Two novel mutations in PADI6 and TLE6 genes cause female infertility due to arrest in embryonic development

The Mammalian Oocyte: A Central Hub for Cellular Reprogramming and Stemness

The mammalian oocyte is pivotal in reproductive biology, acting as a central hub for cellular reprogramming and stemness. It uniquely contributes half of the zygotic nuclear genome and the entirety of the mitochondrial genome, ensuring individual development and health. Oocyte-mediated reprogramming, exemplified by nuclear transfer, resets somatic cell identity to achieve pluripotency and has transformative potential in regenerative medicine. This process is critical for understanding cellular differentiation, improving assisted reproductive technologies, and advancing cloning and stem cell research. During fertilization, the maternal-zygotic transition shifts developmental control from maternal factors to zygotic genome activation, establishing totipotency. Oocytes also harbor reprogramming factors that guide nuclear remodeling, epigenetic modifications, and metabolic reprogramming, enabling early embryogenesis. Structures like mitochondria, lipid droplets, and cytoplasmic lattices contribute to energy production, molecular regulation, and cellular organization. Recent insights into oocyte components, such as ooplasmic nanovesicles and endolysosomal vesicular assemblies (ELVAS), highlight their roles in maintaining cellular homeostasis, protein synthesis, and reprogramming efficiency. By unraveling the reprogramming mechanisms inherent in oocytes, we advance our understanding of cloning, cell differentiation, and stem cell therapy, highlighting their valuable significance in developmental biology and regenerative medicine.

Structural insight into the function of human peptidyl arginine deiminase 6

Peptidyl arginine deiminase 6 (PADI6 or PAD6) is vital for early embryonic development in mice and humans, yet its function remains elusive. PADI6 is less conserved than other PADIs and it is currently unknown whether it has a catalytic function. Here we show that human PADI6 dimerises like hPADIs 2-4, however, does not bind Ca2+ and is inactive in in vitro assays against standard PADI substrates. By determining the crystal structure of hPADI6, we show that hPADI6 is structured in the absence of Ca2+ where hPADI2 and hPADI4 are not, and the Ca-binding sites are not conserved. Moreover, we show that whilst the key catalytic aspartic acid and histidine residues are structurally conserved, the cysteine is displaced far from the active site centre and the hPADI6 active site pocket appears closed through a unique evolved mechanism in hPADI6, not present in the other PADIs. Taken together, these findings provide insight into how the function of hPADI6 may differ from the other PADIs based on its structure and provides a resource for characterising the damaging effect of clinically significant PADI6 variants.

Novel variants in PADI6 genes cause female infertility due to early embryo arrest

PURPOSE

Early embryo arrest is characterized by premature termination of development in preimplantation embryos. Human subcortical maternal complex (SCMC) is a protein complex that is specifically expressed in mammalian oocytes and early embryos and is essential for embryonic cell division. Peptidyl arginine deiminase 6 (PADI6) is proven to be a member of SCMC. Variants in the PADI6 gene have been shown to induce early embryo arrest. In this study, we performed genetic analysis in patients with female infertility due to early embryo arrest to identify the disease-causing gene variants.

METHODS

Whole-exome sequencing and Sanger sequencing were used to identify the variants in the patients and their families. Western blotting and immunofluorescence staining were used to check the effects of the variants on expression and function of PADI6.

RESULTS

We identified a novel homozygous variant (c.358A > C [p.Thr120Pro]) and novel compound-heterozygous variants (c.2044C > T [p.Arg682Trp] and c.707dupT [p.Leu237Alafs*24]) in PADI6 in two infertile individuals with early embryo arrest. We found that these variants resulted in a decrease in the expression level of PADI6, which may lead to abnormal protein function. Immunofluorescence staining also suggested that these variants affected the expression of PADI6.

CONCLUSION

Our study expands the spectrum of genetic defects in female early embryo arrest and further supports the causality between PADI6 variants and female infertility.

