Paul J. Yong

The evolution of gene duplicates.

Gene and genome duplications have given rise to enormous variability among species in the number of genes within their genomes. Gene copies have in turn played important roles in adaptation, having been implicated in the evolution of the immune response, insecticide resistance, efficient protein synthesis, and vertebrate body plans. In this chapter, we discuss the life history of gene duplications, from their first appearance within a population, through the period during which they rise in frequency or disappear, to their long-term fate. At each phase, we discuss the evolutionary processes that have influenced the dynamics of gene duplications and shaped their ultimate roles within a population. We argue that there is no evidence that organisms have evolved strategies to promote gene duplication in order to permit adaptive evolution. In contrast, many mechanisms exist to silence or eliminate duplicated genes, suggesting that selection has acted largely to reduce the rate of gene duplication. We also argue that natural selection has functioned as an effective sieve, increasing the representation of beneficial gene duplicates among those that establish within a population and that play a long-term role in evolution. To refine our understanding of how selection acts on new gene duplications, we provide a model incorporating a single-copy gene, its gene duplicate, and selection either favoring heterozygotes or eliminating deleterious mutations. Although both forms of selection can increase the initial rate of spread of a gene duplicate, the efficacy with which they do so differs dramatically. Heterozygote advantage always increases the rate of spread and can have a large impact. In contrast, masking deleterious mutations never has a large effect on the rate of spread of the duplicate, and this minor effect can be negative as well as positive. In both cases, the degree of linkage between the two gene copies affects the rate of spread of the duplication. Finally, we discuss evolutionary processes that occur over longer periods after a gene duplication has become established within a population. These long-term processes include maintenance, inactivation, and diversification in function. Consideration of each of the short-term and long-term processes affecting duplicated genes illustrates the subtle ways in which selection has acted to shape genomic structure.

Decidual NK Cells Alter In Vitro First Trimester Extravillous Cytotrophoblast Migration: A Role for IFN-γ

Abnormal placentation results in either inadequate (consequences: recurrent miscarriage, intrauterine growth restriction, and preeclampsia) or overzealous (consequences: placenta accreta, increta, and percreta) placentation. NK cells dominate in first trimester decidua and probably control extravillous cytotrophoblast (EVT) invasion. We examined this interaction in a novel way, using NK cells and villous explants from concordant first trimester pregnancies cocultured using a new collagen (two-dimensional) model of placentation. Decidual NK (dNK) cells exerted contact-independent inhibition of normal cytotrophoblast migration, associated with changes in the cytotrophoblast expression of metalloproteases-2 and -9, and plasminogen activator inhibitor-1. dNK cells did not affect EVT proliferation and apoptosis, and cell column formation. dNK cell effects were partially reversed by neutralizing Abs against IFN-γ. We provide ex vivo human evidence of a direct role for dNK in modulating EVT differentiation as they form columns and then migrate from anchoring villi.

Cancer-Associated Mutations in Endometriosis without Cancer

Background Endometriosis, defined as the presence of ectopic endometrial stroma and epithelium, affects approximately 10% of reproductive‐age women and can cause pelvic pain and infertility. Endometriotic lesions are considered to be benign inflammatory lesions but have cancerlike features such as local invasion and resistance to apoptosis. Methods We analyzed deeply infiltrating endometriotic lesions from 27 patients by means of exomewide sequencing (24 patients) or cancer‐driver targeted sequencing (3 patients). Mutations were validated with the use of digital genomic methods in microdissected epithelium and stroma. Epithelial and stromal components of lesions from an additional 12 patients were analyzed by means of a droplet digital polymerase‐chain‐reaction (PCR) assay for recurrent activating KRAS mutations. Results Exome sequencing revealed somatic mutations in 19 of 24 patients (79%). Five patients harbored known cancer driver mutations in ARID1A, PIK3CA, KRAS, or PPP2R1A, which were validated by Safe‐Sequencing System or immunohistochemical analysis. The likelihood of driver genes being affected at this rate in the absence of selection was estimated at P=0.001 (binomial test). Targeted sequencing and a droplet digital PCR assay identified KRAS mutations in 2 of 3 patients and 3 of 12 patients, respectively, with mutations in the epithelium but not the stroma. One patient harbored two different KRAS mutations, c.35G→T and c.35G→C, and another carried identical KRAS c.35G→A mutations in three distinct lesions. Conclusions We found that lesions in deep infiltrating endometriosis, which are associated with virtually no risk of malignant transformation, harbor somatic cancer driver mutations. Ten of 39 deep infiltrating lesions (26%) carried driver mutations; all the tested somatic mutations appeared to be confined to the epithelial compartment of endometriotic lesions.

