Should we perform oocyte accumulation to preserve fertility in women with Turner syndrome? A multicenter study and systematic review of the literature

STUDY QUESTION

Should we perform oocyte accumulation to preserve fertility in women with Turner syndrome (TS)?

SUMMARY ANSWER

The oocyte cryopreservation strategy is not well adapted for all TS women as their combination of high basal FSH with low basal AMH and low percentage of 46,XX cells in the karyotype significantly reduces the chances of freezing sufficient mature oocytes for fertility preservation.

WHAT IS KNOWN ALREADY

An oocyte cryopreservation strategy requiring numerous stimulation cycles is needed to preserve fertility in TS women, to compensate for the low ovarian response, the possible oocyte genetic alterations, the reduced endometrial receptivity, and the increased rate of miscarriage, observed in this specific population. The validation of reliable predictive biomarkers of ovarian response to hormonal stimulation in TS patients is necessary to help practitioners and patients choose the best-personalized fertility preservation strategy.

STUDY DESIGN, SIZE, DURATION

A retrospective bicentric study was performed from 1 January 2011 to 1 January 2023. Clinical and biological data from all TS women who have received from ovarian stimulation for fertility preservation were collected. A systematic review of the current literature on oocyte retrieval outcomes after ovarian stimulation in TS women was also performed (PROSPERO registration number: CRD42022362352).

PARTICIPANTS/MATERIALS, SETTING, METHODS

A total of 14 TS women who had undergone ovarian stimulation for fertility preservation were included, representing the largest cohort of TS patients published to date (n = 14 patients, 24 cycles). The systematic review of the literature identified 34 additional TS patients with 47 oocyte retrieval outcomes after ovarian stimulation in 14 publications (n = 48 patients, n = 71 cycles in total).

MAIN RESULTS AND THE ROLE OF CHANCE

The number of cryopreserved mature oocytes on the first cycle for TS patients was low (4.0 ± 3.7). Oocyte accumulation was systematically proposed to increase fertility potential and was accepted by 50% (7/14) of patients (2.4 ± 0.5 cycles), leading to an improved total number of 10.9 ± 7.2 cryopreserved mature oocytes per patient. In the group who refused the oocyte accumulation strategy, only one patient exceeded the threshold of 10 mature cryopreserved oocytes. In contrast, 57.1% (4/7) and 42.9% (3/7) of patients who have underwent the oocyte accumulation strategy reached the threshold of 10 and 15 mature cryopreserved oocytes, respectively (OR = 8 (0.6; 107.0), P = 0.12; OR= 11 (0.5; 282.1), P = 0.13). By analyzing all the data published to date and combining it with our data (n = 48 patients, n = 71 cycles), low basal FSH and high AMH concentrations as well as a higher percentage of 46,XX cells in the karyotype were significantly associated with a higher number of cryopreserved oocytes after the first cycle. Moreover, the combination of low basal FSH concentration (<5.9 IU/l), high AMH concentration (>1.13 ng/ml), and the presence of 46,XX cells (>1%) was significantly predictive of obtaining at least six cryopreserved oocytes in the first cycle, representing objective criteria for identifying patients with real chances of preserving an adequate fertility potential by oocyte cryopreservation.

LIMITATIONS, REASONS FOR CAUTION

Our results should be analyzed with caution, as the optimal oocyte number needed for successful live birth in TS patients is still unknown due to the low number of reports their oocyte use in the literature to date.

WIDER IMPLICATIONS OF THE FINDINGS

TS patients should benefit from relevant clinical evaluation, genetic counseling and psychological support to make an informed choice regarding their fertility preservation technique, as numerous stimulation cycles would be necessary to preserve a high number of oocytes.

STUDY FUNDING/COMPETING INTEREST(S)

This research received no external funding. The authors declare no conflict of interest.

TRIAL REGISTRATION NUMBER

N/A.

