Omics and Male Infertility: Highlighting the Application of Transcriptomic Data.

Temidayo S Omolaoye,Victor A Omolaoye,Richard K Kandasamy,Stefan S Du Plessis,Mahmood Yaseen Hachim

doi:10.3390/life12020280

Abstract

Male infertility is a multifaceted disorder affecting approximately 50% of male partners in infertile couples. Over the years, male infertility has been diagnosed mainly through semen analysis, hormone evaluations, medical records and physical examinations, which of course are fundamental, but yet inefficient, because 30% of male infertility cases remain idiopathic. This dilemmatic status of the unknown needs to be addressed with more sophisticated and result-driven technologies and/or techniques. Genetic alterations have been linked with male infertility, thereby unveiling the practicality of investigating this disorder from the “omics” perspective. Omics aims at analyzing the structure and functions of a whole constituent of a given biological function at different levels, including the molecular gene level (genomics), transcript level (transcriptomics), protein level (proteomics) and metabolites level (metabolomics). In the current study, an overview of the four branches of omics and their roles in male infertility are briefly discussed; the potential usefulness of assessing transcriptomic data to understand this pathology is also elucidated. After assessing the publicly obtainable transcriptomic data for datasets on male infertility, a total of 1385 datasets were retrieved, of which 10 datasets met the inclusion criteria and were used for further analysis. These datasets were classified into groups according to the disease or cause of male infertility. The groups include non-obstructive azoospermia (NOA), obstructive azoospermia (OA), non-obstructive and obstructive azoospermia (NOA and OA), spermatogenic dysfunction, sperm dysfunction, and Y chromosome microdeletion. Findings revealed that 8 genes (LDHC, PDHA2, TNP1, TNP2, ODF1, ODF2, SPINK2, PCDHB3) were commonly differentially expressed between all disease groups. Likewise, 56 genes were common between NOA versus NOA and OA (ADAD1, BANF2, BCL2L14, C12orf50, C20orf173, C22orf23, C6orf99, C9orf131, C9orf24, CABS1, CAPZA3, CCDC187, CCDC54, CDKN3, CEP170, CFAP206, CRISP2, CT83, CXorf65, FAM209A, FAM71F1, FAM81B, GALNTL5, GTSF1, H1FNT, HEMGN, HMGB4, KIF2B, LDHC, LOC441601, LYZL2, ODF1, ODF2, PCDHB3, PDHA2, PGK2, PIH1D2, PLCZ1, PROCA1, RIMBP3, ROPN1L, SHCBP1L, SMCP, SPATA16, SPATA19, SPINK2, TEX33, TKTL2, TMCO2, TMCO5A, TNP1, TNP2, TSPAN16, TSSK1B, TTLL2, UBQLN3). These genes, particularly the above-mentioned 8 genes, are involved in diverse biological processes such as germ cell development, spermatid development, spermatid differentiation, regulation of proteolysis, spermatogenesis and metabolic processes. Owing to the stage-specific expression of these genes, any mal-expression can ultimately lead to male infertility. Therefore, currently available data on all branches of omics relating to male fertility can be used to identify biomarkers for diagnosing male infertility, which can potentially help in unravelling some idiopathic cases.

Highlights

Infertility affects 15% of couples of reproductive age, from which, 50% of the total cases are attributed to the male factor [1], and of these, about 50% are idiopathic
The small non-coding RNAs (ncRNAs) are present in the sperm nucleus and represent another mechanism of epigenetic control
The current study aims to give an overview of the available evidence on omics and male infertility and to utilize publicly available transcriptomic data to identify the different pathways and biological processes that may be involved in the pathogenesis of male infertility

Summary

Introduction

Infertility affects 15% of couples of reproductive age, from which, 50% of the total cases are attributed to the male factor [1], and of these, about 50% are idiopathic. Making the investigation of the role of epigenetic and genetic modifications in the etiologies of male infertility essential. Epigenetics is the study of heritable modifications in gene function that cannot be explained by changes in DNA sequence [11]. Epigenetic changes affect gene expression in histone tail modifications at some specific amino acid residues. A post-translational modification of these histone proteins serves as the epigenetic mediator in the sperm cell which regulates the gene expression. Epigenetic changes may affect DNA methylation at the CpG site, and the small non-coding RNAs (ncRNAs) and chromatin remodeling. The collective investigation of hormonal dysfunction, epigenetic modifications and genetic alteration has provided an approach to deeply assess male infertility, starting from the formation of germ cells

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