Fumitoshi Ishino

RTL6 (also known as SIRH3 ) is a eutherian-specific metavirus-derived gene highly conserved among placental mammals. We previously demonstrated that RTL6 is expressed in microglia and secreted into the brain extracellular space, where it mediates the trapping and clearance of bacterial lipopolysaccharide (LPS). However, its role in microglial TLR4 signaling remained unclear. To investigate the earliest LPS response, we performed RNA-seq analysis of wild-type and Rtl6 -deficient primary microglia following 10 min of LPS stimulation. Rtl6 -deficient microglia exhibited compensatory upregulation of residual transcripts derived from the untranslated region of Rtl6 , suggesting feedback regulation of Rtl6 expression. Loss of RTL6 attenuated the induction of immediate-early response genes, including Fos, Jun, Nr4a1, Nr4a2, Egr2, and Egr3 , together with broad suppression of interferon-responsive and inflammatory transcriptional programs. Altered neuronal and oligodendrocyte/myelin interaction pathways indicated remodeling of microglial communication networks. Strikingly, genes involved in cell-cycle progression, DNA replication, chromatin assembly, DNA repair, and genome maintenance were coordinately upregulated, including multiple disease-associated microglia (DAM)-related genes. Collectively, these findings indicate that RTL6 couples extracellular LPS sensing to inflammatory transcriptional responses while regulating microglial functional state transitions. Our results identify RTL6 as a previously unrecognized component of the regulatory network governing microglial functional states in placental mammals.

Eutherian mammals possess 11 metavirus-derived genes, collectively known as the sushi-ichi retrotransposon homologue (SIRH)/Retrotransposon Gag-like (RTL) genes. Several members of this group function in microglia, where SIRH3/RTL6, SIRH8/RTL5, and SIRH10/RTL9 mediate innate immune responses against bacterial-, viral-, and fungal-derived pathogen-associated molecular patterns, respectively, whereas SIRH11/RTL4 responds to noradrenaline and is thought to contribute to stress-responsive brain functions. In addition, the retroviral Env-derived gene ERVPb1 has been implicated in yolk sac-derived resident macrophage lineages, suggesting that both Gag- and Env-derived domesticated genes contributed to the evolution of mammalian neuroimmune systems. Microglia are now recognized as central regulators of neural circuit formation, brain homeostasis, and neuroimmune function, and their dysfunction has been implicated in a wide range of neurological and psychiatric disorders. Here, we review current knowledge of virus-derived genes that have shaped the functional evolution of microglia. We also revisit the concept of “Placenta-driven evolution,” which proposes that the relatively hypomethylated developmental environment of extraembryonic tissues, including the placenta and yolk sac, facilitates the retention and functional co-option of virus-derived sequences, thereby accelerating eutherian evolution. Finally, by integrating recent advances in virus-derived genes and retroelement biology, we discuss how this evolutionary framework may extend beyond extraembryonic tissues to other hypomethylated developmental environments, including the germline and preimplantation embryos.

Mammalian placentation represents one of the most striking evolutionary innovations among vertebrates, and accumulating evidence indicates that virus-derived genes—particularly the metavirus-derived PEG10 and PEG11/RTL1—have played indispensable but distinct roles: PEG10 in the emergence of therian viviparity and PEG11/RTL1 in the subsequent differentiation between marsupial and eutherian placental types. Notably, the metavirus-derived SIRH/RTL gene group, which includes PEG10 and PEG11/RTL1, exhibits unique and diverse functions not only in placenta development but also within microglia of the brain. Because microglia originate from yolk sac progenitors, these findings suggest that extraembryonic tissues such as the placenta and yolk sac provided permissive environments that enabled the retention, expression and functional domestication of virus-derived sequences. Once the placenta itself was established through viral gene integration, it may in turn have acted as a powerful driver of eutherian evolution through recurrent acquisition and co-option of additional virus-derived genes—a process we refer to as “placenta-driven evolution.” This perspective offers a unified framework in which viral gene acquisition is viewed as a key driver of genomic innovation, tightly intertwined with the emergence of viviparity, subsequent divergence at the marsupial–eutherian split, and continued diversification of placental structure and function across eutherian lineages.

