Describing patterns of familial cancer risk in subfertile men using population pedigree data.

STUDY QUESTION: Can we simultaneously assess risk for multiple cancers to identify familial multicancer patterns in families of azoospermic and severely oligozoospermic men? SUMMARY ANSWER: Distinct familial cancer patterns were observed in the azoospermia and severe oligozoospermia cohorts, suggesting heterogeneity in familial cancer risk by both type of subfertility and within subfertility type. WHAT IS KNOWN ALREADY: Subfertile men and their relatives show increased risk for certain cancers including testicular, thyroid, and pediatric. STUDY DESIGN, SIZE, DURATION: A retrospective cohort of subfertile men (N = 786) was identified and matched to fertile population controls (N = 5674). Family members out to third-degree relatives were identified for both subfertile men and fertile population controls (N = 337 754). The study period was 1966-2017. Individuals were censored at death or loss to follow-up, loss to follow-up occurred if they left Utah during the study period. PARTICIPANTS/MATERIALS, SETTING, METHODS: Azoospermic (0 × 106/mL) and severely oligozoospermic (<1.5 × 106/mL) men were identified in the Subfertility Health and Assisted Reproduction and the Environment cohort (SHARE). Subfertile men were age- and sex-matched 5:1 to fertile population controls and family members out to third-degree relatives were identified using the Utah Population Database (UPDB). Cancer diagnoses were identified through the Utah Cancer Registry. Families containing ≥10 members with ≥1 year of follow-up 1966-2017 were included (azoospermic: N = 426 families, 21 361 individuals; oligozoospermic: N = 360 families, 18 818 individuals). Unsupervised clustering based on standardized incidence ratios for 34 cancer phenotypes in the families was used to identify familial multicancer patterns; azoospermia and severe oligospermia families were assessed separately. MAIN RESULTS AND THE ROLE OF CHANCE: Compared to control families, significant increases in cancer risks were observed in the azoospermia cohort for five cancer types: bone and joint cancers hazard ratio (HR) = 2.56 (95% CI = 1.48-4.42), soft tissue cancers HR = 1.56 (95% CI = 1.01-2.39), uterine cancers HR = 1.27 (95% CI = 1.03-1.56), Hodgkin lymphomas HR = 1.60 (95% CI = 1.07-2.39), and thyroid cancer HR = 1.54 (95% CI = 1.21-1.97). Among severe oligozoospermia families, increased risk was seen for three cancer types: colon cancer HR = 1.16 (95% CI = 1.01-1.32), bone and joint cancers HR = 2.43 (95% CI = 1.30-4.54), and testis cancer HR = 2.34 (95% CI = 1.60-3.42) along with a significant decrease in esophageal cancer risk HR = 0.39 (95% CI = 0.16-0.97). Thirteen clusters of familial multicancer patterns were identified in families of azoospermic men, 66% of families in the azoospermia cohort showed population-level cancer risks, however, the remaining 12 clusters showed elevated risk for 2-7 cancer types. Several of the clusters with elevated cancer risks also showed increased odds of cancer diagnoses at young ages with six clusters showing increased odds of adolescent and young adult (AYA) diagnosis [odds ratio (OR) = 1.96-2.88] and two clusters showing increased odds of pediatric cancer diagnosis (OR = 3.64-12.63). Within the severe oligozoospermia cohort, 12 distinct familial multicancer clusters were identified. All 12 clusters showed elevated risk for 1-3 cancer types. An increase in odds of cancer diagnoses at young ages was also seen in five of the severe oligozoospermia familial multicancer clusters, three clusters showed increased odds of AYA diagnosis (OR = 2.19-2.78) with an additional two clusters showing increased odds of a pediatric diagnosis (OR = 3.84-9.32). LIMITATIONS, REASONS FOR CAUTION: Although this study has many strengths, including population data for family structure, cancer diagnoses and subfertility, there are limitations. First, semen measures are not available for the sample of fertile men. Second, there is no information on medical comorbidities or lifestyle risk factors such as smoking status, BMI, or environmental exposures. Third, all of the subfertile men included in this study were seen at a fertility clinic for evaluation. These men were therefore a subset of the overall population experiencing fertility problems and likely represent those with the socioeconomic means for evaluation by a physician. WIDER IMPLICATIONS OF THE FINDINGS: This analysis leveraged unique population-level data resources, SHARE and the UPDB, to describe novel multicancer clusters among the families of azoospermic and severely oligozoospermic men. Distinct overall multicancer risk and familial multicancer patterns were observed in the azoospermia and severe oligozoospermia cohorts, suggesting heterogeneity in cancer risk by type of subfertility and within subfertility type. Describing families with similar cancer risk patterns provides a new avenue to increase homogeneity for focused gene discovery and environmental risk factor studies. Such discoveries will lead to more accurate risk predictions and improved counseling for patients and their families. STUDY FUNDING/COMPETING INTEREST(S): This work was funded by GEMS: Genomic approach to connecting Elevated germline Mutation rates with male infertility and Somatic health (Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD): R01 HD106112). The authors have no conflicts of interest relevant to this work. TRIAL REGISTRATION NUMBER: N/A.