Advances in the genetic etiology of female infertility

Human reproduction is a complex process involving gamete maturation, fertilization, embryo cleavage and development, blastocyst formation, implantation, and live birth. If any of these processes are abnormal or arrest, reproductive failure will occur. Infertility is a state of reproductive dysfunction caused by various factors. Advances in molecular genetics, including cell and molecular genetics, and high-throughput sequencing technologies, have found that genetic factors are important causes of infertility. Genetic variants have been identified in infertile women or men and can cause gamete maturation arrest, poor quality gametes, fertilization failure, and embryonic developmental arrest during assisted reproduction technology (ART), and thus reduce the clinical success rates of ART. This article reviews clinical studies on repeated in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) failures caused by ovarian dysfunction, oocyte maturation defects, oocyte abnormalities, fertilization disorders, and preimplantation embryonic development arrest due to female genetic etiology, the accumulation of pathogenic genes and gene pathogenic loci, and the functional mechanism and clinical significance of pathogenic genes in gametogenesis and early embryonic development.

Cryo-EM structure of the human subcortical maternal complex and the associated discovery of infertility-associated variants

The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, three core components of the SCMC, have attracted much attention over the past several years. Evaluating the pathogenicity of a missense variant in the SCMC is limited by the lack of information on its structure, although we recently solved the structure of the mouse SCMC and proposed that reproductive disorders caused by pathogenic variants are related to the destabilization of the SCMC core complex. Here we report the cryogenic electron microscopy structure of the human SCMC and uncover that the pyrin domain of NLRP5 is essential for the stability of SCMC. By combining prediction of SCMC stability and in vitro reconstitution, we provide a method for identifying deleterious variants, and we successfully identify a new pathogenic variant of TLE6 (p.A396T). Thus, on the basis of the structure of the human SCMC, we offer a strategy for the diagnosis of reproductive disorders and the discovery of new infertility-associated variants.

Crystal structure of human peptidylarginine deiminase type VI (PAD6) provides insights into its inactivity

Human peptidylarginine deiminase isoform VI (PAD6), which is predominantly limited to cytoplasmic lattices in the mammalian oocytes in ovarian tissue, is essential for female fertility. It belongs to the peptidylarginine deiminase (PAD) enzyme family that catalyzes the conversion of arginine residues to citrulline in proteins. In contrast to other members of the family, recombinant PAD6 was previously found to be catalytically inactive. We sought to provide structural insight into the human homologue to shed light on this observation. We report here the first crystal structure of PAD6, determined at 1.7 Å resolution. PAD6 follows the same domain organization as other structurally known PAD isoenzymes. Further structural analysis and size-exclusion chromatography show that PAD6 behaves as a homodimer similar to PAD4. Differential scanning fluorimetry suggests that PAD6 does not coordinate Ca2+ which agrees with acidic residues found to coordinate Ca2+ in other PAD homologs not being conserved in PAD6. The crystal structure of PAD6 shows similarities with the inactive state of apo PAD2, in which the active site conformation is unsuitable for catalytic citrullination. The putative active site of PAD6 adopts a non-productive conformation that would not allow protein-substrate binding due to steric hindrance with rigid secondary structure elements. This observation is further supported by the lack of activity on the histone H3 and cytokeratin 5 substrates. These findings suggest a different mechanism for enzymatic activation compared with other PADs; alternatively, PAD6 may exert a non-enzymatic function in the cytoplasmic lattice of oocytes and early embryos.

Proteomic Analysis of Domestic Cat Blastocysts and Their Secretome Produced in an In Vitro Culture System without the Presence of the Zona Pellucida

Domestic cat blastocysts cultured without the zona pellucida exhibit reduced implantation capacity. However, the protein expression profile has not been evaluated in these embryos. The objective of this study was to evaluate the protein expression profile of domestic cat blastocysts cultured without the zona pellucida. Two experimental groups were generated: (1) domestic cat embryos generated by IVF and cultured in vitro (zona intact, (ZI)) and (2) domestic cat embryos cultured in vitro without the zona pellucida (zona-free (ZF group)). The cleavage, morula, and blastocyst rates were estimated at days 2, 5 and 7, respectively. Day 7 blastocysts and their culture media were subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). The UniProt Felis catus database was used to identify the standard proteome. No significant differences were found in the cleavage, morula, or blastocyst rates between the ZI and ZF groups (p > 0.05). Proteomic analysis revealed 22 upregulated and 20 downregulated proteins in the ZF blastocysts. Furthermore, 14 proteins involved in embryo development and implantation were present exclusively in the culture medium of the ZI blastocysts. In conclusion, embryo culture without the zona pellucida did not affect in vitro development, but altered the protein expression profile and release of domestic cat blastocysts.