[EUGIC (Extension of the Use of Gametes in Intra-Conjugal): New uses of gametes within the couple]

OBJECTIVE

New possibilities for using gametes within a couple were created by the French law of August 2, 2021 related to bioethics by opening Assisted Reproductive Technics (ART) to all women. It concerns previously self-preserved gametes, thus avoiding the need for gamete donation. The objective of our study is to evaluate the perception of these new uses by ART practitioners.

METHOD

A questionnaire of twelve short questions was sent to professionals concerned with gamete donation.

RESULTS

One hundred and ten professionals answered the questionnaire. The majority of them approve of the Reception of Oocytes from the Partner (ROPA), notably if there is a medical indication. Requests are rarer for the care of trans* people, and raise more questions. Although less favorable to the use of eggs from trans* men, more of them support the practice when it is an alternative to oocyte donation.

CONCLUSION

The acronym EUGIC (Extension of the Use of Gametes in Intra-Conjugal) makes it possible to group together these new situations generated by the change in the French law.

[What issues, changes and adaptations for French ART centers in the context of the new bioethics law?]

OBJECTIVE

This review intends to introduce the changes of the new Bioethics law in the reproductive field and its application in French ART centers.

MATERIAL AND METHODS

The review details the main provisions of the Bioethics Law of August 2nd 2021 as well as the three decrees published since: the first one on September 29th 2021, which specifies in particular the age conditions to benefit from ART and self-preservation of one's gametes; another decree on December 31st, 2021, to set the terms and conditions for gamete self-preservation activities for non-medical reasons and the last decree on April 14th 2022, relating to the allocation of donated gametes and embryo donation.

RESULTS

Since the law of August 2nd, 2021, access conditions to assisted reproductive technology (ART) have evolved in France. Previously based on pathological infertility or the risk of transmission of a serious disease, ART is now intended to respond to the parental project of a couple formed by a man and a woman, two women or an unmarried woman. With the widening of access conditions, the use of gamete donation will likely increase. The upcoming raise of children born from gamete donation has led the legislator to question their right to access their origin. From September 1st 2022, adults born from gamete donation will be able to request a special administrative authority in order to access the donor's non identifying data (age, physical characteristics, family and professional situation, motivation for the donation…) and/or the donor's identity. Moreover, the new bioethics law opens up the possibility of autologous gamete cryopreservation without medical reasons, under specific age conditions, in order to carry out an assisted reproduction technique later. If gametes are not used, autologous gamete preservation could also allow an increase in gamete donation. However, the modification of gamete donation conditions could suggest a short term decrease in donors' number. Finally, the new bioethics law further opens up research on human embryos and embryonic stem cells.

CONCLUSION

The arrangements introduced by the Bioethics Law promulgated on August 2nd, 2021 represent a major revolution in the field of Reproductive Medicine and are expected to transform the practices of reproductive biology centers and CECOS in France.

[Fertility preservation and access to medically assisted reproduction for Trans people: Guidelines from French Professional Association for Transgender Health]

Many health care professionals are dealing with the issue of transgender people in their medical practice. In the field of reproduction, Trans people can benefit from fertility preservation before the introduction of hormonal treatment or surgery altering their fertility. This article, which is the result of a collaborative work of several reproductive professionals involved in the health of Trans people, provides an overview of the possibilities of fertility preservation and medically assisted reproduction techniques in France for Trans people.

[HLA-C KIR interactions and placental defects: Implications in ART pregnancy issues]

OBJECTIVE

The aim of this review is to update data concerning the impact of HLA-C KIR system on placental disorders and assess the involvement on ART clinical outcomes.

METHOD

Ensuring the maintenance of human pregnancy requires the set up of immunological tolerance to prevent foetus rejection. This phenomenon involves different actors of the immune system: among them, uterine NK cells (uNK) hold specific KIR (killer-cell immunoglobulin-like) receptors linking to HLA molecules on the surface of trophoblastic cells at implantation. Many studies provided evidence that the specific interaction between maternal KIR and foetal HLA-C could influence the process of placentation; according to the KIR haplotype and the type of HLA-C, the interaction could be detrimental for placental function. We reviewed the latest data available regarding HLA-C KIR interactions and ART outcomes.