Detection of neuron-derived cfDNA in blood plasma: a new diagnostic approach for neurodegenerative conditions.

Neurodegenerative diseases, such as Alzheimer's disease (AD), pose significant challenges in early diagnosis, leading to irreversible brain damage and cognitive decline. In this study, we present a novel diagnostic approach that utilizes whole molecule analysis of neuron-derived cell-free DNA (cfDNA) as a biomarker for early detection of neurodegenerative diseases. By analyzing Differential Methylation Regions (DMRs) between purified cortical neurons and blood plasma samples, we identified robust biomarkers that accurately distinguish between neuronal and non-neuronal cfDNA. The use of cfDNA offers the advantage of convenient and minimally invasive sample collection compared to traditional cerebrospinal fluid or tissue biopsies, making this approach more accessible and patient friendly. Targeted sequencing at the identified DMR locus demonstrated that a conservative cutoff of 5% of neuron-derived cfDNA in blood plasma accurately identifies 100% of patients diagnosed with AD, showing promising potential for early disease detection. Additionally, this method effectively differentiated between patients with mild cognitive impairment (MCI) who later progressed to AD and those who did not, highlighting its prognostic capabilities. Importantly, the differentiation between patients with neurodegenerative diseases and healthy controls demonstrated the specificity of our approach. Furthermore, this cfDNA-based diagnostic strategy outperforms recently developed protein-based assays, which often lack accuracy and convenience. While our current approach focused on a limited set of loci, future research should explore the development of a more comprehensive model incorporating multiple loci to increase diagnostic accuracy further. Although certain limitations, such as technical variance associated with PCR amplification and bisulfite conversion, need to be addressed, this study emphasizes the potential of cfDNA analysis as a valuable tool for pre-symptomatic detection and monitoring of neurodegenerative diseases. With further development and validation, this innovative diagnostic strategy has the potential to significantly impact the field of neurodegenerative disease research and patient care, offering a promising avenue for early intervention and personalized therapeutic approaches.

Epigenetic determinants of reproductive potential augment the predictive ability of the semen analysis.

OBJECTIVE: To investigate the power of DNA methylation variability in sperm cells in assessing male fertility potential. DESIGN: Retrospective cohort. SETTING: Fertility care centers. PATIENTS: Male patients seeking infertility treatment and fertile male sperm donors. INTERVENTION: None. MAIN OUTCOME MEASURES: Sperm DNA methylation data from 43 fertile sperm donors were analyzed and compared with the data from 1344 men seeking fertility assessment or treatment. Methylation at gene promoters with the least variable methylation in fertile patients was used to create 3 categories of promoter dysregulation in the infertility treatment cohort: poor, average, and excellent sperm quality. RESULTS: After controlling for female factors, there were significant differences in intrauterine insemination pregnancy and live birth outcomes between the poor and excellent groups across a cumulative average of 2-3 cycles: 19.4% vs. 51.7% (P=.008) and 19.4% vs. 44.8% (P=.03), respectively. Live birth outcomes from in vitro fertilization, primarily with intracytoplasmic sperm injection, were not found to be significantly different among any of the 3 groups. CONCLUSION: Methylation variability in a panel of 1233 gene promoters could augment the predictive ability of semen analysis and be a reliable biomarker for assessing intrauterine insemination outcomes. In vitro fertilization with intracytoplasmic sperm injection appears to overcome high levels of epigenetic instability in sperm.