Retrotransposon Gag-like (RTL) 8A, 8B and 8C are eutherian-specific genes derived from a certain retrovirus. They cluster as a triplet of genes on the X chromosome, but their function remains unknown. Here, we demonstrate that Rtl8a and Rtl8b play important roles in the brain: their double knockout (DKO) mice not only exhibit reduced social responses and increased apathy-like behaviour, but also become obese from young adulthood, similar to patients with late Prader–Willi syndrome (PWS), a neurodevelopmental genomic imprinting disorder. Mouse RTL8A/8B proteins are expressed in the prefrontal cortex and hypothalamus and localize to both the nucleus and cytoplasm of neurons, presumably due to the N-terminal nuclear localization signal-like sequence at the N-terminus. An RNAseq study in the cerebral cortex revealed reduced expression of several GABA type A receptor subunit genes in DKO, in particular Gabrb2, which encodes its β2 subunit. We confirmed the reduction of GABRB2 protein in the DKO cerebral cortex by western blotting. As GABRB2 has been implicated in the aetiology of several neurodevelopmental and neuropsychiatric disorders, it is likely that the reduction of GABRB2 is one of the major causes of the neuropsychiatric defects in the DKO mice.

Retrotransposon Gag-like 4 (RTL4), a gene acquired from a retrovirus, is a causative gene in autism spectrum disorder. Its knockout mice exhibit increased impulsivity, impaired short-term spatial memory, failure to adapt to novel environments, and delayed noradrenaline (NA) recovery in the frontal cortex. However, due to its very low expression in the brain, it remains unknown which brain cells express RTL4 and its dynamics in relation to NA. We addressed these issues using knock-in mice carrying endogenous Rtl4 fused to Venus, which encodes a fluorescent protein. The RTL4-Venus fusion protein was detected as a secreted protein in the midbrain, hypothalamus, hippocampus and amygdala in the postnatal brain. Its signal intensity was high during critical periods of neonatal adaptation to novel environments. It was upregulated by various stimuli, including isoproterenol administration, whereas it was decreased by anesthesia but was maintained by milnacipran administration, suggesting its highly sensitive response to stressors, possible dependence on the arousal state and involvement in the NA reuptake process. In vitro mixed glial culture experiments demonstrated that Rtl4 is a microglial gene and suggested that RTL4 secretion responds rapidly to isoproterenol. Microglial RTL4 plays an important role in the NA response and possibly in the development of the NAergic neuronal network in the brain.

RTL4 , a gene acquired from a retrovirus, is a causative gene in autism spectrum disorder. Its KO mice exhibit increased impulsivity, impaired short-term spatial memory, failure to adapt to novel environments, and delayed noradrenaline (NA) recovery in the frontal cortex. However, due to its very low expression in the brain, it remains unknown which brain cells express RTL4 and its dynamics in relation to NA. Here, using knock-in mice carrying endogenous Rtl4 fused to Venus , we demonstrated that RTL4 is a microglial gene with several important properties. The RTL4-Venus fusion protein was detected as a secreted protein in the midbrain, hypothalamus, hippocampus and amygdala in the postnatal brain. Its signal intensity was high during critical periods of neonatal adaptation to novel environments and was upregulated by various stimuli, such as handling the mice, mild environmental changes and administration of isoproterenol, an agonist of adrenergic beta receptors. It was decreased by anesthesia but was maintained by the administration of milnacipran, an NA reuptake inhibitor. These results suggest that RTL4 intensity depends on the arousal state via NA and is somehow related to the NA reuptake process. In vitro mixed glial culture experiments demonstrated that Rtl4 is a microglial gene and suggested that RTL4 secretion responds rapidly to isoproterenol. Taken together with previous results from Rtl4 KO mice, microglial RTL4 plays an important role in the NA response and it is likely involved in the development of the NAergic neuronal network in the brain.

