Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics

From oxidative imbalance to compromised standard sperm parameters: Toxicological aspect of phthalate esters on spermatozoa

The exponential rise in global male infertility and subfertility-related issues raises severe concern. One of the major contributors is phthalate esters, typical endocrine disruptors affecting millions of lives. The inevitable exposure to phthalates due to their universal application as plasticizers leaves the human population vulnerable to this silent threat. This review explicitly deals with the spermiotoxic effects of different phthalate esters on in vivo and in vitro models and on surveyed human populations to find the most plausible link between global usage of phthalates and poor sperm health. As the free radicals in spermatozoa are prerequisites for their standard structure and functioning, the precise regulation and phthalate-mediated impairment of pro-oxidant:anti-oxidant balance with subsequent loss of structural and functional integrity have also been critically discussed. Furthermore, we also provided future directives, which, if addressed, will fill the still-existing lacunae in phthalate-mediated male reproductive toxicity research.

Quantitative phosphoproteomics reveals GSK3A substrate network is involved in the cryodamage of sperm motility

During sperm cryopreservation, the most significant phenotype of cryodamage is the decrease in sperm motility. Several proteomics studies have already been performed to search for key regulators at the protein level. However, sperm functions are known to be highly regulated by phosphorylation signaling. Here, we constructed a quantitative phosphoproteome to investigate the expression change of phosphorylated sites during sperm cryopreservation. A total of 3107 phosphorylated sites are identified and 848 of them are found to be significantly differentially expressed (DE). Bioinformatics analysis showed that the corresponding genes of these regulated sites are highly associated with sperm motility, providing a connection between the molecular basis and the phenotype of cryodamage. We then performed kinase enrichment analysis and successfully identified glycogen synthase kinase-3α (GSK3A) as the key kinase that may play an important role in the regulation of sperm motility. We further constructed a GSK3A centric network that could help us better understand the molecular mechanism of cryodamage in sperm motility. Finally, we also verified that GSK3A was abnormally activated during this process. The presented phosphoproteome and functional associations provide abundant research resources for us to learn the regulation of sperm functions, as well as to optimize the cryoprotectant for sperm cryopreservation.

Proteomics and metabolomics - Current and future perspectives in clinical andrology

Proteomics and metabolomics are emerging as promising tools to investigate the molecular mechanisms associated with male infertility. Proteins and metabolites play a pivotal role in regulating the molecular pathways associated with physiological functions of spermatozoa. Semen analysis, physical examination and laboratory work up cannot identify the etiology of infertility in 30%-40% of cases, which are classified as idiopathic. Therefore, the application of proteomics and metabolomics in the field of andrology will aid to overcome the limitations of the standard semen analysis. Understanding the molecular pathways associated with male infertility will help in planning ad hoc treatments, contributing to the clinical management of infertile patients. In this review, proteomics and metabolomics studies on spermatozoa and seminal plasma are discussed with a focus on molecular biomarkers associated with male infertility-related conditions.

Proteomic Analyses of Human Sperm Cells: Understanding the Role of Proteins and Molecular Pathways Affecting Male Reproductive Health

Human sperm proteomics research has gained increasing attention lately, which provides complete information about the functional state of the spermatozoa. Changes in the sperm proteome are evident in several male infertility associated conditions. Global proteomic tools, such as liquid chromatography tandem mass spectrometry and matrix-assisted laser desorption/ionization time-of-flight, are used to profile the sperm proteins to identify the molecular pathways that are defective in infertile men. This review discusses the use of proteomic techniques to analyze the spermatozoa proteome. It also highlights the general steps involved in global proteomic approaches including bioinformatic analysis of the sperm proteomic data. Also, we have presented the findings of major proteomic studies and possible biomarkers in the diagnosis and therapeutics of male infertility. Extensive research on sperm proteome will help in understanding the role of fertility associated sperm proteins. Validation of the sperm proteins as biomarkers in different male infertility conditions may aid the physician in better clinical management.

