Molecular Profiling of Spermatozoa Reveals Correlations between Morphology and Gene Expression: A Novel Biomarker Panel for Male Infertility

Genome-Wide microRNA Expression Profiling in Human Spermatozoa and Its Relation to Sperm Quality

BACKGROUND

Sperm samples are separated into bad and good quality samples in function of their phenotype, but this does not indicate their genetic quality.

METHODS

Here, we used GeneChip miRNA arrays to analyze microRNA expression in ten semen samples selected based on high-magnification morphology (score 6 vs. score 0) to identify miRNAs linked to sperm phenotype.

RESULTS

We found 86 upregulated and 21 downregulated miRNAs in good-quality sperm (score 6) compared with bad-quality sperm samples (score 0) (fold change > 2 and p-value < 0.05). MiR-34 (FC × 30, p = 8.43 × 10-8), miR-30 (FC × 12, p = 3.75 × 10-6), miR-122 (FC × 8, p = 0.0031), miR-20 (FC × 5.6, p = 0.0223), miR-182 (FC × 4.83, p = 0.0008) and miR-191 (FC × 4, p = 1.61 × 10-6) were among these upregulated miRNAs. In silico prediction algorithms predicted that miRNAs upregulated in good-quality sperm targeted 910 genes involved in key biological functions of spermatozoa, such as cell death and survival, cellular movement, molecular transport, response to stimuli, metabolism, and the regulation of oxidative stress. Genes deregulated in bad-quality sperm were involved in cell growth and proliferation.

CONCLUSIONS

This study reveals that miRNA profiling may provide potential biomarkers of sperm quality.

The Response of the miRNA Profiles of the Thyroid Gland to the Artificial Photoperiod in Ovariectomized and Estradiol-Treated Ewes

The photoperiod has been considered to be a key environmental factor in sheep reproduction, and some studies have shown that the thyroid gland plays an important role in mammalian reproduction, but the molecular mechanism is still unclear. In this study, we used the artificial-light-controlled, ovariectomized, and estradiol-treated model (OVX + E2 model); healthy and consistent 2-3-year-old Sunite multiparous ewes were collected; and thyroids were collected for testing, combined with RNA-seq technology and bioinformatics analysis, to analyze the effects of different photoperiods (long photoperiod treatment for 42 days, LP42; short photoperiod treatment for 42 days, SP42; SP42 transferred to LP42, SPLP42) on the variations in the miRNA profiles of the thyroid gland. A total of 105 miRNAs were differentially expressed in the thyroid gland, most of which were new miRNAs. Through GO and KEGG enrichment analysis, the results showed that the photoperiod response characteristics of Sunite ewes were affected by Olfactory transduction, Wnt signaling pathways, and Apelin signaling pathways. A different illumination time may have a certain influence on the downstream of these pathways, which leads to the change in animal estrus state. In addition, lncRNA-mRNA-miRNA network analysis revealed the target binding sites of identified miRNAs in DE-circRNA and DE-mRNA, such as Novel_369, Novel_370, Novel_461, and so on. The results of this study will provide some new insights into the function of miRNA and the changes in sheep thyroid glands under different photoperiods.

Unraveling the protective genetic architecture of COVID-19 in the Brazilian Amazon

Despite all the efforts acquired in four years of the COVID-19 pandemic, the path to a full understanding of the biological mechanisms involved in this disease remains complex. This is partly due to a combination of factors, including the inherent characteristics of the infection, socio-environmental elements, and the variations observed within both the viral and the human genomes. Thus, this study aimed to investigate the correlation between genetic host factors and the severity of COVID-19. We conducted whole exome sequencing (WES) of 124 patients, categorized into severe and non-severe groups. From the whole exome sequencing (WES) association analysis, four variants (rs1770731 in CRYBG1, rs7221209 in DNAH17, rs3826295 in DGKE, and rs7913626 in CFAP46) were identified as potentially linked to a protective effect against the clinical severity of COVID-19, which may explain the less severe impact of COVID-19 on the Northern Region. Our findings underscore the importance of carrying out more genomic studies in populations living in the Amazon, one of the most diverse from the point of view of the presence of rare and specific alleles. To our knowledge, this is the first WES study of admixed individuals from the Brazilian Amazon to investigate genomic variants associated with the clinical severity of COVID-19.

