Adaptive Evolution Favoring KLK4 Downregulation in East Asians

Pilot GWAS of caries in African-Americans shows genetic heterogeneity

BACKGROUND

Dental caries is the most common chronic disease in the US and disproportionately affects racial/ethnic minorities. Caries is heritable, and though genetic heterogeneity exists between ancestries for a substantial portion of loci associated with complex disease, a genome-wide association study (GWAS) of caries specifically in African Americans has not been performed previously.

METHODS

We performed exploratory GWAS of dental caries in 109 African American adults (age > 18) and 96 children (age 3-12) from the Center for Oral Health Research in Appalachia (COHRA1 cohort). Caries phenotypes (DMFS, DMFT, dft, and dfs indices) assessed by dental exams were tested for association with 5 million genotyped or imputed single nucleotide polymorphisms (SNPs), separately in the two age groups. The GWAS was performed using linear regression with adjustment for age, sex, and two principal components of ancestry. A maximum of 1 million adaptive permutations were run to determine empirical significance.

RESULTS

No loci met the threshold for genome-wide significance, though some of the strongest signals were near genes previously implicated in caries such as antimicrobial peptide DEFB1 (rs2515501; p = 4.54 × 10- 6) and TUFT1 (rs11805632; p = 5.15 × 10- 6). Effect estimates of lead SNPs at suggestive loci were compared between African Americans and Caucasians (adults N = 918; children N = 983). Significant (p < 5 × 10- 8) genetic heterogeneity for caries risk was found between racial groups for 50% of the suggestive loci in children, and 12-18% of the suggestive loci in adults.

CONCLUSIONS

The genetic heterogeneity results suggest that there may be differences in the contributions of genetic variants to caries across racial groups, and highlight the critical need for the inclusion of minorities in subsequent and larger genetic studies of caries in order to meet the goals of precision medicine and to reduce oral health disparities.

Concise Review: Altered Versus Unaltered Amniotic Membrane as a Substrate for Limbal Epithelial Cells

Limbal stem cell deficiency (LSCD) can result from a variety of corneal disorders, including chemical and thermal burns, infections, and autoimmune diseases. The symptoms of LSCD may include irritation, epiphora, blepharospasms, photophobia, pain, and decreased vision. There are a number of treatment options, ranging from nonsurgical treatments for mild LSCD to various forms of surgery that involve different cell types cultured on various substrates. Ex vivo expansion of limbal epithelial cells (LEC) involves the culture of LEC harvested either from the patient, a living relative, or a cadaver on a substrate in the laboratory. Following the transfer of the cultured cell sheet onto the cornea of patients suffering from LSCD, a successful outcome can be expected in approximately three out of four patients. The phenotype of the cultured cells has proven to be a key predictor of success. The choice of culture substrate is known to affect the phenotype. Several studies have shown that amniotic membrane (AM) can be used as a substrate for expansion of LEC for subsequent transplantation in the treatment of LSCD. There is currently a debate over whether AM should be denuded (i.e., de-epithelialized) prior to LEC culture, or whether this substrate should remain intact. In addition, crosslinking of the AM has been used to increase the thermal and mechanical stability, optical transparency, and resistance to collagenase digestion of AM. In the present review, we discuss the rationale for using altered versus unaltered AM as a culture substrate for LEC. Stem Cells Translational Medicine 2018;7:415-427.

Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin

Sun-exposure is a key environmental variable in the study of human evolution. Several skin-pigmentation genes serve as classical examples of positive selection, suggesting that sun-exposure has significantly shaped worldwide genomic variation. Here we investigate the interaction between genetic variation and sun-exposure, and how this impacts gene expression regulation. Using RNA-Seq data from 607 human skin samples, we identified thousands of transcripts that are differentially expressed between sun-exposed skin and non-sun-exposed skin. We then tested whether genetic variants may influence each individual’s gene expression response to sun-exposure. Our analysis revealed 10 sun-exposure-dependent gene expression quantitative trait loci (se-eQTLs), including genes involved in skin pigmentation (SLC45A2) and epidermal differentiation (RASSF9). The allele frequencies of the RASSF9 se-eQTL across diverse populations correlate with the magnitude of solar radiation experienced by these populations, suggesting local adaptation to varying levels of sunlight. These results provide the first examples of sun-exposure-dependent regulatory variation and suggest that this variation has contributed to recent human adaptation.

Varying levels of sun-exposure across the world have significantly shaped human evolution. Previous analyses have found several skin pigmentation genes with evidence of strong evolutionary pressures throughout human history, manifesting as large differences in the frequency of genomic variants across populations. But even within populations, individuals respond differently to sun-exposure, suggesting variation in addition to the major differences in skin pigmentation across populations. Here we investigated whether genetic variants associate with response to sun-exposure within Europeans. To measure the response we analyzed gene expression in sun-exposed and non-sun-exposed skin, and identified ten genetic variants that associated with the sun-exposure response of nearby genes. One of these genetic variants, which associated with the sun-exposure response of the gene RASSF9, showed evidence of adaptation in humans in response to solar radiation. Together this evidence suggests that the regulation of gene expression is influenced by sun-exposure and that the sun-exposure dependent effect on RASSF9 expression may have had an effect on human fitness. To our knowledge, this is the first example of an environment-dependent regulatory variant with evidence of adaptation in humans.