Expectant Management of Severe Preeclampsia Remote from Term: A Structured Systematic Review

Objective: To compare outcomes associated with expectant vs. interventionist care of severe preeclampsia in observational studies. Data Sources: Medline (01/1980–07/2007), bibliographies of retrieved papers, personal files, Cochrane Database of Systematic Reviews. Study Selection: Expectant or interventionist care of preeclampsia at <34 wk. Tabulation, Integration, Results: Data abstraction independently by two reviewers. Median [IQR] of clinical maternal/perinatal outcomes presented. Results: 72 publications, primarily from tertiary care centres in Dutch and developed world sites. Expectant care of severe preeclampsia <34 wk (39 cohorts, 4,650 women), for which 40% of women are eligible, is associated with pregnancy prolongation of 7–14 d, and few serious maternal complications (median <5%), similar to interventionist care (2 studies, 42 women). Complication rates are higher with HELLP <34wk (12 cohorts, 438 women) and severe preeclampsia <28wk (6 cohorts, 305 women), similar to interventionist care (6 cohorts, 467 women and 2 cohorts, 70 women, respectively). Expectant care of HELLP <34 wk (12 cohorts, 438 women) is associated with fewer days gained (median 5), but more serious maternal morbidity (e.g., eclampsia, median 15%). More than half of women have at least temporary improvement of HELLP. In the developed world, expectant (vs. interventionist) care of severe preeclampsia or HELLP <34 wk is associated with reduced neonatal death and complications. Stillbirth is higher in Dutch and developing world sites where viability thresholds are higher. For preeclampsia <24wk (4 cohorts), perinatal mortality is >80%. No predictors of adverse maternal/perinatal outcomes were identified (13 studies). Conclusions: Future research should establish the best maternal/fetal monito regimen and indications for delivery with expectant care. A definitive RCT is needed.

Clinical aspects, prenatal diagnosis, and pathogenesis of trisomy 16 mosaicism

Introduction: Analysis of data from cases of trisomy mosaicism can provide insight for genetic counselling after prenatal diagnosis and for the elucidation of the pathogenesis of trisomy during pregnancy. Methods: Statistical analysis was carried out on data from 162 cases of pregnancies with prenatal diagnosis of trisomy 16 mosaicism. Results: The majority of cases resulted in live birth (66%) with an average gestational age of 35.7 weeks and average birth weight of −1.93 standard deviations from the population mean. Among the live births 45% had at least one malformation, the most common being VSD, ASD, and hypospadias. The level of trisomy on direct CVS (cytotrophoblast) was associated with more severe intrauterine growth restriction (IUGR) and higher risk of malformation, while the level of trisomy on cultured CVS (chorionic villous stroma) was associated only with more severe IUGR. Similarly, the presence of trisomy on amniocentesis (amniotic fluid) was associated with both IUGR and malformation, while the presence of trisomy in the amniotic mesenchyme was associated only with IUGR. Surprisingly, the degree of trisomy in placental tissues appeared to be independent of the degree of trisomy in amniotic fluid and amniotic mesenchyme. The sex of the fetus was not associated with any outcome variables, although there was an excess of females (sex ratio = 0.45) that may be explained by selection against male mosaic trisomy 16 embryos before the time of CVS (∼9-12 weeks). Conclusion: The levels of trisomy in different fetal-placental tissues are significant predictors of some measures of outcome in mosaic trisomy 16 pregnancies.

Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden

Endometriosis is a significant risk factor for clear cell and endometrioid ovarian cancers and is often found contiguous with these cancers. Using whole‐genome shotgun sequencing of seven clear cell ovarian carcinomas (CCC) and targeted sequencing in synchronous endometriosis, we have investigated how this carcinoma may evolve from endometriosis. In every case we observed multiple tumour‐associated somatic mutations in at least one concurrent endometriotic lesion. ARID1A and PIK3CA mutations appeared consistently in concurrent endometriosis when present in the primary CCC. In several cases, one or more endometriotic lesions carried the near‐complete complement of somatic mutations present in the index CCC tumour. Ancestral mutations were detected in both tumour‐adjacent and ‐distant endometriotic lesions, regardless of any cytological atypia. These findings provide objective evidence that multifocal benign endometriotic lesions are clonally related and that CCCs arising in these patients progress from endometriotic lesions that may already carry sufficient cancer‐associated mutations to be considered neoplasms themselves, albeit with low malignant potential. We speculate that genomically distinct classes of endometriosis exist and that ovarian endometriosis with high mutational burden represents one class at high risk for malignant transformation.