Environmental exposure to industrial air pollution is associated with decreased male fertility.

OBJECTIVE: To understand how chronic exposure to industrial air pollution is associated with male fertility through semen parameters. DESIGN: Retrospective cohort study. PATIENTS: Men in the Subfertility, Health, and Assisted Reproduction cohort who underwent a semen analysis in the two largest healthcare systems in Utah from 2005-2017 with ≥1 measured semen parameter (N = 21,563). INTERVENTION(S): Residential histories for each man were constructed using locations from administrative records linked through the Utah Population Database. Industrial facilities with air emissions of nine endocrine-disrupting compound chemical classes were identified from the Environmental Protection Agency Risk-Screening Environmental Indicators microdata. Chemical levels were linked with residential histories for the 5 years before each semen analysis. MAIN OUTCOME MEASURES: Semen analyses were classified as azoospermic or oligozoospermic (< 15 M/mL) using World Health Organization cutoffs for concentration. Bulk semen parameters such as concentration, total count, ejaculate volume, total motility, total motile count, and total progressive motile count were also measured. Multivariable regression models with robust standard errors were used to associate exposure quartiles for each of the nine chemical classes with each semen parameter, adjusting for age, race, and ethnicity, as well as neighborhood socioeconomic disadvantage. RESULTS: After adjustment for demographic covariates, several chemical classes were associated with azoospermia and decreased total motility and volume. For exposure in the 4th relative to 1st quartile, significant associations were observed for acrylonitrile (ßtotal motility = -0.87 pp), aromatic hydrocarbons (odds ratio [OR]azoospermia = 1.53; ßvolume = -0.14 mL), dioxins (ORazoospermia = 1.31; ßvolume = -0.09 mL; ßtotal motility = -2.65 pp), heavy metals (ßtotal motility = -2.78pp), organic solvents (ORazoospermia = 1.75; ßvolume = -0.10 mL), organochlorines (ORazoospermia = 2.09; ßvolume = -0.12 mL), phthalates (ORazoospermia = 1.44; ßvolume = -0.09 mL; ßtotal motility = -1.21 pp), and silver particles (ORazoospermia = 1.64; ßvolume = -0.11 mL). All semen parameters significantly decreased with increasing socioeconomic disadvantage. Men who lived in the most disadvantaged areas had concentration, volume, and total motility of 6.70 M/mL, 0.13 mL, and 1.79 pp lower, respectively. Count, motile count, and total progressive motile count all decreased by 30-34 M. CONCLUSION(S): Several significant associations between chronic low-level environmental exposure to endocrine-disrupting compound air pollution from industrial sources and semen parameters were observed. The strongest associations were seen for increased odds of azoospermia and declines in total motility and volume. More research is needed to further explore additional social and exposure factors as well as expand on the risk posed to male reproductive health by the studied chemicals.

The impact of socioeconomic status on bulk semen parameters, fertility treatment, and fertility outcomes in a cohort of subfertile men.