RESULTS

The available results highlight a significant increase of preeclampsia risk and recurrent miscarriages when the maternal inhibitory haplotype KIR AA is present, this risk is all the more enhanced when the interaction occurs with foetal HLA-C2. Recent data suggest the consequences of this detrimental interaction in case of DET (double embryo transfer) or use of donor's oocytes in ART practice. On the other hand, maternal KIR AB or BB haplotypes haven't been related to an additional obstetrical risk, as well as the foetal HLA-C1 homozygous allotype.

CONCLUSION

Despite the existence of many confoundings in current literature on the subject, interaction between maternal KIR and foetal HLA-C represent a promising target lead to broaden the spectrum of placental defects etiologies, especially in the reproductive health area.

P-219 Does artificial shrinkage prior to fresh blastocyst transfer improve ongoing pregnancy rate? A prospective double blind randomized controlled trial

Study question

Does artificial shrinkage (AS) of blastocoelic cavity (BC) prior to fresh elective single blastocyst transfer (SBET) increase ongoing pregnancy rate?

Summary answer

Ongoing pregnancy rates were similar with or without AS of blastocoelic cavity. AS does not seem to provide benefit before fresh blastocyst transfer.

What is known already

AS of the vitrified blastocysts enhances success rate in frozen embryo transfer cycles.

In vitro cultured embryos suffer changes in temperature, pH and osmotic pressure. Moreover, manipulations such as pipetting, fertilization, microscopic observations and changes of dishes can induce oxidative stress and apoptosis. The presence of cell free DNA (cfDNA) in blastocyst fluids could be the consequence of its release from dead cells. The quantity of cfDNA in blastocyst fluids could possibly be related to the rate of cell death. It is thus interesting to estimate whether AS of BC could improve the implantation rate in cycles with fresh blastocyst transfer.

Study design, size, duration

Prospective, randomized, double blind controlled study. From May 20th 2018 to June 30th 2021, 150 couples elected for fresh SBET were included in the study and were randomly selected as “AS +” group (n = 100), where AS of blastocoel was performed by laser pulse before fresh blastocyst transfer, and “AS -” group (n = 50), where fresh blastocysts were transferred without any additional intervention.

Participants/materials, setting, methods

On day 5 after fertilization, one blastocyst with a grade of expansion B3, B4, B5 or B6 and type A or B quality trophectoderm (Gardner and Schoolcraft classification, 1999) was selected for transfer. After replacement, the droplet that contained the embryo from day 3 was collected for cfDNA level quantification.

Ongoing pregnancy rate was determined by the visualization of a gestational sac with a foetal heartbeat 6 weeks later and cfDNA was assessed by ALU-qPCR.

Main results and the role of chance

The two groups were similar for age, BMI, infertility duration and cause, stimulation characteristics and embryological parameters. The global ongoing pregnancy rate per transfer after SBET was 49.7 %. The pregnancy rate in the AS + group was slightly higher than in the control group but not significantly (respectively 50.00 % and 48,9 %, p = 0,91).

cfDNA median value in the AS+ group was comparable to the control group (0.493 (0.219; 0.915) mg/ml and 0.595 (0.271; 1.129) mg/ml respectively (p = 0.45)). No link was found between cfDNA rate and clinical pregnancy rate.

Limitations, reasons for caution

Patients included in the study are still followed to evaluate the impact of AS on live birth rate, wastage rate, obstetrical and neonatal complications. cfDNA rate was evaluated in spent culture media and not by blastocentesis, which could provide a more accurate quantification.

Wider implications of the findings

To our knowledge, this is the first prospective randomized controlled study assessing the benefit of AS of BC before fresh blastocyst transfer. The inclusion of live birth rate is crucial to ascertain the interest of this technique and more studies are needed to improve the use of cfDNA in routine.

