Faculty Bibliography

The testis expresses the largest number of genes of any mammalian organ, a finding that has long puzzled molecular biologists. Our single-cell transcriptomic data of human and mouse spermatogenesis provide evidence that this widespread transcription maintains DNA sequence integrity in the male germline by correcting DNA damage through a mechanism we term transcriptional scanning. We find that genes expressed during spermatogenesis display lower mutation rates on the transcribed strand and have low diversity in the population. Moreover, this effect is fine-tuned by the level of gene expression during spermatogenesis. The unexpressed genes, which in our model do not benefit from transcriptional scanning, diverge faster over evolutionary timescales and are enriched for sensory and immune-defense functions. Collectively, we propose that transcriptional scanning shapes germline mutation signatures and modulates mutation rates in a gene-specific manner, maintaining DNA sequence integrity for the bulk of genes but allowing for faster evolution in a specific subset.

During mammalian development, gonadotropin-releasing-hormone-1 neurons (GnRH-1ns) migrate from the developing vomeronasal organ (VNO) into the brain asserting control of pubertal onset and fertility. Recent data suggest that correct development of the olfactory ensheathing cells (OEC) is imperative for normal GnRH-1 neuronal migration. However, the full ensemble of molecular pathways that regulate OEC development remains to be fully deciphered. Loss-of-function of the transcription factor Gli3 is known to disrupt olfactory development, however, if Gli3 plays a role in GnRH-1 neuronal development is unclear. By analyzing Gli3 extra-toe mutants (Gli3^Xt/Xt), we found that Gli3 loss-of-function compromises the onset of achaete-scute family bHLH transcription factor 1 (Ascl-1) positive vomeronasal progenitors and the formation of OEC in the nasal mucosa. Surprisingly, GnRH-1 neurogenesis was intact in Gli3^Xt/Xt mice but they displayed significant defects in GnRH-1 neuronal migration. In contrast, Ascl-1^null mutants showed reduced neurogenesis for both vomeronasal and GnRH-1ns but less severe defects in OEC development. These observations suggest that Gli3 is critical for OEC development in the nasal mucosa and subsequent GnRH-1 neuronal migration. However, the non-overlapping phenotypes between Ascl-1 and Gli3 mutants indicate that Ascl-1, while crucial for GnRH-1 neurogenesis, is not required for normal OEC development. Since Kallmann syndrome (KS) is characterized by abnormal GnRH-1ns migration, we examined whole exome sequencing data from KS subjects. We identified and validated a GLI3 loss-of-function variant in a KS individual. These findings provide new insights into GnRH-1 and OECs development and demonstrate that human GLI3 mutations contribute to KS etiology.Significance statement. The transcription factor Gli3 is necessary for correct development of the olfactory system. However, if Gli3 plays a role in controlling GnRH-1 neuronal development has not been addressed. We found that Gli3 loss-of-function compromises the onset of Ascl-1+ vomeronasal progenitors, formation of olfactory ensheathing cells in the nasal mucosa, and impairs GnRH-1 neuronal migration to the brain. By analyzing Ascl-1^null mutants we dissociated the neurogenic defects observed in Gli3 mutants from lack of olfactory ensheathing cells in the nasal mucosa, moreover, we discovered that Ascl-1 is necessary for GnRH-1 ontogeny. Analyzing human whole exome sequencing data, we identified a GLI3 loss-of-function variant in a KS individual. Our data suggest that GLI3 is a candidate gene contributing to KS etiology.

BACKGROUND/UNASSIGNED:The postpartum period can be a vulnerable time during which many women are prone to mood disturbances. Since telomere length (TL) is known to be associated with dysphoric moods, inflammation, and stress in many populations, this study's objective was to assess the relationships among TL, dysphoric moods, stress, and inflammation during the postpartum period. METHOD/UNASSIGNED:This cross-sectional pilot study is a secondary analysis of data collected in a larger parent study of anti-thyroid peroxidase (TPO) enzyme antibody positive versus negative women. The parent study followed selected mothers every month for 6 postpartum months. From this parent study, a random sample of preserved peripheral blood mononuclear cells from 97 participants collected at 2-4 months postpartum were measured for TL. Data were available on the production of interleukin-6 (IL-6), an inflammatory cytokine, in stimulated ex vivo cultures for 59 of these women. Dysphoric moods and stress were measured. Pearson correlations and linear regressions were performed, controlling for postpartum thyroiditis status and age. RESULTS/UNASSIGNED:There were no statistically significant relationships between TL and demographic factors, stress, depression, or TPO status. There were significant negative correlations between TL and anxiety and a trend for a relationship between TL and IL-6 levels. IL-6 levels were significantly, positively associated with negative moods. CONCLUSIONS/UNASSIGNED:Higher anxiety scores and inflammation were associated with shorter TL. Inflammation was related to anxiety and other dysphoric moods and was marginally associated with shorter TLs.