OBJECTIVE: To study the effect of socioeconomic status on the use of fertility treatment and the rate of live birth in men with subfertility. DESIGN: A retrospective, time-to-event analysis of men with subfertility in Utah stratified by socioeconomic status. SETTING: Patients seen in fertility clinics throughout Utah. PATIENT(S): All men in Utah undergoing semen analysis between 1998 and 2017 at the state's 2 largest health care networks. INTERVENTION(S): Socioeconomic status (defined as area deprivation index of patients' residential location). MAIN OUTCOME MEASURE(S): Categorical use of fertility treatment, the count of fertility treatments (in patients with ≥1 treatment), and live birth after semen analysis. RESULT(S): When controlling for age, ethnicity, and semen parameters (count and concentration), men from low socioeconomic areas were only 60%-70% as likely to use fertility treatment depending on type compared with men from high socioeconomic areas (intrauterine insemination [IUI] hazards ratio [HR] = 0.691 (0.581-0.821), P<.001; in vitro fertilization [IVF] HR = 0.602 (0.466-0.778), P<.001). Of men undergoing fertility treatment, those from low socioeconomic areas had 75%-80% the number of treatments as men from high socioeconomic areas depending on type (IUI incident rate ratio = 0.740 (0.645-0.847), P<.001; IVF incident rate ratios = 0.803 (0.585-1.094), P=.170). When controlling for age, ethnicity, semen parameters, and use of fertility treatment, men from low socioeconomic areas were only 87% as likely to experience a live birth as men from high socioeconomic areas (HR = 0.871 (0.820-0.925), P<.001). Given the overall higher likelihood of live birth in men from high socioeconomic areas, as well as their greater chance of using fertility treatment, we predicted an annual disparity of 5 additional live births in high socioeconomic men compared with low for every 100 men. CONCLUSION(S): Men from low socioeconomic areas undergoing semen analyses are significantly less likely to use fertility treatment and experience a live birth than their counterparts from high socioeconomic areas. Mitigation programs to increase access to fertility treatment may help to reduce this bias; however, our results suggest that additional discrepancies beyond fertility treatment require addressing.

Fertility preservation practices for female oncofertility differ significantly across the USA: results of a survey of SREI members.

PURPOSE: The field of oncofertility has maintained an important focus on improving access, yet standardized practices are lacking. To assess how female cancer patients are provided oncofertility care, we sought to determine provider-level differences and whether there are physician or practice characteristics that predict these variations. METHODS: A cross-sectional survey was sent to SREI members. The survey included fifteen questions about physician practice characteristics and oncofertility cryopreservation protocols. Topics included ovarian stimulation protocols, fertilization techniques, stage of embryo cryopreservation, routine use of pre-implantation genetic testing for aneuploidy (PGT-A), and ovarian tissue cryopreservation (OTC). Statistical analyses assessed whether practice setting, geographic region, time in practice, and mandatory state insurance coverage had effects on cryopreservation protocols. RESULTS: A total of 141 (17%) from diverse REI practice backgrounds completed the survey. The median number of new female oncofertility consults per year was 30 (range 1 to 300). Providers in academic settings treated more patients (median 40 vs. 15, p < 0.001). Providers in academic settings more often use gonadotropin-releasing hormone agonists (85% vs. 52%, p < 0.001) and perform OTC (41% vs. 4%, p < 0.001). Providers in academic practices were less likely to perform intracytoplasmic sperm injection in every cycle (37% vs. 55%, p = 0.032) and less likely to usually advise PGT-A (21% vs. 36%, p = 0.001). Mandated state insurance coverage had no effect on oncofertility practices. CONCLUSION: Oncofertility practices vary among providers. Factors such as practice setting and region may affect the services provided. We do not yet know the best practices in oncofertility patients, and future research is needed.

Single-cell analysis of human testis aging and correlation with elevated body mass index.

Aging men display reduced reproductive health; however, testis aging is poorly understood at the molecular and genomic levels. Here, we utilized single-cell RNA-seq to profile over 44,000 cells from both young and older men and examined age-related changes in germline development and in the testicular somatic cells. Age-related changes in spermatogonial stem cells appeared modest, whereas age-related dysregulation of spermatogenesis and somatic cells ranged from moderate to severe. Altered pathways included signaling and inflammation in multiple cell types, metabolic signaling in Sertoli cells, hedgehog signaling and testosterone production in Leydig cells, cell death and growth in testicular peritubular cells, and possible developmental regression in both Leydig and peritubular cells. Remarkably, the extent of dysregulation correlated with body mass index in older but not in younger men. Collectively, we reveal candidate molecular mechanisms underlying the complex testicular changes conferred by aging and their possible exacerbation by concurrent chronic conditions such as obesity.

The hamster egg penetration test may decrease intracytoplasmic sperm injection utilization while maintaining high conventional fertilization rates.