Trial registration number

NCT02988544

O-141 Mapping of SARS-CoV-2-associated receptors and proteases mRNA in human endometrium during natural and stimulated cycles

Study question

Covid-19 pandemic has significantly affected the assisted reproductive technology (ART) practice. Understanding whether SARS-CoV-2 could infect endometrial tissues during ART is crucial for risk mitigation

Summary answer

Analyses of gene expression profiles of SARS-CoV-2 host entry candidates from microarray data suggest that endometrium should be considered as potential target for SARS-CoV-2 infection.

What is known already

Very few studies analyzed the gene expression profiles of SARS-CoV-2-associated receptors and proteases, mainly focusing on ACE2 and TMPRSS2 expression, resulting incomplete knowledge in different specimens from female genital tract. However, no studies have analyzed the potential impact of controlled ovarian stimulation (COS) protocols during ART procedure on the endometrial gene expression profiles of SARS-CoV-2-associated receptors and proteases

Study design, size, duration

To address this question, we retrospectively examined the gene expression profile of SARS-CoV-2-associated receptors and proteases in endometrial biopsies of a cohort of ART candidates using Affymetrix microarray data

Participants/materials, setting, methods

Human endometrial tissue under natural (n = 62) and COS cycles (n = 42) were analyzed. A focus was particularly made on the renin-angiotensin system relates genes with a prominent role in the virus infection, and gene expression levels of receptors and proteases closely related to SARS-CoV-2 infectionwas also studied.

Main results and the role of chance

Using our large cohort of endometrial samples, we reported a high prevalence of genes related to the ACE2 pathway, including AGT, AGTR1, ANPEP, CTSA, ENPEP, LNPEP, MME, NLN, THOP1, BSG and CTSL during both phases(early- and mid-secretory phase), and mainly during the mid-secretory phase for ACE2. The highest signal intensities were found for CTSA, LNPEP, MME, NLN, BSG and CTSL. The most representative of dual coexpression of SARS-CoV-2-associated receptor and protease in endometrium was BSG-CSTL and BSG-CTSA. It s also important to note high variation of SARS-CoV-2 receptors inter-patients under natural cycle.Globally, the impact of COS on endometrial gene expression profile of SARS-CoV-2-associated receptors and proteases of non Covid-19 patients is low, suggesting no additional potential risks of SARS-CoV-2 infection during stimulated ART procedure compared with natural cycles.

Limitations, reasons for caution

Analyses of Affymetrix microarray gene expression data were performed in non-COVID-19 patients. Whether the SARS-CoV-2 infection changes the endometrial gene expression profile of SARS-CoV-2-associated receptors and proteases is under investigation

Wider implications of the findings

Specimens from female genital tract may be considered as potential targets for SARS-CoV-2.

Trial registration number

not applicable

P–242 Gene expression profiles of SARS-CoV–2-associated receptors and proteases in human early embryonic development and follicular cells

Study question

Are the oocytes, embryos, granulosa and cumulus cells, used during ART, susceptible to the SARS-CoV–2 infection?

Summary answer

Transcriptomic analyses of SARS-CoV–2-associated receptors and proteases strongly suggest that blastocysts are most permissive to SARS-CoV–2 compared with mature oocytes and day 3 embryos.

What is known already

Very few studies analyzed the gene expression profiles of SARS-CoV–2-associated receptors and proteases, mainly focusing on ACE2 and TMPRSS2 expression, resulting in partial knowledge in different specimens from female genital tract. To date, the gene expression profile of SARS-CoV–2 host entry candidates in the entire preimplantation embryos is scarcely available. Moreover, reports on oocyte and granulosa cells susceptibilityto SARS-CoV–2 are very sparse.

