In principle, a new L1 insertion into a lethal gene could initiate a cascade leading to fetal death, although our diploid nature limits such consequences. Many signaling pathways and genes are involved in the process of miscarriage and single gene mutations may cause spontaneous abortion [
6]. Based on a study of 489 single gene knockout mouse models, White et al. [
88] found 29 percent of the genes to be lethal and 13 percent sublethal.
KIF7 (kinesin family member gene 7) was the first human gene associated with fetal lethality when it was found to cause hydrolethalus and acrocallosal syndromes [
89], and since then many other candidate genes have been identified. A review of 50 human studies identified a range of possible causative gene and copy number variations (CNVs) for miscarriage, including
CHRNA1 (cholinergic receptor, nicotinic, alpha polypeptide 1)
, DYNC2H1 (dynein, cytoplasmic 2, heavy chain 1), and
RYR1 (ryanodine receptor 1)
, which were reported by multiple studies [
6]. Several whole exome sequence analyses of euploid miscarriages have been conducted, including a study of 30 fetuses in which mutations in
FGFR3 (fibroblast growth factor receptor 3),
COL2A1 (collagen, type II, alpha 1), and
OFD1 (oral-facial-digital syndrome 1) genes, in addition to structural variants, accounted for 10 percent of the cohort [
90]. Fang et al. [
91] found that expression of VEGF (vascular endothelial growth factor), part of the angiogenesis signaling pathway, was significantly decreased in missed abortion tissue and correlated with increased levels of VEGFR1 (Vascular Endothelial Growth Factor Receptor 1) and Notch-1. Adache et al. [
92] reviewed the key role of the cyclooxygenase (COX)-1 and -2 signaling pathways for repeated failure of embryo implantation. Affected genes found in other studies include KIF14 (kinesin family member 14) [
93], IFT122 (intraflagellar transport 122) [
94], PLCD4 (phospholipase C delta 4), and OSBPL5 (protein-like 5) [
95]. In the case of recurrent miscarriage, cytokine gene polymorphisms, novel HLA alelles, and mutations in inflammatory factors and synaptonemal complex protein 3 (SYCP3) have been implicated. SYCP3 encodes an essential structural component of the synaptonemal complex and its mutation may result in chromosome abnormalities [
96‐
99]. Thus, it is increasingly evident that mutation of any of many cellular pathway genes can initiate miscarriage.
Studies have demonstrated that healthy humans carry many mutated gene alleles [
100]: elevated L1 retrotransposition during early embryogenesis could contribute to this mutation burden. It is possible that during early development epigenetic change or loss of a retrotransposon inhibiting factor could trigger derepression of active retrotransposons increasing the likelihood of an L1 inserting into a lethal gene. Recent studies have revealed the complexity of cellular factors and pathways regulating the activity of human retrotransposons. To date about 80 factors have been identified that limit expression or insertion of retrotransposons in cell culture or mouse models ([
101]; reviewed in [
36]). For example, knockout of DNA Methyltransferase 3 Like (DNMT3L) protein in mouse germ cells was accompanied by epigenetic change, reactivation of retrotransposons, and meiotic collapse [
77]. Loss of TEX19.1 in mice leads to placental growth retardation, increased embryonic lethality, and derepressed retrotransposon expression in placenta and hypomethylated trophectoderm-derived cells, and its loss in mouse pluripotent embryonic stem cells increases retrotransposition of engineered L1 constructs [
60,
102]. To cite another example, using a digital droplet PCR detection strategy, a startling 70-fold increase in retrotransposition of an L1 reporter transgene in a mouse deficient for MOV10L1, a piRNA pathway protein, was claimed by Newkirk et al. [
103].
The impacts of retrotransposons on gene integrity extend beyond simple mutation by insertion: these have been the subjects of many reviews [
18,
32,
104‐
107]. Ongoing retrotransposition events salt genomes with novel splice sites, polyadenylation signals, promoters, and transcription factor binding sites that can alter gene expression. Recombination between retrotransposons causes deletions, duplications, or rearrangements of gene sequence, and this is especially true for Alus [
108]. L1-mediated retrotransposition insertion can also cause deletions up to a megabase at their sites of insertion [
18,
105,
109‐
112]: one example is the deletion of an entire HLA-A gene caused by an SVA insertion that resulted in leukemia [
113]. Retrotransposons are also associated with segmental duplications [
114]; significantly, CNVs have also been linked with human miscarriage [
115,
116]. Even more dramatic non-LTR retrotransposon-mediated genomic rearrangements may occur. L1 endonuclease activity and SVA retrotransposition leading to multiple DNA breaks was proposed as causal for one case of human germline chromothripsis [
117], a phenomenon involving numerous chromosomal rearrangements in a single event, and one that has also been linked with severe congenital defects [
118]. In summary, the mutagenic potential of active human retrotransposons can be significant.