Genetic mechanisms of fertilization failure and early embryonic arrest: a comprehensive review

BACKGROUND

Infertility and pregnancy loss are longstanding problems. Successful fertilization and high-quality embryos are prerequisites for an ongoing pregnancy. Studies have proven that every stage in the human reproductive process is regulated by multiple genes and any problem, at any step, may lead to fertilization failure (FF) or early embryonic arrest (EEA). Doctors can diagnose the pathogenic factors involved in FF and EEA by using genetic methods. With the progress in the development of new genetic technologies, such as single-cell RNA analysis and whole-exome sequencing, a new approach has opened up for us to directly study human germ cells and reproductive development. These findings will help us to identify the unique mechanism(s) that leads to FF and EEA in order to find potential treatments.

OBJECTIVE AND RATIONALE

The goal of this review is to compile current genetic knowledge related to FF and EEA, clarifying the mechanisms involved and providing clues for clinical diagnosis and treatment.

SEARCH METHODS

PubMed was used to search for relevant research articles and reviews, primarily focusing on English-language publications from January 1978 to June 2023. The search terms included fertilization failure, early embryonic arrest, genetic, epigenetic, whole-exome sequencing, DNA methylation, chromosome, non-coding RNA, and other related keywords. Additional studies were identified by searching reference lists. This review primarily focuses on research conducted in humans. However, it also incorporates relevant data from animal models when applicable. The results were presented descriptively, and individual study quality was not assessed.

OUTCOMES

A total of 233 relevant articles were included in the final review, from 3925 records identified initially. The review provides an overview of genetic factors and mechanisms involved in the human reproductive process. The genetic mutations and other genetic mechanisms of FF and EEA were systematically reviewed, for example, globozoospermia, oocyte activation failure, maternal effect gene mutations, zygotic genome activation abnormalities, chromosome abnormalities, and epigenetic abnormalities. Additionally, the review summarizes progress in treatments for different gene defects, offering new insights for clinical diagnosis and treatment.

WIDER IMPLICATIONS

The information provided in this review will facilitate the development of more accurate molecular screening tools for diagnosing infertility using genetic markers and networks in human reproductive development. The findings will also help guide clinical practice by identifying appropriate interventions based on specific gene mutations. For example, when an individual has obvious gene mutations related to FF, ICSI is recommended instead of IVF. However, in the case of genetic defects such as phospholipase C zeta1 (PLCZ1), actin-like7A (ACTL7A), actin-like 9 (ACTL9), and IQ motif-containing N (IQCN), ICSI may also fail to fertilize. We can consider artificial oocyte activation technology with ICSI to improve fertilization rate and reduce monetary and time costs. In the future, fertility is expected to be improved or restored by interfering with or supplementing the relevant genes.

PADI6: What we know about the elusive fifth member of the peptidyl arginine deiminase family

Peptidyl arginine deiminase 6 (PADI6) is a maternal factor that is vital for early embryonic development. Deletion and mutations of its encoding gene in female mice or women lead to early embryonic developmental arrest, female infertility, maternal imprinting defects and hyperproliferation of the trophoblast. PADI6 is the fifth and least well-characterized member of the peptidyl arginine deiminases (PADIs), which catalyse the post-translational conversion of arginine to citrulline. It is less conserved than the other PADIs, and currently has no reported catalytic activity. While there are many suggested functions of PADI6 in the early mouse embryo, including in embryonic genome activation, cytoplasmic lattice formation, maternal mRNA and ribosome regulation, and organelle distribution, the molecular mechanisms of its function remain unknown. In this review, we discuss what is known about the function of PADI6 and highlight key outstanding questions that must be answered if we are to understand the crucial role it plays in early embryo development and female fertility. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.