Genomic and transcriptomic evaluations of infertile or subfertile Arunachali yak sperm

Sperm infertility or subfertility is detrimental to the precious highland germplasm like yak whose population has been gradually declining in India. Understanding the 'omic' landscape of infertile or subfertile yak sperm can reveal some interesting insights. In an attempt to do the same, this study considered the semen of infertile or subfertile yak bulls for whole-genome and transcriptome evaluations. DNA sequencing revealed that the yak sperm genome contains the necessary genes to carry out all the important biological processes related to the growth, development, survival and multiplication of an organism. Interestingly, RNA Seq results highlighted that genes like VAMP7, MYLK, ARAP2 and MARCH6 showed increased expression, while biological processes related to immune response (GO:0043308, GO:0002447, GO:0002278, GO:0043307, GO:0043312, GO:0002283, GO:0043299 and GO:0002446) were significantly overrepresented. These findings hint at a possible role played by immune system in regulating infertility or subfertility in yaks. Further, in-depth studies can validate these findings and help in improving our biological understanding in this area.

Effect of body mass index on semen quality, sperm chromatin integrity and sperm DNA methylation

Obesity represents a growing problem due to its impacts on human health and reproduction. In this study, we analysed semen quality, sperm DNA integrity and gene-specific CpG methylation in 116 healthy men from normal population. The men were divided into three groups according to their body mass index (BMI), and their ejaculates were analysed using standard methods, sperm chromatin structure assay (SCSA), methylation next generation sequencing (NGS) and amplicon sequencing. The sperm methylation NGS revealed six significantly differentially methylated regions (DMRs). Using subsequent targeted amplicon sequencing in 116 men, two of the DMRs were proved as differentially methylated in sperm of men with normal BMI vs. BMI ≥ 25. The DMRs were located in the EPHA8 and ANKRD11 gene. Also, we detected a significant decline in the EPHA8, ANKRD11 and CFAP46 gene methylation in association with increasing BMI values. The genes EPHA8 and ANKRD11 are involved in the nervous system and brain development; the CFAP46 gene plays a role in a flagellar assembly and is associated with sperm motility. Significantly lower rates of motile and progressive motile sperm were observed in men with BMI ≥ 30. Our results show that excess body weight can modify CpG methylation of specific genes, affect sperm motility, and compromise sperm chromatin integrity. These factors can stand behind the observed reduced fertility in men with obesity. The methylation changes might be transmitted to their offspring through sperm, and become a basis for possible developmental and reproductive issues in the next generation.

Different Nuclear Architecture in Human Sperm According to Their Morphology

Human sperm parameters serve as a first step in diagnosing male infertility, but not in determining the potential for successful pregnancy during assisted reproductive technologies (ARTs) procedures. Here, we investigated the relationship between sperm head morphology at high magnification, based on strict morphologic criteria, and the nuclear architecture analyzed by fluorescence in situ hybridization (FISH). We included five men. Two of them had an elevated high-magnification morphology score of 6 points (Score 6) indicating high fertility potential, whereas three had a low score of 0 points (Score 0), indicating low fertility potential. We used FISH to study the inter-telomeric distance and the chromosomal territory area of chromosome 1 (Chr. 1). We then compared these two parameters between subjects with high and low scores. FISH data analysis showed that the inter-telomeric distance (ITD) and chromosomal territory area (CTA) of Chr. 1 were significantly higher in subjects with low scores (score 0) than high scores (score 6). Our results suggest that (i) there is a link between nuclear architecture and sperm head abnormalities, particularly vacuoles; and (ii) it is possible to select spermatozoa with normal nuclear architecture, which might indirectly explain the positive ART outcomes observed with this technique.

Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveals regulatory pathways associated with pig testis function

Long noncoding RNA (lncRNA) and microRNA (miRNA) are known to play pivotal roles in mammalian testicular function and spermatogenesis. However, their impact on porcine male reproduction has yet to be well unraveled. Here, we sequenced and identified lncRNA and miRNA expressed in the testes of Chinese indigenous Banna mini-pig inbred line (BMI) and introduced Western Duroc (DU) and Large White (LW) pigs. By pairwise comparison (BMI vs DU, BMI vs LW, and DU vs LW), we found the gene expression differences in the testes between Chinese local pigs and introduced Western commercial breeds were more striking than those between introduced commercial breeds. Furthermore, we found 1622 co-differentially expressed genes (co-DEGs), 122 co-differentially expressed lncRNAs (co-DELs), 39 co-differentially expressed miRNAs (co-DEMs) in BMI vs introduced commercial breeds (DU and LW). Functional analysis revealed that these co-DEGs and co-DELs/co-DEMs target genes were enriched in male sexual function pathways, including MAPK, AMPK, TGF-β/Smad, Hippo, NF-kappa B, and PI3K/Akt signaling pathways. Additionally, we established 10,536 lncRNA-mRNA, 11,248 miRNA-mRNA pairs, and 62 ceRNA (lncRNA-miRNA-mRNA) networks. The ssc-miR-1343 had the most interactive factors in the ceRNA network, including 20 mRNAs and 3 lncRNAs, consisting of 56 ceRNA pairs. These factors played extremely important roles in the regulation of testis function as key nodes in the interactive regulatory network. Our results provide insight into the functional roles of lncRNAs and miRNAs in porcine testis and offer a valuable resource for understanding the differences between Chinese indigenous and introduced Western pigs.

