Multiple Genomic Events Altering Hominin Sialic Acid Biology Predated the Common Ancestor of Humans and Neanderthals

Multiple Genomic Events Altering Hominin Sialic Acid Biology Predated the Common Ancestor of Humans and Neanderthals

Naazneen Khan¹, Stevan Springer¹, Marc de Manuel Montero², Stephane Peyrégne³, Kay Prüfer³, Tomas Marques-Bonet², Pascal Gagneux¹ and Ajit Varki¹

¹Center for Academic Research and Training in Anthropogeny (CARTA), Glycobiology Research and Training Center (GRTC), Departments of Medicine, Pathology, Cellular & Molecular Medicine and Anthropology, UC San Diego, La Jolla CA, USA.
²Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, Spain.
³Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

Using immunochemical approaches (Sarich & Wilson), and then protein sequencing (Goodman, Doolittle and others) it was conclusively shown by the 1970s that chimpanzees were our closest living evolutionary cousins.  For the next two decades, the popular assumption (King & Wilson, 1975) was that humans and chimpanzees differed primarily in terms of expression of otherwise nearly identical genes and proteins. It was then suggested by Olson that gene loss might also be an engine of evolutionary change (“Less is More”). Contemporaneous with this suggestion came the first report of a human-specific and human-universal gene loss resulting in a clear structural and biochemical difference between humans and chimpanzees: pseudogenization of the CMAH gene, which resulted in loss of the common mammalian sialic acid (Sia) called Neu5Gc, and an excess of the precursor Sia called Neu5Ac. As sialic acids can have highly diverse presentations and are displayed at >100mM concentrations on most cell surfaces, this event constituted a major change in many aspects of biology, including “self-associated molecular patterns”, which are known to modulate innate immune cells via engagement of CD33-related Siglec receptors.  This Alu-mediated mutation appears to have been fixed ~2-3 million years ago and may have contributed to the origin of the genus Homo. We now know that gene expression changes and gene loss are not the only mechanisms involved in human evolution, and (perhaps not surprisingly, in retrospect), all possible genomic mechanisms are operative.

In this regard, human genomic events altering >10 other genes involved in Sia biology have been discovered, which also appeared to be human-specific, i.e., not found in then available limited chimpanzee genomic data––suggesting that Sia biology might represent a "hotspot" in hominin evolution. However, the possibility of ascertainment bias due to the number and quality of human genomes compared with those of other hominids could not be ruled out. Availability of many more hominid genomes including ancient DNA of extinct hominins now allows fresh analysis, and better evolutionary timing of these events. All known human genomic changes in CD33-related SIGLEC gene cluster (affecting 8 of 13 members of this class of genes) are found in African populations, indicating that they predated the common ancestor of modern humans. Comparisons with 147 “great ape” genomes indicate that all these changes are indeed unique to hominins. There was no evidence for strong selection after the Human-Neanderthal/Denisovan common ancestor, ~500 kya.  Consistent with these observations, Neanderthal and Denisovan genomes include almost all the major changes found in modern humans. Genome-level analyses can miss domain-specific rapid evolution within functional regions of specific proteins.  Indeed, Sia-binding domains of CD33-related Siglecs prominent on innate immune cells harbor higher rates of evolution relative to those of the other hominids and of the adjacent/underlying/more proximal structural C2-set domains. The CMAH mutation likely induced changes in self-associated molecular patterns, setting in motion multiple events, including emergence of human-specific pathogens that coat themselves with Neu5Ac-containing molecular mimics of human glycans, to suppress immune responses via Siglec engagement. The resulting “hot spot” in hominin Sia biology apparently occurred in the Homo lineage prior to the common ancestor of Humans and Neanderthals. Multiple genomic changes in the CD33rSIGLEC gene cluster may also be relevant to unusual human-specific expression change of CD33rSiglecs in locations such as placental trophoblast (SIGLEC6); pancreatic islets (SIGLEC7); ovarian fibroblasts (SIGLEC11/16); amniotic epithelium (SIGLEC5/14); microglia (SIGLEC11/16 and CD33); mucosal epithelial surfaces (SIGLEC12 and 13); NK cells (SIGLEC17); and, T cells (SIGLECs 5/14,7,9).