Genetic variants underlying developmental arrests in human preimplantation embryos

Developmental arrest in preimplantation embryos is one of the major causes of assisted reproduction failure. It is briefly defined as a delay or a failure of embryonic development in producing viable embryos during ART cycles. Permanent or partial developmental arrest can be observed in the human embryos from one-cell to blastocyst stages. These arrests mainly arise from different molecular biological defects, including epigenetic disturbances, ART processes, and genetic variants. Embryonic arrests were found to be associated with a number of variants in the genes playing key roles in embryonic genome activation, mitotic divisions, subcortical maternal complex formation, maternal mRNA clearance, repairing DNA damage, transcriptional, and translational controls. In this review, the biological impacts of these variants are comprehensively evaluated in the light of existing studies. The creation of diagnostic gene panels and potential ways of preventing developmental arrests to obtain competent embryos are also discussed.

Embryonic arrest: causes and implications

PURPOSE OF REVIEW

Embryonic arrest is a key determinant of the number of euploid blastocysts obtained after IVF. Here, we review factors that are implicated in the developmental arrest of preimplantation embryos and their relevance for assisted reproduction outcomes.

RECENT FINDINGS

Among the treatment options available to infertile women, IVF is the one associated with most favorable outcomes. The cumulative pregnancy rates in women undergoing IVF are determined by aneuploidy rate (age), ovarian response to stimulation (ovarian reserve), and the rate of embryo developmental arrest. Mutations in maternal effect genes, especially those encoding for subcortical maternal complex, have been implicated in human embryo developmental arrest. In addition, perturbation of biological processes, such as mitochondrial unfolded protein response and long noncoding RNA regulatory pathways, may play a role. However, how each of these factors contributes to embryos' arrest in different cohorts and age groups has not been determined.

SUMMARY

Arrest of human embryos during preimplantation development is a common occurrence and is partly responsible for the limited number of euploid blastocysts obtained in assisted reproduction cycles. Although genetic and metabolic causes have been implicated, the mechanisms responsible for human embryo developmental arrest remain poorly characterized.

NLRP7 participates in the human subcortical maternal complex and its variants cause female infertility characterized by early embryo arrest

Successful human reproduction requires normal oocyte maturation, fertilization, and early embryo development. Early embryo arrest is a common phenomenon leading to female infertility, but the genetic basis is largely unknown. NLR family pyrin domain-containing 7 (NLRP7) is a member of the NLRP subfamily. Previous studies have shown that variants of NLRP7 are one of the crucial causes of female recurrent hydatidiform mole, but whether NLRP7 variants can directly affect early embryo development is unclear. We performed whole-exome sequencing in patients who experienced early embryo arrest, and five heterozygous variants (c.251G > A, c.1258G > A, c.1441G > A, c. 2227G > A, c.2323C > T) of NLRP7 were identified in affected individuals. Plasmids of NLRP7 and subcortical maternal complex components were overexpressed in 293 T cells, and Co-IP experiments showed that NLRP7 interacted with NLRP5, TLE6, PADI6, NLRP2, KHDC3L, OOEP, and ZBED3. Injecting complementary RNAs in mouse oocytes and early embryos showed that NLRP7 variants influenced the oocyte quality and some of the variants significantly affected early embryo development. These findings contribute to our understanding of the role of NLRP7 in human early embryo development and provide a new genetic marker for clinical early embryo arrest patients. KEY MESSAGES: Five heterozygous variants of NLRP7 (c.1441G > A; 2227G > A; c.251G > A; c.1258G > A; c.2323C > T) were identified in five infertile patients who experienced early embryo arrest. NLRP7 is a component of human subcortical maternal complex. NLRP7 variants lead to poor quality of oocytes and early embryo development arrest. This study provides a new genetic marker for clinical early embryo arrest patients.

