Sperm mosaicism: implications for genomic diversity and disease

Abstract

While sperm mosaicism has few consequences for men, the offspring and future generations are unwitting recipients of gonadal cell mutations, often yielding severe disease. Recent studies, fueled by emergent technologies, show that sperm mosaicism is a common source of de novo mutations (DNMs) that underlie severe pediatric disease as well as human genetic diversity. Sperm mosaicism can be divided into three types: Type I arises during sperm meiosis and is non-age dependent; Type II arises in spermatogonia and increases as men age; and Type III arises during paternal embryogenesis, spreads throughout the body, and contributes stably to sperm throughout life. Where Types I and II confer little risk of recurrence, Type III may confer identifiable risk to future offspring. These mutations are likely to be the single largest contributor to human genetic diversity. New sequencing approaches may leverage this framework to evaluate and reduce disease risk for future generations.

Keywords: advanced paternal age; human variation; primordial germ cells; sperm mosaicism; spermatogonial stem cells.

Figure 1.

Anatomy of the spermatogonial stem cell (SSC) niche. (A) Human testes contain a web of seminiferous tubules, which are the site of spermatogenesis. They connect to the epididymis and the ductus deferens (or vas deferens) as a portal to ejaculation. (B) Cross-section of a seminiferous tubule. SSCs proliferate and self-renew, producing spermatocytes, which undergo meiosis and, depending on their progression, are distinguished as primary or secondary. Following secondary meiotic division, spermatids differentiate into mature sperm (or spermatozoa) that will shed into the lumen of the seminiferous tubule prior to ejaculation.

Figure 2.

Temporal resolution of sperm mosaicism. (A) Sperm mosaic mutations can arise at any point during sperm lineage, starting from the zygote, before or after the establishment of the primordial germ cells (PGCs), which are the embryonic progenitors of spermatogonial stem cells (SSCs), or during spermatogenesis. We broadly distinguish three types of sperm mosaicism, Types I (sperm), II (SSC), and III (embryonic), and further subdivide Types II and III into IIa, IIb, IIIa, and IIIb. Type III mutations arise during early embryogenesis prior to (IIIa) or after (IIIb) the establishment of the PGC population. Type IIa and IIb mutations arise within the SSCs and are distinguished by their impact on cellular proliferation. Type I mutations arise during the last stages of spermatogenesis and by definition are only ever-present in a few sperm of the same meiotic division. (B) In the testicular stem cell niche, Type I mutations are the only type absent from SSCs. Type IIa includes mutations that do not impact the fitness of SSCs and stay contained within their lineage. Type IIb, also referred to as ‘selfish sperm’ mutations, provides a selective advantage to an SSC within the niche; however, this is at the cost of offspring, as these mutations typically result in severe congenital disorders (e.g., Apert, Noonan, and Costello syndromes). Finally, Type III is present in several SSCs due to their developmental origin. They are typically found throughout the seminiferous tubules and across the two testes, resulting in measurable allelic fractions in bulk sperm samples. (C) The different types of sperm mosaicism result in distinct recurrence risk patterns. Type I and Type IIa mutations result in no or infinitesimally small recurrence risk within a family; as they are random, their recurrence across the population is as expected by chance. Type IIb mutations result in overproliferation within the stem cell niche, however, this results in little recurrence risk within a family. Like cancer mutations, however, due to their selection advantage, the same FGFR2/3, RET, HRAS, or KRAS mutations are found more frequently across the population than expected by chance. Finally, Type III mutations can exhibit high recurrence risk within a family (up to 25%), but their recurrence across the population is as expected by chance.

Figure 3.

The timing of a mutation and its selective potential determine abundance in sperm. Schematic of the developing lineage of germ cells and the soma. The different types of sperm mosaicism are labeled and occur prior to or following Primordial Germ Cell (PGC) specification (Types IIIa and IIIb, respectively), within the SSCs (Type II), or are present only within one or two sperm cells (Type I). Only Type IIb mutations exhibit positive selection. The abundance of a mutation among sperm cells is a function of its timing during development and the presence or absence of positive selection. Note that for simplicity all mutations are shown to occur in separate sperm lineages. However, in reality, individual sperm lineages will show a combination of all types of sperm mosaicism.

Figure 4.

Paternal mutations in offspring are largely due to age-dependent sperm mosaicism. (A) Single nucleotide variants (SNVs) occurring during spermatogenesis or oogenesis of the parents are present in the respective germ cells prior to conception (parental mosaic de novo SNVs, i.e. dSNVs) and will reside on the paternal or maternal haplotype of the embryo, respectively. dSNVs that occur following conception are defined as zygotic, and should be stochastically distributed across both haplotypes. Currently, we further assume that Type III mutations appear at similar rates in the male and female germ cell lineage. Thus the imbalance (80:20%) of dSNVs in favor of the paternal haplotype must derive from Type I and II sperm mosaicism. (B) Type III mutations are determined during embryonic development and should remain constant with age. Similarly, the stochastic nature of Type I is likely independent of age effects. Thus, the observed increase of dSNVs with paternal age should derive mostly from Type II mutations that accumulate with each cell cycle. (C) As a consequence of the increase of Type II mutations with age, the relative contribution of Types I and III decreases. Likewise, the average intrafamilial recurrence risk of a given dSNV decreases with age.

Figure 5.

Sperm mosaicism contributes to human genomic diversity. (A) In a simplified assumption that each sperm contributes 100 mutations before conception and a stable paternal age at conception, each man will transmit 50 of these private variants to the next generation. In the fourth generation, if each man has one son, this will amount to a total of 188 private variants that are only found in any one individual within this generation. Ultimately, this will increase to double the number of DNMs, with ~100 arising from prior generations and ~100 arising from the most recent generation. (B) Assuming that each man has two sons, using a similar rate of ~100 sperm mosaic mutations, sperm mosaicism will contribute 144 private variants (not shared with any sibling or cousin) per person, or 1152 across all 16 offspring in the fourth generation. The total contribution in the population now numbers 1152 novel variants.