Study design, size, duration

To address this question, we retrospectively examined the gene expression profiles of SARS-CoV–2-associated receptors and proteases in human granulosa cells (GCs), cumulus cells (CCs), mature oocytes, day 3 embryos, blastocysts and trophectoderm cells obtained from our previously described Affymetrix microarray data.

Participants/materials, setting, methods

Human GCs and CCs (n = 17), mature oocytes (n = 6), and preimplantation embryos (n = 20) were analyzed. The comparison of gene expression levels of receptors and proteases closely related to SARS-CoV–2 infection. For each gene, the number of samples with the probe set ‘present’, based on the detection call, was analyzed. Each probe set was classified according to the signal intensity value median, as low (&lt;100), medium (100–200) or high expression level (&gt;200).

Main results and the role of chance

ACE2, BSG, CTSL, CTSA were detectable at high expression level in all mature oocyte samples, while only CTSL was strongly expressed in all day 3 embryos. The most representative dual co-expression of SARS-CoV–2-associated receptor and protease (60% of samples) during the embryonic genome activation stage (EGA) was ACE2-CTSL and BSG-CTSL. In blastocysts, ACE2, BSG, CTSL, CTSA and FURIN were detectable in the entire cohort at high expression level, and the prevalence of the different dual co-expression of SARS-CoV–2-associated proteases and receptors was optimal (100% of samples). Interestingly, only CTSL was detectable in all trophectoderm samples and a prevalence of 60% was found for the BSG-CTSL co-expression. ACE2, BSG, CTSL and CTSA were present at high expression level in CCs samples. In contrast, ACE2 and BSG expression was very low while CTSL and CTSA showed a high expression level in GCs.A prevalence of 100% was reported for ACE2-CTSL, ACE2-CTSA co-expression for both cell types. In addition, BSG-CTSL and BSG-CTSA co-expression were also present in all CCs against ∼70% in GCs samples. This data suggest a potential risks of SARS-CoV–2 infection either GC or early embryo development.

Limitations, reasons for caution

Analyses of Affymetrix microarray gene expression data were performed in non-COVID–19 patients. Whether the SARS-CoV–2 infection change the gene expression profile of SARS-CoV–2-associated receptors and proteases is under investigation.

Wider implications of the findings: Specimens from female genital tract may be considered as potential targets for SARS-CoV–2.

Trial registration number

Not applicable

[Assessment of genital microbiota: An emerging approach in assisted reproductive techniques]

The genital microbiota actively participates in women's reproductive health. Indeed, a genital dysbiosis (microbial imbalance associated with adverse effects on host health) can lead to vaginal infections (such as mycoses or bacterial vaginosis). Recent data reported that genital dysbiosis (e.g. vaginal or endometrial) was associated with fewer chances of live births in assisted reproductive technologies (ART), via decreased pregnancy rates and an increased risk of miscarriages. The presence or diversity of certain bacterial strains (in particular Gardenellavaginalis, Proteobacteria, Lactobacillusjensenii, Lactobacilluscrispatus or Atopobiumvaginae) within the genital microbiota seem to be associated with the outcomes of ART cycles, suggesting new approaches to improve ART results. In this review, we aim at presenting the state of art on the association between the female genital microbiota and ART success. The diagnostic and therapeutic approaches (i.e. probiotics, antibiotic therapy and transplantation of vaginal microbiota) in the management of patients with altered microbiota will also be discussed. The confirmation of these data in the coming years could significantly improve the management of infertile patients in ART with a more personalized approach partially based on the female genital microbiotic profile.

[Endometrial receptivity in assisted reproductive techniques: An aspect to investigate in embryo implantation failure]

Infertility affects between 8 and 12% of reproductive-age couples worldwide. Despite improvements in assisted reproductive techniques (ART), live birth rates are still limited. In clinical practice, imaging and microscopy are currently widely used, but their diagnostic effectiveness remains limited. In research, the emergence of innovative techniques named OMICS would improve the identification of the implantation window, while progressing in the understanding of the pathophysiological mechanisms involved in embryo implantation failures. To date, transcriptomic analysis seems to be the most promising approach in clinical research. The objective of this review is to present the results obtained with the different approaches available in clinical practice and in research to assess endometrial receptivity in patients undergoing ART.