A complex heterozygous mutation in PADI6 causes early embryo arrest: A case report

Background: The PADI6 gene is a component of the subcortical maternal effect complex (SCMC). Mutations in the PADI6 gene, which was the first gene discovered to impact the activation process of the human embryonic genome, have been shown to induce early embryo arrest. Case: A 29-year-old lady with primary infertility underwent in vitro fertilization embryo transfer (IVF-ET) for tubal reasons, who had normal hormone levels and ovarian reserve. A Progestin-Primed Ovarian Stimulation (PPOS) protocol of Ovarian stimulation with IVF was performed. The total of Gonadotropin (Gn) stimulation with u-FSH was 2100 IU, which lasted for 10 days. When three follicles measuring less than 18 mm in diameter were seen, r-hCG 250 ug and triptorelin acetate 0.2 mg were injected to trigger oocyte maturation. Nineteen oocytes (including thirteen MII oocytes) were picked up 37 h after the trigger, and seven of these were normal fertilized. Unfortunately, these many embryos were stopped at the 1- or 2-cell stage, hence this infertile patient's IVF treatment won't result in an embryo transfer. Using whole-exome sequencing, a complex heterozygous mutation in PADI6 was discovered: c. 1247T>C [p.Ile416Thr] in exon 12 of PADI6, and c. 2009_2010del [p.Glu670GlyfsTer48] in exon 17 of PADI6. Conclusion: We found a complex heterozygous mutation in the PADI6 gene (c. 1247T>C; c. 2009_2010del) that caused embryos were arrested at the 1- or 2- cell stage. The discovery in this patient adds to the evidence showing the PADI6 gene mutation causes early embryo arrest in humans.

Role of the PADI family in inflammatory autoimmune diseases and cancers: A systematic review

The peptidyl arginine deiminase (PADI) family is a calcium ion-dependent group of isozymes with sequence similarity that catalyze the citrullination of proteins. Histones can serve as the target substrate of PADI family isozymes, and therefore, the PADI family is involved in NETosis and the secretion of inflammatory cytokines. Thus, the PADI family is associated with the development of inflammatory autoimmune diseases and cancer, reproductive development, and other related diseases. In this review, we systematically discuss the role of the PADI family in the pathogenesis of various diseases based on studies from the past decade to provide a reference for future research.

Peptidylarginine deiminase enzymes and citrullinated proteins in female reproductive physiology and associated diseases†

Citrullination, the post-translational modification of arginine residues, is catalyzed by the four catalytically active peptidylarginine deiminase (PAD or PADI) isozymes and alters charge to affect target protein structure and function. PADs were initially characterized in rodent uteri and, since then, have been described in other female tissues including ovaries, breast, and the lactotrope and gonadotrope cells of the anterior pituitary gland. In these tissues and cells, estrogen robustly stimulates PAD expression resulting in changes in levels over the course of the female reproductive cycle. The best-characterized targets for PADs are arginine residues in histone tails, which, when citrullinated, alter chromatin structure and gene expression. Methodological advances have allowed for the identification of tissue-specific citrullinomes, which reveal that PADs citrullinate a wide range of enzymes and structural proteins to alter cell function. In contrast to their important physiological roles, PADs and citrullinated proteins are also involved in several female-specific diseases including autoimmune disorders and reproductive cancers. Herein, we review current knowledge regarding PAD expression and function and highlight the role of protein citrullination in both normal female reproductive tissues and associated diseases.

Common dysmorphic oocytes and embryos in assisted reproductive technology laboratory in association with gene alternations