Sperm morphology value in assisted reproduction: dismantling an enigma and key takeaways for the busy clinician

The ideal morphology of the sperm cell was initially described based on the characteristics of sperm able to migrate through the endocervical canal assuming these had the best fertilization potential. Sperm morphology assessment has moved over the years toward stricter criteria based on the findings from studies that underline its value in successful reproductive outcomes. While treatment options are clear for some conditions related to abnormal sperm morphology, the value of sperm morphology in assisted reproduction requires further investigation. The objective of this review is to offer care providers updated guidance for choosing appropriate treatment strategies based on sperm morphology assessment and morphological deviations. Issues to be considered for a reliable determination and interpretation of sperm morphology using the current thresholds and criteria are discussed. In addition, key knowledge on morphological abnormalities relevant to the clinical care of infertile patients, distinguishing between monomorphic and polymorphic forms as well as the isolated or non-isolated occurrence of teratozoospermia in semen is presented. Furthermore, the impact of impaired morphology on assisted reproductive technique outcomes is summarized in light of the latest research.

Effect of Micronutrients and L-Carnitine as Antioxidant on Sperm Parameters, Genome Integrity, and ICSI Outcomes: Randomized, Double-Blind, and Placebo-Controlled Clinical Trial

The evaluation of sperm DNA integrity is recommended in the sixth edition of the 2021 World Health Organization guidelines. Oxidative stress has been identified as a crucial factor leading to genome decay, lipid peroxidation, and nucleoprotein oxidation. This double-blind, placebo-controlled clinical trial aimed to assess the effect of oral antioxidant treatment (Fertilis), which contains L-carnitine and some micronutrients, in the improvement of conventional sperm parameters, sperm DNA integrity and in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) outcomes. A total of 263 participants were enrolled and randomly divided into two groups: 131 participants received the antioxidant treatment, while 132 participants received a placebo. The male partners in both groups underwent the antioxidant treatment or the placebo for a duration of three months. For each participant, we performed a hormonal test, an infectious test, a spermogram, a TUNEL assay for sperm DNA fragmentation, a toluidine blue staining for sperm DNA decondensation, and an IVF/ICSI procedure. Sperm characteristics analysis (volume, count, motility, and vitality), sperm DNA fragmentation, and sperm DNA decondensation were assessed and compared to the results preceding the antioxidant treatment. The study outcome revealed a significant decrease in the DNA fragmentation index and a significant increase in sperm motility after 3 months of treatment (p = 0.01 and p = 0.02, respectively). Additionally, a significant improvement in clinical pregnancy rate (p = 0.01) and life birth rate (p = 0.031) was observed. No significant changes were observed in conventional sperm parameters (volume, count, and vitality) or sperm DNA decondensation (SDI). Antioxidant therapy has a beneficial impact on achieving pregnancy, whether through spontaneous conception or assisted reproductive procedures (ART).

Integration of omics studies indicates that species-dependent molecular mechanisms govern male fertility

BACKGROUND

Comparative and comprehensive omics studies have recently been conducted to provide a comprehensive understanding of the biological mechanisms underlying infertility. However, because these huge omics datasets often contain irrelevant information, editing strategies for summarizing and filtering the data are necessary prerequisite steps for identifying biomarkers of male fertility. Here, we attempted to integrate omics data from spermatozoa with normal and below-normal fertility from boars and bulls, including transcriptomic, proteomic, and metabolomic data. Pathway enrichment analysis was conducted and visualized using g:Profiler, Cytoscape, EnrichmentMap, and AutoAnnotation to determine fertility-related biological functions according to species.

RESULTS

In particular, gamete production and protein biogenesis-associated pathways were enriched in bull spermatozoa with below-normal fertility, whereas mitochondrial-associated metabolic pathways were enriched in boar spermatozoa with normal fertility. These results indicate that below-normal fertility may be determined by aberrant regulation of protein synthesis during spermatogenesis, and the modulation of reactive oxygen species generation to maintain capacitation and the acrosome reaction governs boar sperm fertility.

CONCLUSION

Overall, this approach demonstrated that distinct molecular pathways drive sperm fertility in mammals in a species-dependent manner. Moreover, we anticipate that searching for species-specific signaling pathways may aid in the discovery of fertility-related biomarkers within large omics datasets.

Genomic testing for copy number and single nucleotide variants in spermatogenic failure

PURPOSE

To identify clinically significant genomic copy number (CNV) and single nucleotide variants (SNV) in males with unexplained spermatogenic failure (SPGF).

MATERIALS AND METHODS

Peripheral blood DNA from 97/102 study participants diagnosed with oligozoospermia, severe oligozoospermia, or non-obstructive azoospermia (NOA) was analyzed for CNVs via array comparative genomic hybridization (aCGH) and SNVs using whole-exome sequencing (WES).