Objective: Retrotransposons are a group of abundant, repetitive sequences, which originated from ancient retroviral infections of our ancestral genomes. They are silenced by epigenetic marks throughout most of life, but become activated during early embryo development, with reprogramming of the epigenome. Some retrotransposons play regulatory roles during early development. Non-Long Terminal Repeat (LTR) retrotransposons (e.g. LINE-1) regulate gene expression during early mouse embryo development. LTR retrotransposons, such as the human endogenous retrovirus HERV-W and HERV-FRD (Syncytin-1 and Syncytin-2), mediate placentation¹. We hypothesized that aneuploidy, which disrupts implantation, would affect expression of retrotransposons during early human development.
Design(s): Prospective laboratory study.
Material(s) and Method(s): Blastocysts donated by patients who underwent IVF/PGT-A at NYU Langone FC were thawed, stripped of zona pellucidae by laser (to remove sperm or cumulus) and their genomic DNA and mRNA separated by the G&Tseq protocol² with modifications. mRNA expression and gene copy number were measured by RT-qPCR and qPCR using Bio-Rad CFX96 thermocycler and iQ SYBY Green mix, and the DELTADELTACq method was used to express their levels relative to GAPDH and 5S RNA, respectively. Data were analyzed by Mann Whitney U test and Student's T-test with GraphPad Prism 8 software.
Result(s): Syncytin-1 was expressed in all human embryos, but its expression in euploid embryos (n=2) was significantly higher than in aneuploid embryos (n=6) (median 1.943 vs 0.316, P= 0.0019). Expression of Syncytin-2 also was extremely higher in euploid compared to aneuploid embryos (median 2.155 vs. 0.1124, P= 0.0003). The copy number of ALU sequences in aneuploid embryos was greater than in euploid embryos (mean 0.943+/-0.067 vs 0.807+/-0.0716, T-test P=0.0486), but LINE1 copy number or expression did not differ between euploid and aneuploid embryos (mean 0.787+/-0.069 vs 0.904+/-0.094, T-test P= 0.1778).
Conclusion(s): We compared expression of a number of retrotransposons between euploid and aneuploid human blastocysts, and discovered that the human endogenous retrovirus, Syncytin-1 and Syncytine-2, are markedly decreased in aneuploid compared to euploid embryos. Given the crucial role of Syncytins in formation of human placenta, our data provide a possible mechanism of implantation failure in euploid embryos, and suggest a possible biomarker for implantation. References: 1. Soygur B, Moore H. Expression of Syncytin 1 (HERV-W), in the preimplantation human blastocyst, embryonic stem cells and trophoblast cells derived in vitro. Hum Reprod. 2016 Jul; 31(7):1455-61. 2. Macaulay IC, Teng MJ, Haerty W, Kumar P, Ponting CP, Voet T. Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq. Nat Protoc. 2016 Nov; 11(11):2081-103.
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Objective: Clinical guidelines on the optimal duration of controlled ovarian stimulation and ideal follicle size were developed for fresh embryo transfer cycles. Whether these apply to freeze all cycles remain unclear. We evaluated the impact of lead follicle size and duration of stimulation on the probability of euploid embryos in women undergoing IVF/PGT-A Design: Cross-sectional study
Material(s) and Method(s): Data from 721 patients undergoing at least two cycles of COS for IVF with preimplantation genetic testing for aneuploidy (PGT-A) via Next Generation Sequencing (NGS) (1859 cycles). Mixed-effect logistic regression, which can account for correlations among repeated outcomes within sample patients, was used to evaluate the association between independent variables and probability of achieving euploid embryos. We first conducted a mixed-effect logistic regression in a univariate manner. All variables then were evaluated in a multivariate model to control for confounding effects. Significant variables to p<0.05 were retained in the final model. p-values <0.05 were considered significant. Statistical analyses were performed using "nlme" and "lme4" package from R project. Results are reported as odds ratios (OR) with 95% confidence intervals (CI).
Result(s): Increasing sum (1.034 [1.022 1.046]/p<0.001) and mean diameter (1.129 [1.046 1.219] p=0.002) of the 5 largest follicles increased the probability of forming euploid embryos. Increasing days of stimulation showed a non-significant trend toward lower chance of forming euploid embryos (0.976 [0.923 1.031]/p=0.382) (Table 1).