NLRP7 is increased in human idiopathic fetal growth restriction and plays a critical role in trophoblast differentiation

Fetal growth restriction (FGR) the leading cause of perinatal mortality and morbidity is highly related to abnormal placental development, and placentas from FGR pregnancies are often characterized by increased inflammation. However, the mechanisms of FGR-associated inflammation are far from being understood. NLRP7, a member of a family of receptors involved in the innate immune responses, has been shown to be associated with gestational trophoblastic diseases. Here, we characterized the expression and the functional role of NLRP7 in the placenta and investigated its involvement in the pathogenesis of FGR. We used primary trophoblasts and placental explants that were collected during early pregnancy, and established trophoblast-derived cell lines, human placental villi, and serum samples from early pregnancy (n = 38) and from FGR (n = 40) and age-matched controls (n = 32). Our results show that NLRP7 (i) is predominantly expressed in the trophoblasts during the hypoxic period of placental development and its expression is upregulated by hypoxia and (ii) increases trophoblast proliferation ([³H]-thymidine) and controls the precocious differentiation of trophoblasts towards syncytium (syncytin 1 and 2 and β-hCG production and xCELLigence analysis) and towards invasive extravillous trophoblast (2D and 3D cultures). We have also demonstrated that NLRP7 inflammasome activation in trophoblast cells increases IL-1β, but not IL-18 secretion. In relation to the FGR, we demonstrated that major components of NLRP7 inflammasome machinery are increased and that IL-1β but not IL-18 circulating levels are increased in FGR. Altogether, our results identified NLRP7 as a critical placental factor and provided evidence for its deregulation in FGR. NLRP7 inflammasome is abundantly expressed by trophoblast cells. It is regulated by a key parameter of placental development, hypoxia. It controls trophoblast proliferation, migration, and invasion and exhibits anti-apoptotic role. NLRP7 machinery is deregulated in FGR pregnancies. KEY MESSAGES: NLRP7 inflammasome is abundantly expressed by trophoblast cells. It is regulated by a key parameter of placental development, hypoxia. It controls trophoblast proliferation, migration, and invasion and exhibits anti-apoptotic role. NLRP7 machinery is deregulated in FGR pregnancies.

Inhibition of human placental endothelial cell proliferation and angiogenesis by netrin-4

INTRODUCTION

Netrin-4 is a secreted member of the laminin-related protein family, known to be involved in axonal guidance and endothelial cell survival, proliferation, and migration. We have recently reported the cellular localization of netrin-4 and its receptor neogenin in human first trimester and term placenta. A strong expression of netrin-4 was observed in trophoblast and in endothelial cells, suggesting a potential role of this protein in placental angiogenesis. In relation to human pregnancy, it has been reported that circulating netrin-4 were increased in fetal umbilical cord blood of intrauterine growth restriction IUGR compared to normal pregnancy suggesting an adverse effect of this protein on placental and fetal development. The aim of this study was to determine the role of netrin-4 in placental angiogenesis.

METHODS

The effects of netrin-4 on proliferation, migration, tube-like organization, and spheroid sprouting of human placental microvascular endothelial cells (HPEC) were studied.

RESULTS

We demonstrated that netrin-4 inhibits HPEC proliferation, tube-like formation, migration and spheroid sprouting, suggesting a direct role of netrin-4 in the regulation of intra-villus angiogenesis.

DISCUSSION

This is the first report of an anti-angiogenic activity of netrin-4 in human placenta. This study brings new insights into netrin-4 roles in placental angiogenesis and suggests possible involvements of netrin-4 in angiogenesis-related pathologies such as IUGR.

[PROK1, prognostic marker of embryo implantation?]