RESULTS

Of the 2544 CNVs identified in individuals with SPGF, > 90% were small, ranging from 0.6 to 75 kb. Thirty, clinically relevant genomic aberrations, were detected in 28 patients (~ 29%). These included likely diagnostic CNVs in 3/41 NOA patients (~ 7%): 1 hemizygous, intragenic TEX11 deletion, 1 hemizygous DDX53 full gene deletion, and 1 homozygous, intragenic STK11 deletion. High-level mosaicism for X chromosome disomy (~ 10% 46,XY and ~ 90% 47,XXY) was also identified in 3 of 41 NOA patients who previously tested normal with conventional karyotyping. The remaining 24 CNVs detected were heterozygous, autosomal recessive carrier variants. Follow-up WES analysis confirmed 8 of 27 (30%) CNVs (X chromosome disomy excluded). WES analysis additionally identified 13 significant SNVs and/or indels in 9 patients (~ 9%) including X-linked AR, KAL1, and NR0B1 variants.

CONCLUSION

Using a combined genome-wide aCGH/WES approach, we identified pathogenic and likely pathogenic SNVs and CNVs in 15 patients (15%) with unexplained SPGF. This value equals the detection rate of conventional testing for aneuploidies and is considerably higher than the prevalence of Y chromosome microdeletions. Our results underscore the importance of comprehensive genomic analysis in emerging diagnostic testing of complex conditions like male infertility.

The relevance of sperm morphology in male infertility

This brief report concerns the role of human sperm morphology assessment in different fields of male infertility: basic research, genetics, assisted reproduction technologies, oxidative stress. One of the best methods in studying sperm morphology is transmission electron microscopy (TEM) that enables defining the concept of sperm pathology and classifying alterations in non-systematic and systematic. Non-systematic sperm defects affect head and tail in variable ratio, whereas the rare systematic defects are characterized by a particular anomaly that marks most sperm of an ejaculate. TEM analysis and fluorescence in situ hybridization represent outstanding methods in the study of sperm morphology and cytogenetic in patients with altered karyotype characterizing their semen quality before intracytoplasmic sperm injection. In recent years, the genetic investigations on systematic sperm defects, made extraordinary progress identifying candidate genes whose mutations induce morphological sperm anomalies. The question if sperm morphology has an impact on assisted fertilization outcome is debated. Nowadays, oxidative stress represents one of the most important causes of altered sperm morphology and function and can be analyzed from two points of view: 1) spermatozoa with cytoplasmic residue produce reactive oxygen species, 2) the pathologies with inflammatory/oxidative stress background cause morphological alterations. Finally, sperm morphology is also considered an important endpoint in in vitro experiments where toxic substances, drugs, antioxidants are tested. We think that the field of sperm morphology is far from being exhausted and needs other research. This parameter can be still considered a valuable indicator of sperm dysfunction both in basic and clinical research.

Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis

Chronic epididymitis (CE) refers to a long-lasting inflammatory condition of the epididymis, which is considered the most common site of intrascrotal inflammation and an important aetiological factor of male infertility. Recent studies demonstrate that small RNAs secreted from epididymal epithelium modulate embryo development and offspring phenotypes via sperm transmission, and the resulting modifications may lead to transgenerational inheritance. However, to date, the genome-wide analysis of small RNA together with the transcriptomic expression profiles of human epididymis and CE is still lacking. In this study, we facilitated next-generation sequencing and bioinformatics to comprehensively analyze the small RNA and mRNA in an integrative way and identified signatures associated with CE. Both of the small RNA and mRNA expression data demonstrated relatively larger molecular differences among the segmental region of the epididymides, including caput, corpus, and cauda, than that of the inflammatory conditions. By comparing the inflamed caputs to the controls, a total of 1727 genes (1220 upregulated and 507 downregulated; 42 most significant genes, adjusted P <0.05) and 34 miRNAs (23 upregulated and 11 downregulated) were identified as differentially expressed. In silico functional enrichment analysis showed their roles in regulating different biological activities, including leukocyte chemotaxis, extracellular milieu reconstruction, ion channel and transporter-related processes, and nervous system development. Integrative analysis of miRNA and mRNA identified a regulatory network consisting of 22 miRNAs and 31 genes (miRNA-mRNA) which are strong candidates for CE. In addition, analysis about other species of small RNA, including (miRNA), piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA), Y RNA, and rsRNA identified the distinct expression pattern of tsRNA in CE. In summary, our study performed small RNA and miRNA profiling and integrative analysis in human CE. The findings will help to understand the role of miRNA-mRNA in the pathogenesis of CE and provide molecular candidates for the development of potential biomarkers for human CE.