This was a cohort study of in vitro fertilization (IVF) subjects at the University of Utah, Salt Lake City (UT, USA) utilizing partner sperm. Cycles where both the hamster egg penetration test (HEPT) and semen analysis were performed within 2 years prior to IVF cycles were stratified into four groups based on a normal or an abnormal HEPT and morphology. The mean conventional and intracytoplasmic sperm injection (ICSI) fertilization rates were calculated in each group. We performed a univariate analysis on the primary outcome comparing clinically interesting subjects. We performed a cost-effectiveness analysis of a policy of HEPT versus universal ICSI in couples with an abnormal morphology. Among patients with a normal HEPT, there was no difference in the mean conventional fertilization rates between those with a normal and an abnormal morphology. There was no difference in the mean conventional fertilization rates between subjects with a normal morphology without a hamster test and those with a normal HEPT without a morphology assessment. In 1000 simulated cycles with an abnormal morphology, a policy of HEPT was cost saving compared to universal ICSI, yet produced similar fertilization rates. The HEPT is similar to the World Health Organization edition 5 (WHO-5) morphology in predicting successful conventional fertilization while allowing decreased utilization of ICSI. A policy of HEPT for males with abnormal morphology saves cost in selecting couples for a fertilization method.

Proton-pump inhibitor use does not affect semen quality in subfertile men.

Proton-pump inhibitors (PPIs) are among the most widely used drugs worldwide. PPI use has recently been linked to adverse changes in semen quality in healthy men; however, the effects of PPI use on semen parameters remain largely unknown specifically in cases with male factor infertility. We examined whether PPI use was associated with detrimental effects on semen parameters in a large population of subfertile men. We retrospectively reviewed data from 12 257 subfertile men who had visited our fertility clinic from 2003 to 2013. Patients who reported using any PPIs for >3 months before semen sample collection were included; 7698 subfertile men taking no medication served as controls. Data were gathered on patient age, medication use, and conventional semen parameters; patients taking any known spermatotoxic medication were excluded. Linear mixed-effect regression models were used to test the effect of PPI use on semen parameters adjusting for age. A total of 248 patients (258 samples) used PPIs for at least 3 months before semen collection. In regression models, PPI use (either as the only medication or when used in combination with other nonspermatotoxic medications) was not associated with statistically significant changes in semen parameters. To our knowledge, this is the largest study to compare PPI use with semen parameters in subfertile men. Using PPIs was not associated with detrimental effects on semen quality in this retrospective study.

Review: Diagnosis and impact of sperm DNA alterations in assisted reproduction.

Sperm nuclear and chromatin abnormalities are common among infertile men and are known to influence natural reproduction. These abnormalities are also considered detrimental to normal fertilization, embryo development, and successful implantation and pregnancies following assisted reproductive treatment (ART). Abnormalities in the sperm nucleus can be broadly classified into sperm chromosomal abnormalities (aneuploidies) and sperm DNA abnormalities such as abnormal packing, DNA integrity, or DNA fragmentation. For the past 30 years, numerous tests have been developed to quantify these abnormalities in sperm. In this chapter, we review the causes of sperm DNA and chromosomal abnormalities, describe the commonly used tests to evaluate these abnormalities, and finally review the impact of these abnormalities on male fertility and ART outcomes. We also performed a comprehensive meta-analysis and systematic review from the existing literature to summarize the effect of sperm DNA fragmentation on ART outcomes such as fertilization rate, embryo quality, and clinical pregnancies. A review of the literature presented in this chapter suggests that sperm nuclear and chromatin abnormalities are associated with male infertility, and they reduce the probability of a successful pregnancy following ART.

Impacts of Abstinence Time on Semen Parameters in a Large Population-based Cohort of Subfertile Men.