Amorphic or defected oocytes and embryos are commonly observed in assisted reproductive technology (ART) laboratories. It is believed that a proper gene expression at each stage of embryo development contributes to the possibility of a decent-quality embryo leading to successful implantation. Many studies reported that several defects in embryo morphology are associated with gene expressions during in vitro fertilization (IVF) treatment. There is lacking literature review on summarizing common morphological defects about gene alternations. In this review, we summarized the current literature. We selected 64 genes that have been reported to be involved in embryo morphological abnormalities in animals and humans, 30 of which were identified in humans and might be the causes of embryonic changes. Five papers focusing on associations of multiple gene expressions and embryo abnormalities using RNA transcriptomes were also included during the search. We have also reviewed our time-lapse image database with over 3000 oocytes/embryos to show morphological defects possibly related to gene alternations reported previously in the literature. This holistic review can better understand the associations between gene alternations and morphological changes. It is also beneficial to select important biomarkers with strong evidence in IVF practice and reveal their potential application in embryo selection. Also, identifying genes may help patients with genetic disorders avoid unnecessary treatments by providing preimplantation genetic testing for monogenic/single gene defects (PGT-M), reduce embryo replacements by less potential, and help scientists develop new methods for oocyte/embryo research in the near future.

Genetics of Oocyte Maturation Defects and Early Embryo Development Arrest

Various pathogenic factors can lead to oogenesis failure and seriously affect both female reproductive health and fertility. Genetic factors play an important role in folliculogenesis and oocyte maturation but still need to be clarified. Oocyte maturation is a well-organized complex process, regulated by a large number of genes. Pathogenic variants in these genes as well as aneuploidy, defects in mitochondrial genome, and other genetic and epigenetic factors can result in unexplained infertility, early pregnancy loss, and recurrent failures of IVF/ICSI programs due to poor ovarian response to stimulation, oocyte maturation arrest, poor gamete quality, fertilization failure, or early embryonic developmental arrest. In this paper, we review the main genes, as well as provide a description of the defects in the mitochondrial genome, associated with female infertility.

A novel variant in TLE6 is associated with embryonic developmental arrest (EDA) in familial female infertility

This study aims to identify genetic causes of familial female infertility characterized by embryonic developmental arrest (EDA) and repeated implantation failure (RIF) with oocyte donation IVF cycle. We used Whole-exome sequencing and Sanger validation to find causative genes in an Iranian consanguineous family that had 3 infertile daughters, 4 fertile daughters, and 2 fertile sons. All patients in this consanguineous family exhibited typical manifestations of unexplained RIF and EDA. Genetic analysis identified a homozygous missense variant (c.G1054C:p.G352R) in exon 13 of the TLE6 gene that cosegregated with the EDA phenotype in an autosomal recessive pattern. Other members of the family, the gene carriers, remain clinically asymptomatic and fertile. Our findings identify a novel nonsynonymous variant, c.G1054C:p.G352R, in the TLE6 gene within a consanguineous Iranian family with autosomal-recessive female infertility and broaden the genetic spectrum of TLE6-associated EDA.

A novel homozygous mutation in the PADI6 gene causes early embryo arrest

Background

It has been proved that mutations in the PADI6 gene can cause early embryo arrest. This study describes a newly discovered mutation in PADI6 that expands the genetic spectrum of early embryo arrest.

Methods

Peripheral blood of a patient diagnosed with early embryo arrest was collected for whole-exome sequencing. Sanger sequencing was performed to confirm this mutation. The effects of the variant were investigated in human embryonic kidney 293T (HEK293T) cells using western blotting, real-time quantitative polymerase chain reaction, and immunofluorescence.

Results

A novel homozygous mutation in PADI6 was identified in the proband. The patient carried a frameshift insertion mutation c.558dupA (p.Thr187Asnfs*48), which was located in the protein arginine deiminase middle domain. The variant destroyed PADI6 protein expression and reduced PADI6 mRNA expression in HEK293T cells.

Conclusions

The newly identified mutation in PADI6 accounts for early embryo arrest. It expands the spectrum of genetic causes and phenotypes of infertility in humans. These findings also provide an additional possible diagnostic marker for patients with recurrent in vitro fertilization/intracytoplasmic sperm injection failure.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12978-022-01495-7.

Some infertile patients experience multiple in vitro fertilization/intracytoplasmic sperm injection (IVF/ICSI) failure owing to recurrent early embryo arrest. However, the underlying mechanisms remain largely unknown. Due to the development of whole-exome sequencing, early embryo arrest has been confirmed as a type of Mendelian disease. This study aimed to identify the genetic cause of early embryo arrest in patients and to expand the genetic spectrum. Furthermore, it can help doctors offer better suggestions to such patients and prevent patients from suffering from multiple IVF/ICSI failures.