A Critical Review of Proteomic Studies in Gestational Diabetes Mellitus

Gestational diabetes mellitus is a progressive and complex pregnancy complication, which threatens both maternal and fetal health. It is urgent to screen for specific biomarkers for early diagnosis and precise treatment, as well as to identify key moleculars to better understand the pathogenic mechanisms. In the present review, we comprehensively summarized recent studies of gestational diabetes using mass spectrometry-based proteomic technologies. Focused on the entire experimental design and proteomic results, we showed that these studies have covered a broad range of research contents in terms of sampling time, sample types, and outcome associations. Although most of the studies only stayed in the stage of initial discovery, several proteins were further verified to be efficient for disease diagnosis. Functional analysis of all the combined significant proteins also showed that a small number of proteins are known to be involved in the regulation of insulin or indirect signaling pathways. However, many factors such as diagnostic criteria, sample processing, proteomic method, and statistical method can greatly affect the identification of reproducible and reliable protein candidates. Thus, we further provided constructive suggestions and recommendations for carrying out proteomic or follow-up studies of gestational diabetes or other pregnancy complications in the future.

Proteomics analysis of asthenozoospermia and identification of glucose-6-phosphate isomerase as an important enzyme for sperm motility

Asthenozoospermia, in which sperm motility is affected, is one of the primary causes of male infertility. However, the exact mechanism responsible for the defective motility remains unknown. It is important to identify the precise proteins or pathways involved in sperm motility. The present study analyzed five asthenozoospermic sperm samples and five healthy controls using TMT-based quantitative method and identified 152 differentially expressed proteins, with 84 upregulated and 68 downregulated in asthenozoospermia. Four proteins (GPI, MDH1, PGAM1 and PGAM2) were found in several over-represented energy metabolism pathways using bioinformatics analysis. Glucose-6-phosphate isomerase (GPI), a rate-limiting enzyme converting glucose-6-phosphate to fructose-6-phosphate, was found to be significantly decreased in asthenozoospermia by Western blotting and ELISA on an extended sample size. Furthermore, substitution of glucose with fructose-6-phosphate significantly promoted asthenozoospermic sperm motility in vitro. Taken together, our results suggest that the poor motility of sperm in asthenozoospermia may partly result from defects in GPI-associated energy metabolism. SIGNIFICANCE: To identify the key proteins or pathways involved in sperm motility, the accurate TMT-based quantitative method was applied to characterize protein profiles of asthenozoospermic sperm. GPI, an enzyme involved in energy metabolism, was found to be differentially abundant, and validated by extended sample analysis. The supplement of the product of GPI, fructose-6-phosphate, could significantly improve sperm motility. Our study could provide new insights into the molecular basis of sperm motility and the improvement of motility in asthenozoospermia.

Quantitative Proteomic Analysis of Human Seminal Plasma from Normozoospermic and Asthenozoospermic Individuals

Seminal plasma is a complex mixture of secretions from various glands in the male genital tract. Compared to sperm cells, it contains important proteins that are both directly and indirectly associated with sperm motility. Here, we constructed quantitative proteomes of human seminal plasma from three normozoospermic and asthenozoospermic individuals. A total of 524 proteins were identified, and 366 of them were found to be quantified in all six samples. We first investigated the absolute expression features of these proteins and found that the variations of protein identification among different samples and other published datasets were mainly due to some lowly expressed proteins. By integration of various proteomic datasets and bioinformatics databases, we comprehensively annotated the biological functions, physiological originations, and disease associations of these proteins. We found that our dataset could benefit the studies of both male infertility and other male diseases. Finally, based on the relative expression values determined by chemical labeling, we identified a total of 29 differentially expressed proteins, which could be used as candidate targets for studying the molecular bases of sperm motility or developing precise diagnostic biomarkers of asthenozoospermia. We further successfully verified the expression trends of four representative proteins by Western blotting. Compared to a previous dataset based on label-free quantification, our results showed that most of the important proteins could be identified in the sample collected only once for each individual, providing the bases for personalized examination of seminal plasma proteins in clinic.