In spite of improvements in assisted reproductive technology (ART) during the last 30 years, the rate of pregnancy remains constrained, as only about 25 % of embryo transfer lead to successful pregnancies, even with an average of two embryos replaced. Embryo selection is currently based on the establishment of morphokinetic scores, a method that obviously exhibits limitations. Therefore, the assessment of embryo development potency by criteria of higher predictive value is mandatory in order to increase the rates of pregnancy. Nowadays, there is increasing evidence that angiogenic factors might contribute to the success of the implantation and to the pregnancy outcome. Among these factors, prokineticin 1 (PROK1) and its receptors (PROKRs) constitute new targets that showed over the last ten years strong biological features directly linked to ovarian physiology, endometrial receptivity, embryo implantation and thus successful pregnancies. In ART, the rates of circulating PROK1 were reported in 2012 as significantly linked to the quality of embryonic cohort, as well as to the rates of pregnancy. Our preliminary data suggest a high potential of this cytokine in the success of implantation and pregnancy, and strongly overtones the emergency to investigate the value of its measurement in conditioned media of oocytes and embryo cultures in ART.

EG-VEGF controls placental growth and survival in normal and pathological pregnancies: case of fetal growth restriction (FGR)

Identifiable causes of fetal growth restriction (FGR) account for 30 % of cases, but the remainders are idiopathic and are frequently associated with placental dysfunction. We have shown that the angiogenic factor endocrine gland-derived VEGF (EG-VEGF) and its receptors, prokineticin receptor 1 (PROKR1) and 2, (1) are abundantly expressed in human placenta, (2) are up-regulated by hypoxia, (3) control trophoblast invasion, and that EG-VEGF circulating levels are the highest during the first trimester of pregnancy, the period of important placental growth. These findings suggest that EG-VEGF/PROKR1 and 2 might be involved in normal and FGR placental development. To test this hypothesis, we used placental explants, primary trophoblast cultures, and placental and serum samples collected from FGR and age-matched control women. Our results show that (1) EG-VEGF increases trophoblast proliferation ([(3)H]-thymidine incorporation and Ki67-staining) via the homeobox-gene, HLX (2) the proliferative effect involves PROKR1 but not PROKR2, (3) EG-VEGF does not affect syncytium formation (measurement of syncytin 1 and 2 and β hCG production) (4) EG-VEGF increases the vascularization of the placental villi and insures their survival, (5) EG-VEGF, PROKR1, and PROKR2 mRNA and protein levels are significantly elevated in FGR placentas, and (6) EG-VEGF circulating levels are significantly higher in FGR patients. Altogether, our results identify EG-VEGF as a new placental growth factor acting during the first trimester of pregnancy, established its mechanism of action, and provide evidence for its deregulation in FGR. We propose that EG-VEGF/PROKR1 and 2 increases occur in FGR as a compensatory mechanism to insure proper pregnancy progress.

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.

Revisiting the role of hCG: new regulation of the angiogenic factor EG-VEGF and its receptors

Endocrine gland-derived vascular endothelial growth factor (EG-VEGF) is an angiogenic factor reported to be specific for endocrine tissues, including the placenta. Its biological activity is mediated via two G protein-coupled receptors, prokineticin receptor 1 (PROKR1) and prokineticin receptor 2 (PROKR2). We have recently shown that (i) EG-VEGF expression peaks between the 8th and 11th weeks of gestation, (ii) its mRNA and protein levels are up-regulated by hypoxia, (iii) EG-VEGF is a negative regulator of trophoblast invasion and (iv) its circulating levels are increased in preeclampsia (PE), the most threatening pathology of pregnancy. Here, we investigated the regulation of the expression of EG-VEGF and its receptors by hCG, a key pregnancy hormone that is also deregulated in PE. During the first trimester of pregnancy, hCG and EG-VEGF exhibit the same pattern of expression, suggesting that EG-VEGF is potentially regulated by hCG. Both placental explants (PEX) and primary cultures of trophoblasts from the first trimester of pregnancy were used to investigate this hypothesis. Our results show that (i) LHCGR, the hCG receptor, is expressed both in cyto- and syncytiotrophoblasts, (ii) hCG increases EG-VEGF, PROKR1 and PROKR2 mRNA and protein expression in a dose- and time-dependent manner, (iii) hCG increases the release of EG-VEGF from PEX conditioned media, (iv) hCG effects are transcriptional and post-transcriptional and (v) the hCG effects are mediated by cAMP via cAMP response elements present in the EG-VEGF promoter region. Altogether, these results demonstrate a new role for hCG in the regulation of EG-VEGF and its receptors, an emerging regulatory system in placental development.