Novel Homozygous PADI6 Variants in Infertile Females with Early Embryonic Arrest

Early embryonic arrest denotes premature termination of development in preimplantation embryos, which is one of the major phenotypes of recurrent assisted reproduction failure. Padi6 is proven to be a member of the subcortical maternal complex (SCMC) in mice, which is essential in oocyte maturation and embryogenesis. We and other groups previously found that biallelic mutations in PADI6 caused female infertility manifesting as early embryonic arrest. In this study, we identified two novel homozygous variants (p.Cys163Arg, and p. Trp475*) of PADI6 in two infertile patients from a cohort of 75 females with the phenotype of early embryonic arrest. An in vitro expression study indicated severe decrease of PADI6, which might destruct the stability of SCMC. Our study expands the mutational spectrum of PADI6 and further supports the causality between PADI6 mutations and female infertility.

Molecular tools for the genomic assessment of oocyte’s reproductive competence

The most important factor associated with oocytes' developmental competence has been widely identified as the presence of chromosomal abnormalities. However, growing application of genome-wide sequencing (GS) in population diagnostics has enabled the identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting IVF outcomes and reproductive fitness. Indeed, GS analysis in families with history of isolated infertility has recently led to the discovery of new genes and variants involved in specific human infertility endophenotypes that impact the availability and the functionality of female gametes by altering unique mechanisms necessary for oocyte maturation and early embryo development. Ongoing advancements in analytical and bioinformatic pipelines for the study of the genetic determinants of oocyte competence may provide the biological evidence required not only for improving the diagnosis of isolated female infertility but also for the development of novel preventive and therapeutic approaches for reproductive failure. Here, we provide an updated discussion and review of the progresses made in preconception genomic medicine in the identification of genetic factors associated with oocyte availability, function, and competence.

Novel biallelic mutations in PADI6 in patients with early embryonic arrest

Peptidyl arginine deiminase, type VI (PADI6) is a member of the subcortical maternal complex (SCMC), which plays vital roles in mammalian embryogenesis. Most mutations in SCMC members have been reported to cause human embryonic arrest, and a total of 15 mutations in PADI6 have been shown to be responsible for early embryonic arrest according to previous studies. However, the genetic factors behind this phenotype remain to be understood in further detail. Here, we identified 13 novel mutations and 4 previously reported mutations of PADI6 in 14 patients who were diagnosed with abnormal embryonic development caused by early arrest, embryonic fragmentation, and recurrent implantation failure. Most of the mutations were predicted by in silico analysis to be deleterious or damaging to the function of PADI6. In addition, the total and East Asian population frequencies of the mutations were low or absent in the gnomAD database. Our study expands the mutational spectrum in PADI6 and will provide precise targets for genetic counseling in the future.

Gene mutations associated with fertilization failure after in vitro fertilization/intracytoplasmic sperm injection

Fertilization failure during assisted reproductive technologies (ART) is often unpredictable, as this failure is encountered only after in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) have been performed. The etiology of fertilization failure remains elusive. More and more mutations of genes are found to be involved in human fertilization failure in infertile patients as high throughput sequencing techniques are becoming widely applied. In this review, the mutations of nine important genes expressed in sperm or oocytes, PLCZ1, ACTL7A, ACTL9, DNAH17, WEE2, TUBB8, NLRP5, ZP2, and TLE6, were summarized and discussed. These abnormalities mainly have shown Mendelian patterns of inheritance, including dominant and recessive inheritance, although de novo mutations were present in some cases. The review revealed the crucial roles of each reported gene in the fertilization process and summarized all known mutations and their corresponding phenotypes. The review suggested the mutations might become promising targets for precision treatments in reproductive medicine. Moreover, our work will provide some helpful clues for genetic counseling, risk prediction, and optimizing clinical treatments for human infertility by supplying the useful and timely information on the genetic causes leading to fertilization failure.