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Post: The ‘Omics In Male Fertility Diagnostics


The 'Omics In Male Fertility Diagnostics

The emerging fields of epigenomics, genomics, transcriptomics, proteomics, and metabolomics have added to the ability to diagnose and treat male infertility by uncovering the various biological processes involved in this condition.

Image Credit: Shidlovski/


Infertility is a problem for one in seven couples of reproductive age, and a male factor is implicated in half the cases. The advent of sophisticated assisted reproduction techniques (ART) has not solved it due largely to the severely limited knowledge of the various components of infertility. Most treatment approaches today consist of repeating the same therapy repeatedly, hoping for a better outcome, in lieu of actual knowledge of what is going wrong – though this could apply to most modern treatments for most long-term medical conditions.Recommended:

The use of OMICS technologies has allowed scientists to gain more knowledge about the multiple factors that may be at fault in male infertility, in a short time and at a relatively low cost. Among these, epigenomics studies heritable changes in gene expression in the absence of actual changes in the gene sequence itself.

Male Age and Fertility

Genomics relates to the full set of gene expression in a cell type or tissue, while proteomics deals with all protein-level changes occurring from a single genome. Metabolomics examines the concentration of various metabolites and the changes in these levels while keeping the environment in a predefined state.

All types of biological compounds can be studied using these platforms, thus allowing scientists to evaluate the genetic blueprint, its expression, the information encoded and translated into protein form, as well as the results of such protein expression.


Genomics began with karyotyping, looking for genetic factors related to infertility. The finding that some regions of the Y chromosome were deleted in cases of spermatogenesis failure was another important milestone. Again, genomics helps diagnose cases of congenital bilateral absence of the vas deferens (CBAVD), a condition occurring in one in a hundred infertile men and due to mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene resulting in obstructive azoospermia.

The finding of abnormal chromosomes in infertile men at up to ten times higher frequency than in other men is striking. Up to 6 in a hundred men with primary infertility will have major chromosomal anomalies and over 2 in a hundred men with secondary infertility. Chromosomal polymorphism has also been found to occur in a high percentage of infertile men, especially in the sex chromosomes.

Aneuploidy of sperm cells can be identified with fluorescent in situ hybridization (FISH), a tool commonly used to detect specific regions of the chromosome linked to male infertility. Though very expensive and disabling the sperm used for any use in ART, the knowledge of such chromosomal ploidy defects could help patients decide whether to proceed with intracytoplasmic sperm injection

Along with a sperm count and motility criteria, many chromosomes containing redundant or polymorphic sequences are linked to severe infertility and the paucity of progressively motile spermatozoa in the processed specimen. This may indicate that such sequences could harbor genes required for sperm function.


Epigenomics suggests that male infertility could cause epigenetic effects in pregnancies via ART. Another finding is the impaired replacement of DNA histones by protamines causing abnormal localization of histones in infertile men. Such studies have also shown possibly damaging effects produced during the processes of ART, such as sumoylation, along with methylation changes due to endocrine-disrupting chemicals (EDCs) that disrupt spermatogenesis.

Besides environmental EDCs, obesity and diabetes are also associated with male infertility via epigenetic sperm changes. Post-transcriptional epigenetics could also contribute to this issue via the modulation of protein translation by short non-coding ribonucleic acids (sRNAs), including microRNAs. Expressed in germ cells and taking part in sperm production, these sRNAs are often altered in expression in infertile or subfertile men.

Stress can alter the sperm sRNA profile of sperm via the packaging of such altered molecules into the epididymosomes that help regulate the contents of the lumen of the epididymis, where sperm maturation occurs along with epigenetic changes. Testicular sperm may be spared the adverse impact of such abnormal sRNA on fertilization and future events.  

DNA methylation and gene transcription patterns may be predictive of the success rates of some ART procedures, and several epigenetic markers on sperm cells have been associated with sperm abnormalities.


Proteomics has shown more than 6,000 sperm proteins within multiple functional pathways, localized in regions linked to their site of origin in the male gonads. It has been possible to establish the proteome signatures in normal semen samples using stable-protein pairs. Still, a very variable picture is obtained from infertile men due to the primitive system now in use to classify the phenotypic features of male infertility.

For instance, in men with asthenozoospermia, estrogen production, structural and signaling/regulatory proteins in the sperm are all affected in various combinations. Similar alterations are found in other proteins in other parts of the male reproductive tract, including the seminal plasma and testicular tissue.


Metabolomics is sometimes considered the most likely to reflect the actual state of function of the phenotype of a cell or tissue compared to the other omics described above. One such change is the generation of high levels of reactive oxygen species (ROS) in infertile men, linked to impaired sperm morphology, low concentration and poor motility, and higher levels of DNA fragmentation. ROS could thus serve as biomarkers of infertility.

One study distinguished patients with and without sperm production and subclassified the latter into those with impaired spermatogenesis, arrest of sperm maturation, and Sertoli-only syndrome, using only ROS. Other scientists have used gas chromatography-mass spectrometry (GC-MS) for metabolomic profiling to differentiate non-obstructive azoospermia with and without sperm.


Despite the promising initial findings of metabolomics and proteomics in classifying types of male infertility, much remains to be done before clinically valid profile panels become available. Omics is unquestionably a target of importance for the study of male infertility without overly invasive testing and may help screen patients for counseling and selection of the right therapies. With a better knowledge base, it will eventually become possible to use omics to make valuable clinical decisions.


  • Egea, R. R. et al. (2014). OMICS: Current and Future Perspectives in Reproductive Medicine and Technology. Journal of Human Reproductive Sciences.
  • Krzastek, S. C. et al. (2019). Future Diagnostics in Male Infertility: Genomics, Epigenetics, Metabolomics and Proteomics. Translational Andrology and Urology.

Further Reading

  • All Fertility Content
  • Fertility and Age
  • Male Age and Fertility

Last Updated: May 5, 2022

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.

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