Proteomics of reproduction: Prospects and perspectives

In recent years, proteomics has been used widely in reproductive research in order to understand the molecular mechanisms related to gametes at the cellular level and the role of proteins involved in fertilization. Network and pathway analysis using bioinformatic tools have paved way to obtain a wider picture on the possible pathways associated with the key differentially expressed proteins (DEPs) and its implication in various infertility scenarios. A brief overview of advanced techniques and bioinformatic tools used for reproductive proteomics is presented. Key findings of proteomic-based studies on male and female reproduction are also presented. Furthermore, the chapter sheds light on the cellular pathways and potential biomarkers associated with male and female infertility. Proteomics coupled with bioinformatic analysis provides an ideal platform for non-invasive management of infertility in couples.

Bioinformatics Analysis of Transcriptomic Data Reveals Refined Functional Networks for the Self-Renewal of Mouse Spermatogonial Stem Cells

Spermatogonial stem cells (SSCs) are exquisitely regulated to reach a balance between proliferation and differentiation in the niche of seminiferous epithelium. Several extrinsic factors such as GDNF are reported to switch the transition, activating various intrinsic signaling pathways. Transcriptomics analysis could provide a comprehensive landscape of gene expression and regulation. Here, we reanalyzed a previously published transcriptome of two cell types (standing for self-renewing and differentiating SSCs correspondingly). First, we proposed a new parameter, the expression index, to sort the genes considering both absolute and relative expression levels. Using a dynamic statistical model, we identified a list of 1119 candidate genes for SSC self-renewal with the best enrichment of canonical markers. Finally, based on interaction relations, we further optimized the list and constructed a refined network containing integrated information of interactions, expression alternations, biological functions, and disease associations. Further annotation of the 521 refined genes involved in the network revealed an enrichment of well-studied signaling pathways. We believe that the refined network could help us better understand the regulation of SSCs' fates, as well as find novel regulators or targets for SSC self-renewal or preservation of male fertility.

Update on the proteomics of male infertility: A systematic review

Objective

To assess the role of differentially expressed proteins as a resource for potential biomarker identification of infertility, as male infertility is of rising concern in reproductive medicine and evidence pertaining to its aetiology at a molecular level particularly proteomic as spermatozoa lack transcription and translation. Proteomics is considered as a major field in molecular biology to validate the target proteins in a pathophysiological state. Differential expression analysis of sperm proteins in infertile men and bioinformatics analysis offer information about their involvement in biological pathways.

Materials and methods

Literature search was performed on PubMed, Medline, and Science Direct databases using the keywords ‘sperm proteomics’ and ‘male infertility’. We also reviewed the relevant cross references of retrieved articles and included them in the review process. Articles written in any language other than English were excluded.

Results

Of 575 articles identified, preliminary screening for relevant studies eliminated 293 articles. At the next level of selection, from 282 studies only 80 articles related to male infertility condition met the selection criteria and were included in this review.

Conclusion

In this molecular era, sperm proteomics has created a platform for enhanced understanding of male reproductive physiology as a potential tool for identification of novel protein biomarkers related to sperm function in infertile men. Therefore, it is believed that proteomic biomarkers can overcome the gaps in information from conventional semen analysis that are of limited clinical utility.

The Glial Cell-Derived Neurotrophic Factor (GDNF)-responsive Phosphoprotein Landscape Identifies Raptor Phosphorylation Required for Spermatogonial Progenitor Cell Proliferation