OBJECTIVE: To assess the effects of abstinence time on semen parameters in normozoospermic and oligozoospermic men using a large cohort of subfertile men. MATERIALS AND METHODS: From 2002 to 2013, we retrospectively reviewed data from 15,623 patients seen at our fertility clinic. Data on patient age and semen parameters were extracted along with abstinence time. Abstinence time was categorized into 4 groups (≤2 days; >2 and ≤5 days; >5 and ≤7 days; and >7 days). Semen samples were further categorized as normozoospermic or oligozoospermic based on concentration. Age-adjusted linear mixed effect regression models were used to test the effect of abstinence categories on semen parameters. RESULTS: Data from 11,782 encounters (10,095 patients) were used for the final analysis after excluding patients <18 years old, azoospermic samples, and those missing all semen parameters. Mean age was 32.4 (standard deviation: 6.5) and median abstinence time was 4.0 days. There were 9840 normozoospermic and 1939 oligozoospermic samples. In normozoospermic men, longer abstinence was associated with increases in ejaculate volume, concentration, total sperm count, and total motile sperm count. However, in oligozoospermic men, longer abstinence time was not associated with improvements in semen parameters except ejaculate volume. CONCLUSION: The effects of abstinence are different on semen parameters in normozoospermic and oligozoospermic patients. Longer abstinence does not improve most semen parameters in oligozoospermic samples. The World Health Organization recommendations for 2-7 days of abstinence may not be beneficial for subfertile patients when timing is a factor.

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons.

To better understand transcriptional regulation during human oogenesis and preimplantation development, we defined stage-specific transcription, which highlighted the cleavage stage as being highly distinctive. Here, we present multiple lines of evidence that a eutherian-specific multicopy retrogene, DUX4, encodes a transcription factor that activates hundreds of endogenous genes (for example, ZSCAN4, KDM4E and PRAMEF-family genes) and retroviral elements (MERVL/HERVL family) that define the cleavage-specific transcriptional programs in humans and mice. Remarkably, mouse Dux expression is both necessary and sufficient to convert mouse embryonic stem cells (mESCs) into 2-cell-embryo-like ('2C-like') cells, measured here by the reactivation of '2C' genes and repeat elements, the loss of POU5F1 (also known as OCT4) protein and chromocenters, and the conversion of the chromatin landscape (as assessed by transposase-accessible chromatin using sequencing (ATAC-seq)) to a state strongly resembling that of mouse 2C embryos. Thus, we propose mouse DUX and human DUX4 as major drivers of the cleavage or 2C state.

Optimization of microelectrophoresis to select highly negatively charged sperm.

PURPOSE: The sperm membrane undergoes extensive surface remodeling as it matures in the epididymis. During this process, the sperm is encapsulated in an extensive glycocalyx layer, which provides the membrane with its characteristic negative electrostatic charge. In this study, we develop a method of microelectrophoresis and standardize the protocol to isolate sperm with high negative membrane charge. METHODS: Under an electric field, the percentage of positively charged sperm (PCS), negatively charged sperm (NCS), and neutrally charged sperm was determined for each ejaculate prior to and following density gradient centrifugation (DGC), and evaluated for sperm DNA damage, and histone retention. Subsequently, PCS, NCS, and neutrally charged sperm were selected using an ICSI needle and directly analyzed for DNA damage. RESULTS: When raw semen was analyzed using microelectrophoresis, 94 % were NCS. In contrast, DGC completely or partially stripped the negative membrane charge from sperm resulting PCS and neutrally charged sperm, while the charged sperm populations are increased with an increase in electrophoretic current. Following DGC, high sperm DNA damage and abnormal histone retention were inversely correlated with percentage NCS and directly correlated with percentage PCS. NCS exhibited significantly lower DNA damage when compared with control (P < 0.05) and PCS (P < 0.05). When the charged sperm population was corrected for neutrally charged sperm, sperm DNA damage was strongly associated with NCS at a lower electrophoretic current. CONCLUSION: The results suggest that selection of NCS at lower current may be an important biomarker to select healthy sperm for assisted reproductive treatment.

Micro-electrophoresis: a noninvasive method of sperm selection based on membrane charge.