Conclusion(s): Allowing the lead follicles to exceed 18mm increases the total number of euploid embryos formed per cycle, presumably by enabling retrieval of additional mature oocytes. Evidence of a detrimental effect of excessive follicle size was not evident in our study, though the number of cycles with follicles exceeding 24 mm was limited. The non-significant trend toward decreased euploid embryos following prolonged stimulation may reflect the effects of poor responders. [Figure presented]
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Objective: Posthumous assisted reproduction (PAR) raises complicated ethical and legal issues. ASRM recommends that assisted reproductive technology (ART) and fertility preservation (FP) programs develop written policies regarding cases of PAR, though little is known about adoption of such policies and how they have been implemented. Our objective was to assess the presence and content of policies toward PAR using oocytes and embryos amongSociety for Assisted Reproductive Technology (SART) member clinics in the U.S.
Design(s): Cross-sectional questionnaire-based study.
Material(s) and Method(s): Our study consists of three phases of communication: email-, postal mail-, and phone-based survey. We report on the first phase of anonymous email survey responses. Surveys were emailed to ASRM-member medical directors of all SART member clinics (n=332) during March and April 2019 using a modified Dillman Method; contact information was acquired from SART and ASRM membership data. The survey included 23 multiple-choice and 3 opened-ended questions assessing practice characteristics (practice type, location, IVF cycle volume), presence of a clinic policy towards PAR, and the content of such policy. Descriptive data are presented as %, with Fisher's exact test used where appropriate, and thematic content analysis was applied to open-ended responses.
Result(s): The first phase of the study received 39 clinic responses (12% response rate). Respondents were distributed across the U.S.; average volume of IVF cycles per year ranged from < 250 to > 1500. More than one-third (35.9%, n=14) of clinics reported participating in any cases of PAR over the past five years, and 5.1% (n=2) reported participation in more than five cases. Participation in cases of PAR was not significantly associated with practice type or IVF cycle volume (p>0.05). 57.9% (n=22) had written policies towards PAR using oocytes or embryos, while 36.8% (n=14) reported they did not have a policy. Practice type, IVF cycle volume, FP volume, and prior participation in cases of PAR were not significantly associated with the presence of a policy (p>0.05). Of those with a policy, 52.4% (n=11) reported they had used that policy, 66.7% (n=10) without a policy reported they had considered adopting one, and 60.0% (n=9) reported they had received a request for PAR services. Only 44% (n=15) of clinics specified that patients not expected to survive to use oocytes due to terminal illness were eligible for oocyte cryopreservation, while 50.0% (n=17) did not specify. Open-ended comments suggested need for case-by-case appraisal and firm consent polices regarding gamete disposition.
Conclusion(s): Our preliminary results suggest that SART programs are receiving an increasing number of requests for PAR services, but many SART programs lack PAR policies, and those with policies do not always follow ASRM recommendations. As PAR cases become more common, clinics should be equipped to manage the complexities of PAR. More data are needed as this study continues, and future research is needed to understand barriers to the creation and implementation of these increasingly needed policies.
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Objective: During preimplantation embryo development, the telomere aging clock resets and 2-cell genes establish totipotency. Like most long -lived cells, oocytes have short telomeres, but telomeres elongate markedly during early embryo development, even in the absence of telomerase (1). Recent studies report that the retrotransposon, LINE-1, is activated after fertilization, when telomeres elongate. Retrotransposons protect chromosome ends in many species, so we hypothesized that inhibiting retrotransposition of LINE-1 during mouse early embryos would disrupt telomere reprogramming in mouse preimplantation embryos. We also evaluated the effect of LINE-1 on the 2-cell, totipotency genes.
Design(s): Laboratory experiment
Material(s) and Method(s): Sixty thawed mouse zygotes (B6C3F1 X B6D2F1) (Embryotech Laboratories) were grouped (15 zygotes/group) and cultured in Global medium containing 0.4% BSA with or without 1muM of the reverse transcriptase inhibitor, AZT, for up to 15 (mid 2-cell stage) or 24 hours (late 2-cell stage). DNA and mRNA were isolated from embryos. Gene expression was measured by RT-qPCR, and LINE-1 copy number and telomere length were measured by qPCR. Data (Mean+/-SEM) was analized with GraphPad Prism 8 software by one-way ANOVA Tukey's multiple comparisons test.
