in chromosome Xq23, which was incorrectly given as rs146662057 and should have been rs146662075. These errors have now been corrected in both the PDF and HTML versions of the Article.

16.
Nat Commun ; 9(1): 321, 2018 01 22.
Article in English | MEDLINE | ID: mdl-29358691

ABSTRACT

The reanalysis of existing GWAS data represents a powerful and cost-effective opportunity to gain insights into the genetics of complex diseases. By reanalyzing publicly available type 2 diabetes (T2D) genome-wide association studies (GWAS) data for 70,127 subjects, we identify seven novel associated regions, five driven by common variants (LYPLAL1, NEUROG3, CAMKK2, ABO, and GIP genes), one by a low-frequency (EHMT2), and one driven by a rare variant in chromosome Xq23, rs146662057, associated with a twofold increased risk for T2D in males. rs146662057 is located within an active enhancer associated with the expression of Angiotensin II Receptor type 2 gene (AGTR2), a modulator of insulin sensitivity, and exhibits allelic specific activity in muscle cells. Beyond providing insights into the genetics and pathophysiology of T2D, these results also underscore the value of reanalyzing publicly available data using novel genetic resources and analytical approaches.


Subject(s)
Chromosomes, Human, X/genetics , Genetic Predisposition to Disease/genetics , Genome-Wide Association Study , Polymorphism, Single Nucleotide , Alleles , Gene Regulatory Networks/genetics , Genotype , Humans , Insulin Resistance/genetics , Male , Models, Genetic , Risk Factors
17.
Methods Mol Biol ; 1451: 81-91, 2016.
Article in English | MEDLINE | ID: mdl-27464802

ABSTRACT

Herein we present several strategies for testing the function of cis-regulatory elements using the PhiC31 integrase system. Firstly, we present two different strategies to analyze the activity of candidate enhancer elements. Targeted integration of candidate enhancers into the same genomic location circumvents the variability-associated random integration and position effects. This method is suitable for testing of candidate enhancers identified through computational or other analyses a priori. Secondly, we present methodology for targeted integration of BACs into the same genomic location(s). By using additional reporters integrated into a BAC, this enables experimental testing whether cis-regulatory elements are functional in the sequence inserted in the BAC.


Subject(s)
Integrases/metabolism , Regulatory Sequences, Nucleic Acid/genetics , Transgenes/genetics , Animals , Integrases/genetics , Zebrafish/genetics
18.
Curr Opin Genet Dev ; 33: 71-6, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26433090

ABSTRACT

In recent years, studies of cis-regulatory mechanisms have evolved from a predominant focus on promoter regions to the realization that spatial and temporal gene regulation is frequently driven by long-range enhancer clusters that operate within chromosomal compartments. This increased understanding of genome function, together with the emergence of technologies that enable whole-genome sequencing of patients' DNAs, open the prospect of dissecting the role of cis-regulatory defects in human disease. In this review we discuss how recent epigenomic studies have provided insights into the function of transcriptional enhancers. We then present examples that illustrate how integrative genomics can help uncover enhancer sequence variants underlying Mendelian and common polygenic human disease.


Subject(s)
Enhancer Elements, Genetic , Gene Expression Regulation , Genetic Diseases, Inborn/genetics , Transcription, Genetic , Epigenesis, Genetic/genetics , Genetic Diseases, Inborn/pathology , Humans
19.
Nature ; 507(7493): 455-461, 2014 Mar 27.
Article in English | MEDLINE | ID: mdl-24670763

ABSTRACT

Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.


Subject(s)
Atlases as Topic , Enhancer Elements, Genetic/genetics , Gene Expression Regulation/genetics , Molecular Sequence Annotation , Organ Specificity , Cell Line , Cells, Cultured , Cluster Analysis , Genetic Predisposition to Disease/genetics , HeLa Cells , Humans , Polymorphism, Single Nucleotide/genetics , Promoter Regions, Genetic/genetics , RNA, Messenger/biosynthesis , RNA, Messenger/genetics , Transcription Initiation Site , Transcription Initiation, Genetic
20.
Development ; 141(3): 715-24, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24449846

ABSTRACT

Zebrafish transgenesis is increasingly popular owing to the optical transparency and external development of embryos, which provide a scalable vertebrate model for in vivo experimentation. The ability to express transgenes in a tightly controlled spatio-temporal pattern is an important prerequisite for exploitation of zebrafish in a wide range of biomedical applications. However, conventional transgenesis methods are plagued by position effects: the regulatory environment of genomic integration sites leads to variation of expression patterns of transgenes driven by engineered cis-regulatory modules. This limitation represents a bottleneck when studying the precise function of cis-regulatory modules and their subtle variants or when various effector proteins are to be expressed for labelling and manipulation of defined sets of cells. Here, we provide evidence for the efficient elimination of variability of position effects by developing a PhiC31 integrase-based targeting method. To detect targeted integration events, a simple phenotype scoring of colour change in the lens of larvae is used. We compared PhiC31-based integration and Tol2 transgenesis in the analysis of the activity of a novel conserved enhancer from the developmentally regulated neural-specific esrrga gene. Reporter expression was highly variable among independent lines generated with Tol2, whereas all lines generated with PhiC31 into a single integration site displayed nearly identical, enhancer-specific reporter expression in brain nuclei. Moreover, we demonstrate that a modified integrase system can also be used for the detection of enhancer activity in transient transgenesis. These results demonstrate the power of the PhiC31-based transgene integration for the annotation and fine analysis of transcriptional regulatory elements and it promises to be a generally desirable tool for a range of applications, which rely on highly reproducible patterns of transgene activity in zebrafish.


Subject(s)
Chromosomal Position Effects/genetics , Gene Targeting , Mutagenesis, Insertional/genetics , Transgenes/genetics , Zebrafish/genetics , Animals , Animals, Genetically Modified , Base Sequence , Brain/metabolism , Enhancer Elements, Genetic/genetics , Gene Expression Regulation , Gene Transfer Techniques , Genes, Reporter/genetics , Genetic Loci/genetics , Genome/genetics , Integrases/metabolism , Lens, Crystalline/metabolism , Molecular Sequence Data , Reproducibility of Results , Xenopus laevis/genetics
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