Cytokine-dependent renewal of stem cells is a fundamental requisite for tissue homeostasis and regeneration. Spermatogonial progenitor cells (SPCs) including stem cells support life-long spermatogenesis and male fertility, but pivotal phosphorylation events that regulate fate decisions in SPCs remain unresolved. Here, we described a quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of SPCs following sustained stimulation with glial cell-derived neurotrophic factor (GDNF), an extrinsic factor supporting SPC proliferation. Stimulated SPCs contained 3382 identified phosphorylated proteins and 12141 phosphorylation sites. Of them, 325 differentially phosphorylated proteins and 570 phosphorylation sites triggered by GDNF were highly enriched for ERK1/2, GSK3, CDK1, and CDK5 phosphorylating motifs. We validated that inhibition of GDNF/ERK1/2-signaling impaired SPC proliferation and increased G2/M cell cycle arrest. Significantly, we found that proliferation of SPCs requires phosphorylation of the mTORC1 component Raptor at Ser⁸⁶³ Tissue-specific deletion of Raptor in mouse germline cells results in impaired spermatogenesis and progressive loss of spermatogonia, but in vitro increased phosphorylation of Raptor by raptor over-expression in SPCs induced a more rapidly growth of SPCs in culture. These findings implicate previously undescribed signaling networks in governing fate decision of SPCs, which is essential for the understanding of spermatogenesis and of potential consequences of pathogenic insult for male infertility.

Protein Bioinformatics Databases and Resources

Many publicly available data repositories and resources have been developed to support protein-related information management, data-driven hypothesis generation, and biological knowledge discovery. To help researchers quickly find the appropriate protein-related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.

The need to revisit published data: A concept and framework for complementary proteomics

Tandem proteomic strategies based on large-scale and high-resolution mass spectrometry have been widely applied in various biomedical studies. However, protein sequence databases and proteomic software are continuously updated. Proteomic studies should not be ended with a stable list of proteins. It is necessary and beneficial to regularly revise the results. Besides, the original proteomic studies usually focused on a limited aspect of protein information and valuable information may remain undiscovered in the raw spectra. Several studies have reported novel findings by reanalyzing previously published raw data. However, there are still no standard guidelines for comprehensive reanalysis. In the present study, we proposed the concept and draft framework for complementary proteomics, which are aimed to revise protein list or mine new discoveries by revisiting published data.

Quantitative phosphoproteomics analysis reveals a key role of insulin growth factor 1 receptor (IGF1R) tyrosine kinase in human sperm capacitation

One of the most important changes during sperm capacitation is the enhancement of tyrosine phosphorylation. However, the mechanisms of protein tyrosine phosphorylation during sperm capacitation are not well studied. We used label-free quantitative phosphoproteomics to investigate the overall phosphorylation events during sperm capacitation in humans and identified 231 sites with increased phosphorylation levels. Motif analysis using the NetworKIN algorithm revealed that the activity of tyrosine phosphorylation kinases insulin growth factor 1 receptor (IGF1R)/insulin receptor is significantly enriched among the up-regulated phosphorylation substrates during capacitation. Western blotting further confirmed inhibition of IGF1R with inhibitors GSK1904529A and NVP-AEW541, which inhibited the increase in tyrosine phosphorylation levels during sperm capacitation. Additionally, sperm hyperactivated motility was also inhibited by GSK1904529A and NVP-AEW541 but could be up-regulated by insulin growth factor 1, the ligand of IGF1R. Thus, the IGF1R-mediated tyrosine phosphorylation pathway may play important roles in the regulation of sperm capacitation in humans and could be a target for improvement in sperm functions in infertile men.

Impact of precise modulation of reactive oxygen species levels on spermatozoa proteins in infertile men

Background

Elevated levels of reactive oxygen species (ROS) are detected in 25% to 80% of infertile men. They are involved in the pathology of male infertility. Understanding the effect of increasing levels of ROS on the differential expression of sperm proteins is important to understand the cellular processes and or/pathways that may be implicated in male infertility. The aim of this study was to examine differentially expressed proteins (DEPs) in spermatozoa from patients with low, medium and high ROS levels.

Methods

A total of 42 infertile men presenting for infertility and 17 proven fertile men were enrolled in the study. ROS levels were measured by chemiluminescence assay. Infertile men were divided into Low (0- < 93 RLU/s/10⁶ sperm) (n = 11), Medium (>93-500 RLU/s/10⁶ sperm) (n = 17) and High ROS (>500 RLU/s/10⁶ sperm) group (n = 14). All fertile men had ROS levels between 4-50 RLU/s/10⁶ sperm. 4 subjects from fertile group and 4 each from the Low, Medium and High ROS were pooled. Protein extraction, protein estimation, gel separation of the proteins, in-gel digestion, LTQ-orbitrap elite hybrid mass spectrometry system was conducted. The DEPs, the cellular localization and pathways of DEPs involved were examined utilizing bioinformatics tools.