OBJECTIVE: To develop a technique with the potential of isolating genetically fit sperm for assisted reproductive technology (ART) treatment without compromising its structural or functional competence. DESIGN: Observational study. SETTING: University hospital. PATIENT(S): Fifty patients undergoing infertility diagnosis and 88 couples undergoing ART treatment. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Under an electric field, the percentage of positively charged sperm (PCS), negatively charged sperm (NCS), and neutrally charged sperm was determined for each ejaculate before and after density gradient centrifugation (DGC), and evaluated for sperm DNA damage, histone retention, and couples' ART outcomes. Subsequently, PCS, NCS, and neutrally charged sperm were selected using an intracytoplasmic sperm injection needle and directly analyzed for DNA damage. RESULT(S): There was a reduction in the NCS population (95.10% ± 0.94% vs. 54.48% ± 2.39%) and an increase in the PCS population (4.28% ± 0.58% vs. 42.52% ± 2.36%) after DGC. The DNA damage was inversely proportional to %NCS (r(2) = -0.242) and directly proportional to the %PCS (r(2) = 0.206). When sperm were picked according to their charge and directly analyzed, sperm DNA damage was lower in the NCS population (3.9% ± 1.5%) compared with control (17.3% ± 3.2%) and %PCS populations (27.8% ± 6.0%). The %NCS was positively associated with fertilization rate (r(2) = 0.469) and blastocyst development (r(2) = 0.308) and inversely associated with embryo arrest (r(2) = -0.253). Implantation rate and clinical pregnancies were higher in patient groups with increased NCS. CONCLUSION(S): Selection of NCS through micro-electrophoresis has the potential to isolate sperm relatively free of DNA damage to be used in ART.

The sperm epigenome: implications for the embryo.

Recent advances, including the human genome project and numerous studies of cancer and other diseases, have shown that the genetic code is not simply limited to the sequence of the four bases of DNA but also includes epigenetic programming, heritable changes that affect gene expression [Riggs A, Martinssen R, Russo V (2007) Introduction. In: Riggs A, Martinssen R, Russo V (eds) Epigenetics mechanisms of gene regulation. Cold Spring Harbor Press, New York]. The science of epigenetics is important in understanding many diseases and biological processes, including in identifying the causes of disease and better understanding the mechanisms by which the environment can affect gene expression [Carrell Fertil Steril 97 (2):267-274, 2012]. This chapter will focus on the epigenome of sperm and particularly highlight the potential role of the sperm epigenome in embryogenesis.The sperm epigenome is unique and highly specialized because of the unique nature and function of sperm and because of the diverse requirements for successful fertilization. Due to the need for motility, sperm chromatin must be compacted and highly organized. During spermiogenesis the chromatin is packaged tightly into the sperm head by the replacement of most histones with protamines. This allows for protection of the DNA from the hostile environment in the female reproductive tract. Remaining histones can have chemical modifications to the tails of the protein that either facilitate or repress gene transcription. Sperm, like embryonic stem cells, have a unique pattern of histone modifications that includes both activating and silencing marks in the promoters of genes associated with development. These bivalent marks, along with DNA hypomethylation, comprise a unique state in which the key genes are "poised" for possible activation in embryogenesis. Sperm epigenetic abnormalities have been linked with multiple diseases including male factor infertility and poor embryogenesis.

Sperm aneuploidy testing using fluorescence in situ hybridization.

Sperm aneuploidy screening has been used as a tool in diagnosis and determining treatment options for male factor infertility since the development of human sperm karyotyping by injection into hamster and mouse oocytes in the 1970s. From these studies and subsequent work with interphase chromosome analysis, at risk populations of men with teratozoospermia, oligozoospermia, and men with translocations, have since been identified. The current technique is an application of fluorescent in situ hybridization (FISH) on interphase sperm nuclei with careful enumeration of the labeled chromosomes to determine sperm ploidy. Typically, five to seven chromosomes are evaluated in individual ejaculates to determine the percent of aneuploid sperm present. This protocol will detail the procedures for: preparation of specimens, exposure of the sperm nuclei to the FISH probes, hybridization, destaining, and scoring criteria.

The marmoset and cotton rat as animal models for the study of sperm chromatin packaging.