Retrotransposon Gag-like (RTL) 8A, 8B and 8C are eutherian-specific genes derived from a certain retrovirus. They clustered as a triplet of genes on the X chromosome, but their function remains unknown. Here, we demonstrate that Rtl8a and Rtl8b play important roles in the brain: their double knockout (DKO) mice not only exhibit reduced social responses and increased apathy-like behavior, but also become obese from young adulthood. Mouse RTL8A/8B proteins are expressed in the prefrontal cortex and hypothalamus and localize to both the nucleus and cytoplasm of neurons, presumably due to the N-terminal nuclear localization signal-like sequence at the N-terminus. An RNAseq study in the cerebral cortex revealed reduced expression of several GABA type A receptor subunits, in particular the β2 subunit of Gabrb2, in DKO. We confirmed the reduction of GABRB2 protein in the DKO cerebral cortex by Western blotting. As GABRB2 has been implicated in the etiology of several neurodevelopmental disorders, it is likely that the reduction of GABRB2 is one of the major causes of the neuropsychiatric defects in the DKO mice.

Retrotransposon Gag-like (RTL) genes play a variety of essential and important roles in the eutherian placenta and brain. It has recently been demonstrated that RTL5 and RTL6 (also known as sushi-ichi retrotransposon homolog 8 (SIRH8) and SIRH3) are microglial genes that play important roles in the brain’s innate immunity against viruses and bacteria through their removal of double-stranded RNA and lipopolysaccharide, respectively. In this work, we addressed the function of RTL9 (also known as SIRH10). Using knock-in mice that produce RTL9-mCherry fusion protein, we examined RTL9 expression in the brain and its reaction to fungal zymosan. Here, we demonstrate that RTL9 plays an important role, degrading zymosan in the brain. The RTL9 protein is localized in the microglial lysosomes where incorporated zymosan is digested. Furthermore, in Rtl9 knockout mice expressing RTL9ΔC protein lacking the C-terminus retroviral GAG-like region, the zymosan degrading activity was lost. Thus, RTL9 is essentially engaged in this reaction, presumably via its GAG-like region. Together with our previous study, this result highlights the importance of three retrovirus-derived microglial RTL genes as eutherian-specific constituents of the current brain innate immune system: RTL9, RTL5 and RTL6, responding to fungi, viruses and bacteria, respectively.

PEG10 and PEG11/RTL1 are paternally expressed, imprinted genes that play essential roles in the current eutherian developmental system and are therefore associated with developmental abnormalities caused by aberrant genomic imprinting. They are also presumed to be retrovirus-derived genes with homology to the sushi-ichi retrotransposon GAG and POL, further expanding our comprehension of mammalian evolution via the domestication (exaptation) of retrovirus-derived acquired genes. In this manuscript, we review the importance of PEG10 and PEG11/RTL1 in genomic imprinting research via their functional roles in development and human disease, including neurodevelopmental disorders of genomic imprinting, Angelman, Kagami-Ogata and Temple syndromes, and the impact of newly inserted DNA on the emergence of newly imprinted regions. We also discuss their possible roles as ancestors of other retrovirus-derived RTL/SIRH genes that likewise play important roles in the current mammalian developmental system, such as in the placenta, brain and innate immune system.

Eutherians have 11 retrotransposon Gag-like (RTL)/sushi-ichi retrotransposon homolog (SIRH) genes presumably derived from a certain retrovirus. Accumulating evidence indicates that the RTL/SIRH genes play a variety of roles in the current mammalian developmental system, such as in the placenta, brain, and innate immune system, in a eutherian-specific manner. It has been shown that the functional role of Paternally Expressed 10 (PEG10) in placental formation is unique to the therian mammals, as are the eutherian-specific roles of PEG10 and PEG11/RTL1 in maintaining the fetal capillary network and the endocrine regulation of RTL7/SIRH7 (aka Leucine Zipper Down-Regulated in Cancer 1 (LDOCK1)) in the placenta. In the brain, PEG11/RTL1 is expressed in the corticospinal tract and hippocampal commissure, mammalian-specific structures, and in the corpus callosum, a eutherian-specific structure. Unexpectedly, at least three RTL/SIRH genes, RTL5/SIRH8, RTL6/SIRH3, and RTL9/SIRH10, play important roles in combating a variety of pathogens, namely viruses, bacteria, and fungi, respectively, suggesting that the innate immunity system of the brain in eutherians has been enhanced by the emergence of these new components. In this review, we will summarize the function of 10 out of the 11 RTL/SIRH genes and discuss their roles in eutherian development and evolution.