Cristina Joana Marques

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

Methylation at the 5′ position of cytosine in DNA has important roles in genome function and is dynamically reprogrammed during early embryonic and germ cell development. The mammalian genome also contains 5-hydroxymethylcytosine (5hmC), which seems to be generated by oxidation of 5-methylcytosine (5mC) by the TET family of enzymes that are highly expressed in embryonic stem (ES) cells. Here we use antibodies against 5hmC and 5mC together with high throughput sequencing to determine genome-wide patterns of methylation and hydroxymethylation in mouse wild-type and mutant ES cells and differentiating embryoid bodies. We find that 5hmC is mostly associated with euchromatin and that whereas 5mC is under-represented at gene promoters and CpG islands, 5hmC is enriched and is associated with increased transcriptional levels. Most, if not all, 5hmC in the genome depends on pre-existing 5mC and the balance between these two modifications is different between genomic regions. Knockdown of Tet1 and Tet2 causes downregulation of a group of genes that includes pluripotency-related genes (including Esrrb, Prdm14, Dppa3, Klf2, Tcl1 and Zfp42) and a concomitant increase in methylation of their promoters, together with an increased propensity of ES cells for extraembryonic lineage differentiation. Declining levels of TETs during differentiation are associated with decreased hydroxymethylation levels at the promoters of ES cell-specific genes together with increased methylation and gene silencing. We propose that the balance between hydroxymethylation and methylation in the genome is inextricably linked with the balance between pluripotency and lineage commitment.

Genomic imprinting in disruptive spermatogenesis.

The possibility of imprinting disease transmission by assisted reproductive technologies has been raised after births of children with Angelmans and Beckwith-Wiedemanns syndromes. To investigate whether imprinting defects were associated with disturbed spermatogenesis, we studied two oppositely imprinted genes in spermatozoan DNA from normozoospermic and oligozoospermic patients. In the mesodermal specific transcript gene (MEST), bisulphite genomic sequencing showed that maternal imprinting was correctly erased in all 123 patients. However, methylation of the H19 gene did not change in any of 27 normozoospermic individuals (0%, 95% CI 0-13%), compared with methylation changes in eight moderate (17%, 8-31%, p=0.026) and 15 severe (30%, 18-45%, p=0.002) oligozoospermic patients. Our data suggest an association between abnormal genomic imprinting and hypospermatogenesis, and that spermatozoa from oligozoospermic patients carry a raised risk of transmitting imprinting errors.

Abnormal methylation of imprinted genes in human sperm is associated with oligozoospermia

Genomic imprinting marks in the male germ line are already established in the adult germinal stem cell population. We studied the methylation patterns of H19 and MEST imprinted genes in sperm of control and oligozoospermic patients, by bisulphite genomic sequencing. We here report that 7 out of 15 (46.7%) patients with a sperm count below 10 x 10(6)/ml display defective methylation of H19 and/or MEST imprinted genes. In these cases, hypomethylation was observed in 5.54% (1.2-8.3%) and complete unmethylation in 2.95% (0-5.9%) of H19 clones. Similarly, for the CTCF-binding site 6, hypomethylation occurred in 4.8% (1.2-8.9%) and complete unmethylation in 3.7% (0-6.9%) of the clones. Conversely, hypermethylation occurred in 8.3% (3.8-12.2%) and complete methylation in 6.1% (3.8-7.6%) of MEST clones. Of the seven patients presenting imprinting errors, two had both H19 hypomethylation and MEST hypermethylation, whereas five displayed only one imprinted gene affected. The frequency of patients with MEST hypermethylation was highest in the severe oligozoospermia group (2/5 patients), whereas H19 hypomethylation was more frequent in the moderate oligozoospermia (2/5 patients). In all cases, global sperm genome methylation analysis (LINE1 transposon) suggested that defects were specific for imprinted genes. These findings could contribute to an explanation of the cause of Silver-Russell syndrome in children born with H19 hypomethylation after assisted reproductive technologies (ART). Additionally, unmethylation of the CTCF-binding site could lead to inactivation of the paternal IGF2 gene, and be linked to decreased embryo quality and birth weight, often associated with ART.

Mutational Characterization of Steroid 21-Hydroxylase Gene in Portuguese patients with Congenital Adrenal Hyperplasia

Congenital adrenal hyperplasia (CAH) due to steroid 21-hydroxylase deficiency is a common inherited disorder of adrenal hormone biosynthesis due to mutations in the 21-hydroxylase gene, CYP21A2. Genotyping for ten of the most frequent mutations was performed in 84 Portuguese CAH patients: 10 salt-wasters, 6 simple-virilizers and 68 non-classical patients. The patients were diagnosed by a level of 17-hydroxyprogesterone above 10 ng/ml either in basal conditions or after an ACTH 0,25 mg IV Test. A variety of genotyping techniques were used to detect these ten mutations. CYP21A2 mutations were detected in 91.7% (77/84) of the patients. The frequency of alleles carrying two or more CYP21A2 mutations (9.5% - 16/168) is higher than in other populations. The most frequent mutations identified in our population were V281L (41.7%) and deletions/conversions involving the promoter region of the CYP21A2 gene (28.3%). A decreased frequency of IVS2-12C/A>G mutation (5.6%) was the most characteristic feature of our population. This study allow the characterization of the mutational spectrum of CAH patients, mainly non-classical CAH, with 21-hydroxylase deficiency from Portugal showing specific genetic features of this population which reveals differences with worldwide countries.