Result(s): As expected, AZT inhibited LINE-1 copy number in late 2-cell embryos compared to controls (1.000+/-0.113 vs 1.942+/-0.089, P<0.0001). Telomeres were longer in late 2-cell (1.563+/-0.107) than mid 2-cell embryos (1.128+/-0.059) (P=0.001), consistent with prior observations of progressive telomere elongation during early development(1). AZT blocked telomere elongation between mid- and late-2 cell stages stage (1.152+/-0.039 vs 1.000+/-0.107, P=0.1994). Telomere length of late 2-cell embryos exposed to AZT was shorter than untreated controls (1.000+/-0.107 vs 1.563+/-0.107, P=0.0002). Transcripts of LINE-1, as well as the 2-cell genes, DUX and Zscan4, were highly expressed in mid- 2-cell compared to late 2-cell embryos (P <0.0001), regardless of inhibition of LINE-1. This suggests that 2-cell genes are activated at synthesis phase of the 2-cell stage. Moreover, AZT decreased expression of DUX, Zscan4d and LINE-1 in mid- 2-cell embryos (0.312+/-0.021, 0.727+/-0.055 and 1.266+/-0.066 respectively) compared to control embryos (1.913+/-0.197, 1.912+/-0.202 and 1.913+0.216 respectively, P<0.001).
Conclusion(s): The retrotransposon, LINE-1, regulates telomere lengthening during preimplantation embryo development- inhibition of LINE-1 synthesis by AZT blocks telomere elongation. AZT also inhibits the 2-cell genes, DUX and Zscan4d, suggesting that LINE-1 is essential not only for telomere reprogramming but also for the establishment of totipotency during early development. References: 1. Liu L, Bailey SM, Okuka M, Munoz P, Li C, Zhou L, Wu C, Czerwiec E, Sandler L, Seyfang A, Blasco MA, Keefe DL. Telomere lengthening early in development. Nat Cell Biol. 2007 Dec; 9(12):1436-41.
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Objective: Treatment of chronic endometritis (CE) improves implantation rates in patients undergoing assisted reproductive technology (ART), but causative organisms are difficult to identify and the most effective treatment regimen remains undefined¹. Our objective was to identify the optimal duration and choice of antimicrobial agent(s) on clearance of CE.
Design(s): Retrospective cohort study of patients between 1/2017 and 12/2018 at a single academic center with an endometrial biopsy (EMB) showing CE.
Material(s) and Method(s): All patients diagnosed with CE (defined as >1 plasma cell/HPF, stained for CD138) on EMB followed by test of cure biopsy (TOC) were included. Antimicrobial agents prescribed and length of course were recorded. Regimens were classified as 14 days or less versus 15 days or more (up to 21 days), and by spectra of coverage: Gram positive, Gram negative, Anaerobe, Atypical and Anti-fungal. Primary outcome was presence or absence of CE on TOC. If a patient remained positive on TOC, subsequent treatment(s) were included as separate course(s) for analysis. Statistical analysis included chi square test of independence and a stepwise multiple logistic regression, with p < 0.05 significant.
Result(s): 144 women with an initial EMB positive for CE received a total of 225 treatment courses. 11 TOC results were unavailable, leaving 214 courses of treatment with known TOC outcomes. The most common indication for EMB was failed frozen embryo transfer(s) (FET) (mean 0.98+/-1.00, range 0-7), euploid pregnancy loss or recurrent pregnancy loss. The mean age of women in the cohort was 36.90+/-3.93 years (range 27-47). Mean number of courses required for clearance was 1.55+/-0.88 (range 0-6). All courses included antimicrobials providing gram positive and negative coverage. 62.6% (134/214) included anaerobic coverage and 66.3% (142/214) included atypical agent(s). 2 courses included anti-fungals. Including anaerobic coverage did not affect outcome (58.2% with vs 61.3% without, p = 0.67), nor did use of an atypical agent (59.2% with vs 59.67% without, p=1.00). Antibiotic regimens lasting 14 days or less (n=155) had lower rates of CE clearance when compared to those lasting 15 days or more (54.8% vs 71.2%, p < 0.03). Stepwise multiple logistic regression showed that only length of antimicrobial course retained a significant impact on TOC (B -0.762, p < 0.027, Omnibus test for variance p <0.024, Hosmer-Lemeshow test for fit p = 0.99).
Conclusion(s): CE is a treatable but poorly defined inflammatory process, which may affect ART success. Ideally, CE is cleared with the first course of antibiotics. Our results show that longer courses (15-21 days) are more effective, regardless of antimicrobial choice. This suggests that patients do not need to take less tolerable agents to achieve high clearance rates, and highlights the need for further, prospective analyses. References: ¹: Cicinelli E, et al. Prevalence of chronic endometritis in repeated unexplained implantation failure and the IVF success rate after antibiotic therapy. Human Reproduction 2015;30(2):323-330.
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With more women than ever waiting until a more advanced age to have children, there exists a newfound urgency to identify the various implications aging has on human reproduction, and understand the disrupted biological processes that result in these changes. In this review, we focus on one recent area of study: the age related epigenetic changes that have been found in female reproductive organs, and the effect these changes may contribute to reproductive outcomes.