Results

1035 proteins were identified in the 3 groups by global proteomic analysis. Of these, 305 were DEPs. 51 were unique to the Low ROS group, 47 Medium ROS group and 104 were unique to the High ROS group. 6 DEPs were identified by Uniprot and DAVID that had distinct reproductive functions and they were expressed only in 3 ROS groups but not in the control.

Conclusions

We have for the first time demonstrated the presence of 6 DEPs with distinct reproductive functions only in men with low, medium or high ROS levels. These DEPs can serve as potential biomarkers of oxidative stress induced male infertility.

Electronic supplementary material

The online version of this article (doi:10.1186/1559-0275-12-4) contains supplementary material, which is available to authorized users.

Proteomics and integrative genomics for unraveling the mysteries of spermatogenesis: the strategies of a team

The strikingly complex structural organization of the mammalian testis in vivo creates particular difficulties for studies of its organization, function and regulation. These difficulties are particularly pronounced for investigations of the molecular communication networks within the seminiferous tubules that govern spermatogenesis. The use of classical molecular and cell biology approaches to unravel this complexity has proved problematic, due to difficulties in maintaining differentiated germ cells in vitro, in particular. The lack of a suitable testing ground has led to a greater reliance on high-quality proteomic and genomic analyses as a prelude to the in vitro antx1d in vivo testing of hypotheses. In this study, we highlight the options currently available for research, as used in our laboratory, in which proteomic and integrative genomic strategies are applied to the study of spermatogenesis in mammals. We will comment on results providing insight into the molecular mechanisms underlying normal and pathological spermatogenesis and new perspectives for the treatment of male infertility in humans. Finally, we will discuss the relevance of our strategies and the unexpected potential and perspectives they offer to teams involved in the study of male reproduction, within the framework of the Human Proteome Project.

SIGNIFICANCE

Integrative genomics is becoming a powerful strategy for discovering the biological significance hidden in proteomic datasets. This work introduces some of the integrative genomic concepts and works used by our team to gain new insight into mammalian spermatogenesis, a remarkably sophisticated process. We demonstrate the relevance of these integrative approaches to understand the cellular cross talks established between the somatic Sertoli cells and the germ cell lineage, within the seminiferous epithelium. Our work also contributes to new knowledge on the pathophysiology of testicular function, with promising clinical applications. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.

Sperm nuclear proteome and its epigenetic potential

The main function of the sperm cell is to transmit the paternal genetic message and epigenetic information to the embryo. Importantly, the majority of the genes in the sperm chromatin are highly condensed by protamines, whereas genes potentially needed in the initial stages of development are associated with histones, representing a form of epigenetic marking. However, so far little attention has been devoted to other sperm chromatin-associated proteins that, in addition to histones and protamines, may also have an epigenetic role. Therefore, with the goal of contributing to cover this subject we have compiled, reviewed and report a list of 581 chromatin or nuclear proteins described in the human sperm cell. Furthermore, we have analysed their Gene Ontology Biological Process enriched terms and have grouped them into different functional categories. Remarkably, we show that 56% of the sperm nuclear proteins have a potential epigenetic activity, being involved in at least one of the following functions: chromosome organization, chromatin organization, protein-DNA complex assembly, DNA packaging, gene expression, transcription, chromatin modification and histone modification. In addition, we have also included and compared the sperm cell proteomes of different model species, demonstrating the existence of common trends in the chromatin composition in the mammalian mature male gamete. Taken together, our analyses suggest that the mammalian sperm cell delivers to the offspring a rich combination of histone variants, transcription factors, chromatin-associated and chromatin-modifying proteins which have the potential to encode and transmit an extremely complex epigenetic information.