In the human, canonical histones are largely replaced by protamine 1 (P1) and protamine 2 (P2) during late spermatogenesis. Recent studies have demonstrated that abnormal replacement of the histones is associated with severe male infertility and has profound implications for early embryogenesis. In this review the hispid cotton rat and the common marmoset are evaluated as animal models for the study of chromatin packaging in sperm. The DNA sequences of protamine 1 and protamine 2 in the cotton rat are also reported. We have found that the P1 and P2 genes share a 64% and 56% amino acid identity with human, respectively. The hispid cotton rat expresses both protamines, has a similar P1:P2 ratio, and a gene sequence homologous to human, thus making it a possible model organism for chromatin studies. The common marmoset also expresses both protamine genes and has a very similar spermatogenetic characteristic to man. This review considers both animals as possible models to study the mechanisms of protamine regulation and the effects of altered expression caused by environmental or physiological perturbations.

Disease progression and solid tumor survival: a transcriptome decoherence model.

Networks of genes are typically generated from expression changes observed between control and test conditions. Nevertheless, within a single control state many genes show expression variance across biological replicates. These transcripts, typically termed unstable, are usually excluded from analyses because their behavior cannot be reconciled with biological constraints. Grouped as pairs of covariant genes they can however show a consistent response to the progression of a disease. We present a model of coherence arising from sets of covariant genes that was developed in-vitro then tested against a range of solid tumors. DGPMs, Decoherence Gene Pair Models, showed changes in network topology reflective of the metastatic transition. Across a range of solid tumor studies the model generalizes to reveal a richly connected topology of networks in healthy tissues that becomes sparser as the disease progresses reaching a minimum size in the advanced tumors with minim survivability.

Identification of human sperm transcripts as candidate markers of male fertility.

To date, there has been little progress towards identifying markers of normal male fertility. The need to supplement current subjective methods that rely on variable semen parameters to assess fertility status continues to be acknowledged. Several studies have shown that spermatozoal RNAs can describe characteristic failures of the spermatogenic pathway among infertile males. In spite of the inherent heterogeneity of semen that describe the "normal" fertile male, this holds the promise of developing markers that could help identify the ever elusive idiopathic infertile male. Through the analyses of the spermatozoal transcriptome from 24 donors of proven fertility, we identified a series of transcripts that were consistently present among all individuals. The heterogeneous nature of the samples, reflected by their semen parameters, was mirrored by the variability of the observed array signal. Nevertheless, clusters of invariable transcript pairs were identified. These were founded by a single central member that was linked in constant proportion even though the absolute level of each member of the transcript pair often varied among individuals. The presence of pairs of stable transcripts suggests that among the heterogeneity observed in the sperm transcriptome, a distinct set is strictly regulated.

Sequence alterations in the YBX2 gene are associated with male factor infertility.

OBJECTIVE: To investigate YBX2 gene alterations in men with severe defects in spermatogenesis, including azoospermia or severe oligozoospermia, and protamine deregulation. MSY2 has been identified as a central component in the regulation of spermatogenesis in mice, but the potential role of its human orthologue, YBX2 or "Contrin," in human infertility is not known. DESIGN: A prospective cohort study. SETTING: University infertility clinic and associated research laboratory. PATIENT(S): A total of 288 men were evaluated. Diagnoses were made of complete azoospermia, severe oligozoospermia, and protamine deregulation, or men were of known paternity. INTERVENTION(S): Deoxyribonucleic acid (from peripheral blood) and semen samples were collected and analyzed for gene mutations and semen parameters respectively. MAIN OUTCOME MEASURE(S): YBX2 gene alterations. RESULT(S): YBX2 sequence analysis revealed 15 polymorphic sites, of which seven polymorphisms were present at a statistically higher frequency in one or both of the patient populations than in controls. Of these seven, two resulted in an amino acid substitution in the highly conserved cold shock domain and one resulted in a highly significant synonymous change in exon 8 of infertile patients. The frequency of single nucleotide polymorphisms was significantly elevated in patients with infertility, particularly in men with abnormal protamine expression. CONCLUSION(S): These data indicate a significant association between gene alterations in the YBX2 gene and abnormal spermatogenesis in humans, including a potential role in altering protamine expression, and implicate YBX2 gene alterations as a potential cause of male factor infertility.