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.

Genomic signatures: tracing the origin of retroelements at the nucleotide level

We investigate the nucleotide sequences of 23 retroelements (4 mammalian retroviruses, 1 human, 3 yeast, 2 plant, and 13 invertebrate retrotransposons) in terms of their oligonucleotide composition in order to address the problem of relationship between retrotransposons and retroviruses, and the coadaptation of these retroelements to their host genomes. We have identified by computer analysis over-represented 3-through 6-mers in each sequence. Our results indicate retrotransposons are heterogeneous in contrast to retroviruses, suggesting different modes of evolution by slippage-like mechanisms. Moreover, we have calculated the Observed/Expected number ratio for each of the 256 tetramers and analysed the data using a multivariate approach. The tetramer composition of retroelement sequences appears to be influenced by host genomic factors like methylase activity.

The complete genome sequence of the gram-positive bacterium Bacillus subtilis

Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

Retroviral oligonucleotide distributions correlate with biased nucleotide compositions of retrovirus sequences, suggesting a duplicative stepwise molecular evolution

A computer-assisted analysis was made of 24 complete nucleotide sequences selected from the vertebrate retroviruses to represent the ten viral groups. The conclusions of this analysis extend and strengthen the previously made hypothesis on the Moloney murine leukemia virus: The evolution of the nucleotide sequence appears to have occurred mainly through at least three overlapping levels of duplication: (1) The distributions of overrepresented (3-6)-mers are consistent with the universal rule of a trend toward TG/CT excess and with the persistence of a certain degree of symmetry between the two strands of DNA. This suggests one or several original tandemly repeated sequences and some inverted duplications. (2) The existence of two general core consensuses at the level of these (3-6)-mers supports the hypothesis of a common evolutionary origin of vertebrate retroviruses. Consensuses more specific to certain sequences are compatible with phylogenetic trees established independently. The consensuses could correspond to intermediary evolutionary stages. (3) Most of the (3-6)-mers with a significantly higher than average frequency appear to be internally repeated (with monomeric or oligomeric internal iterations) and seem to be at least partly the cause of the bias observed by other researchers at the level of retroviral nucleotide composition. They suggest a third evolutionary stage by slippage-like stepwise local duplications.

Evolutionary divergence plots of homologous proteins

A simple and efficient method is described for analyzing quantitatively multiple protein sequence alignments and finding the most conserved blocks as well as the maxima of divergence within the set of aligned sequences. It consists of calculating the mean distance and the root-mean-square distance in each column of the multiple alignment, averaging the values in a window of defined length and plotting the results as a function of the position of the window. Due attention is paid to the presence of gaps in the columns. Several examples are provided, using the sequences of several cytochromes c, serine proteases, lysozymes and globins. Two distance matrices are compared, namely the matrix derived by Gribskov and Burgess from the Dayhoff matrix, and the Risler Structural Superposition Matrix. In each case, the divergence plots effectively point to the specific residues which are known to be essential for the catalytic activity of the proteins. In addition, the regions of maximum divergence are clearly delineated. Interestingly, they are generally observed in positions immediately flanking the most conserved blocks. The method should therefore be useful for delineating the peptide segments which will be good candidates for site-directed mutagenesis and for visualizing the evolutionary constraints along homologous polypeptide chains.