Impact of a Multidisciplinary Vulvodynia Program on Sexual Functioning and Dyspareunia

INTRODUCTION For many years, multidisciplinary approaches, which integrate psychological, physical, and medical treatments, have been shown to be effective for the treatment of chronic pain. To date, there has been anecdotal support, but little empirical data, to justify the application of this multidisciplinary approach toward the treatment of chronic sexual pain secondary to provoked vestibulodynia (PVD). AIM This study aimed to evaluate a 10-week hospital-based treatment (multidisciplinary vulvodynia program [MVP]) integrating psychological skills training, pelvic floor physiotherapy, and medical management on the primary outcomes of dyspareunia and sexual functioning, including distress. METHOD A total of 132 women with a diagnosis of PVD provided baseline data and agreed to participate in the MVP. Of this group, n = 116 (mean age 28.4 years, standard deviation 7.1) provided complete data at the post-MVP assessment, and 84 women had complete data through to the 3- to 4-month follow-up period. RESULTS There were high levels of avoidance of intimacy (38.1%) and activities that elicited sexual arousal (40.7%), with many women (50.4%) choosing to focus on their partners sexual arousal and satisfaction at baseline. With treatment, over half the sample (53.8%) reported significant improvements in dyspareunia. Following the MVP, there were strong significant effects for the reduction in dyspareunia (P = 0.001) and sex-related distress (P < 0.001), and improvements in sexual arousal (P < 0.001) and overall sexual functioning (P = 0.001). More modest but still statistically significant were improvements in sexual desire, lubrication, orgasmic function, and sexual satisfaction. All improvements were retained at 2- to 3-month follow-up. CONCLUSION This study provides strong support for the efficacy of a multidisciplinary approach (psychological, pelvic floor physiotherapy, and medical management) for improving dyspareunia and all domains of sexual functioning among women with PVD. The study also highlights the benefits of incorporating sexual health education into general pain management strategies for this population.

Prediction of pediatric outcome after prenatal diagnosis and expectant antenatal management of congenital cystic adenomatoid malformation.

Objective: To determine whether the congenital cystic adenomatoid malformation (CCAM) volume ratio (CVR) is associated with fetal and postnatal outcome after prenatal diagnosis and antenatal expectant management in a provincial tertiary referral center that does not offer fetal surgery. Methods: Retrospective cohort of 71 consecutive cases of prenatally diagnosed CCAM meeting study criteria (1996–2004). CVR was calculated on the initial ultrasound at the referral center, and associated with hydrops (Fisher’s exact test) and a composite adverse postnatal outcome consisting of death, intubation for respiratory distress, extracorporeal membrane oxygenation, non-elective surgery for symptomatology, or respiratory infection requiring hospital admission (Mann-Whitney test). Results: A CVR >1.6 was significantly associated with hydrops (p = 0.003). In addition, the CVR was significantly associated with the composite adverse postnatal outcome (p = 0.004) at a mean age of follow-up of 41 months (range <1–117 months). For CVR and postnatal outcome, the area-under-the-curve receiver operating characteristic was 0.81 (95% CI 0.69–0.93, p = 0.006), and choosing a CVR cut-off of <0.56, the negative predictive value was 100% (95% CI 0.85–1.00). Conclusion: In a provincial referral center with antenatal expectant management of CCAM, the CVR was associated with hydrops and postnatal outcome, with a CVR <0.56 predictive of good prognosis after birth.

New developments in the medical treatment of endometriosis

Endometriosis affects 1 in 10 women of reproductive-age. The current treatments are surgical and hormonal but have limitations, including the risk of recurrence, side effects, contraceptive action for women who desire pregnancy, and cost. New treatments include gonadotropin-releasing hormone analogues, selective progesterone (or estrogen) receptor modulators, aromatase inhibitors, immunomodulators, and antiangiogenic agents. Further research is needed into central sensitization, local neurogenesis, and the genetics of endometriosis to identify additional treatment targets. A wider range of medical options allows for the possibility of precision health and a more personalized treatment approach for women with endometriosis.

Pelvic Floor Tenderness in the Etiology of Superficial Dyspareunia

OBJECTIVE To calculate the prevalence of pelvic floor tenderness in the population of women with pelvic pain and to determine its implications for symptoms of pelvic pain. METHODS We conducted a retrospective review of patients with pelvic pain at a tertiary referral centre. Pelvic floor tenderness was defined as levator ani tenderness on at least one side during single digit pelvic examination. The prevalence of pelvic floor tenderness in this cohort of women with pelvic pain was compared with the prevalence in a cohort of women without pain attending a gynaecology clinic. In the women with pelvic pain, multiple regression was performed to determine which variables were independently associated with pelvic floor tenderness. RESULTS The prevalence of pelvic floor tenderness was 40% (75/189) in the cohort with pelvic pain, significantly greater than the prevalence of 13% (4/32) in the cohort without pain (OR 4.61; 95% CI 1.55 to 13.7, P = 0.005). On multiple logistic regression, superficial dyspareunia (OR 4.45; 95% CI 1.86 to 10.7, P = 0.001), abdominal wall pain (OR 4.04; 95% CI 1.44 to 11.3, P = 0.005), and bladder base tenderness (OR 4.65; 95% CI 1.87 to 11.6, P = 0.001) were independently associated with pelvic floor tenderness. Pelvic floor tenderness was similarly present in women with or without underlying endometriosis. CONCLUSION Pelvic floor tenderness is common in women with pelvic pain, with or without endometriosis, and is a contributor to superficial dyspareunia. Pelvic floor tenderness was also associated with abdominal wall pain and bladder base tenderness, suggesting that nervous system sensitization is involved in the etiology of pelvic floor tenderness.