Genetic regulation on ex vivo differentiated natural killer cells from human umbilical cord blood CD34 + cells

Natural killer (NK)-cells are a lymphocyte population playing a critical role in the immune surveillance against tumors and virally infected cells. The development of human hematopoietic stem cells (hHSC) into fully differentiated NK-cells pass through discrete stages of differentiation involving a variety of factors such as cytokines, membrane factors, and transcription factors (TFs). Because there is lack of studies in this field, we decided to perform an extended analysis of TFs during in vitro differentiation of NK-cells. At several points of differentiation, cells were characterized by their mRNA expression either for NK-cell cell markers, for a number of mature NK-cell receptors or a large panel of TFs. Our data suggests that some TFs (ID2, EGR-2 and T-BET) play a role in NK-cell commitment, differentiation and maturation. Although delayed on its expression, BLIMP1 also seems to be involved in differentiation and maturation of NK cells, but not in NK-cell commitment. E4BP4 and TOX are more related with initial stages of NK-cell commitment. PU.1, MEF, Ikaros, EGR-1, BCL11B and IRF-2 revealed less involvement in maturation and were more associated with NK-cell commitment and pNK cell production. GATA-3 showed a differential role during the ontogeny of NK-cells. We show that assessment of the transcripts present in the differentiating NK-cells demonstrated, a pattern of preserved and differential gene expression remarkably similar to that seen in mice except for E4BP4 that showed constant downregulation throughout the culture period. A thorough understanding of NK-cell developmental mechanisms is important as it may enable future therapeutic manipulation.

Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications

DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.

DNA methylation imprinting errors in spermatogenic cells from maturation arrest azoospermic patients

Imprinting errors have been described in spermatozoa from infertile patients with oligozoospermia and azoospermia. However, little is known about methylation of imprinted genes in other spermatogenic cells from azoospermic patients. Therefore, we aimed to evaluate the methylation status of single CpGs located in the differentially methylated regions (DMRs) of two imprinted genes, one paternally (H19) and one maternally (MEST) methylated, in primary spermatocytes of azoospermic patients presenting complete (MAc, n = 7) and incomplete (MAi, n = 8) maturation arrest, as well as in other spermatogenic cells from MAi patients that presented focus of complete spermatogenesis in some seminiferous tubules. We observed H19 imprinting errors in primary spermatocytes from one MAi patient and MEST imprinting errors in one MAi and two MAc patients. Additionally, H19 imprinting errors were observed in elongated spermatids/spermatozoa from one MAi patient. Nevertheless, no statistical differences were found for H19 and MEST global methylation levels (percentage of methylated and unmethylated CpGs, respectively) between patients with complete and incomplete MA and also between MA groups and a control group. These results provide further evidence that imprinting errors occur in spermatogenic cells from patients presenting impaired spermatogenesis, as we and others have previously described in ejaculated and testicular spermatozoa. As paternal imprinting errors can be transmitted to the embryo by the sperm cell, they can provide a possible explanation for poor embryo development and/or low pregnancy rates as correct expression of imprinted genes is crucial for embryo and placental development and function. Therefore, in cases with male factor infertility where unsuccessful in vitro fertilization (IVF) treatments are recurrent, analysis of imprinting marks in spermatozoa might be a useful diagnostic tool.

Sperm Epigenetic Profile

Spermatogenesis is a unique process by which diploid mitotically dividing spermatogonia give rise to mature haploid male gametes by a process involving several complex events such as proliferation (mitotic divisions of spermatogonia), meiotic divisions, and differentiation steps. During this process, several epigenetic modifications of the paternal genome occur, which lead to a compacted nuclear structure and transcriptionally inactive genome. It involves histone variants and histone to protamine exchanges. In addition, sperm carry important epigenetic information such as paternal imprinting marks that are crucial for the normal development of the future embryo.

Estudo do imprinting genómico em espermatozóides de pacientes com oligozoospermia

In the present study, we evaluated the methylation status of H19 gene DMR (Differentially Methylated Region) using sodium bisulphite treatment of DNA, cloning of PCR (Polymerase Chain Reaction) products and automated DNA sequencing. We studied 69 clones from 5 sperm samples obtained from males with normal sperm counts (≥ 20 x 106 Sz/mL) and 31 clones from 2 sperm samples isolated from patients with severe oligozoospermia (< 5 x 106 Sz/mL). In sperm cells from severe oligozoospermic patients, we observed that the majority of clones (26/31, 83.9%) presented incomplete methylation, in contrast to clones obtained from sperm from normozoospermic males (33/69, 47.8%). In severe oligozoospermia, the average of unmethylated CpGs was of 4.1, ranging between 1 to 17 affected CpGs, while in normozoospermia the average was of 0.7, ranging from 1 to 3 affected CpGs, being statistically significant the difference between the two groups (p=0.001). The simultaneous demethylation of multiple CpGs occurred in 5/33 (15.2%) of the clones with incomplete methylation in the normozoospermia group, while in severe oligozoospermia the majority of the cases (19/26, 73.1%) presented associated demethylation simultaneously. Concomitantly, for each CpG position, the level of methylation deficit in normozoospermia was always inferior than 10% with the exception of CpG 6 and 9 (12 and 14%, respectively), while in severe oligozoospermia the majority of cases presented values of demethylation superior than 20% (P = 0.000-0.044). The complete demethylation of CTCF protein binding site (CpG 4-8) was only found in severe oligozoospermic cases (3/31, 9.7%). In conclusion, sperm from severe oligozoospermic patients present high rates of genomic imprinting errors, leading to the possibility of transmission of these errors to the offspring during ICSI (Intracytoplasmic Sperm Injection) treatments. In the absence of methylation at H19 DMR, CTCF protein might bind to the paternal allele and, consequently, promote the transmission of two active H19 and two inactive IGF2 alleles. This situation could negatively affect the in vitro development of preimplantation embryo. Thus, these results suggest the importance of a previous study of genomic imprinting in sperm before the ICSI procedure, in order to evaluate the existence of any risk.