A Genome-Wide Association Study Identifies the Skin Color Genes IRF4, MC1R, ASIP, and BNC2 Influencing Facial Pigmented Spots

Predictive accuracy of genetic variants for eye color in a Kazakh population using the IrisPlex system

OBJECTIVE

This study assesses the accuracy of the IrisPlex system, a genetic eye color prediction tool for forensic analysis, in the Kazakh population. The study compares previously published genotypes of 515 Kazakh individuals from varied geographical and ethnohistorical contexts with phenotypic data on their eye color, introduced for the first time in this research.

RESULTS

The IrisPlex panel's effectiveness in predicting eye color in the Kazakh population was validated. It exhibited slightly lower accuracy than in Western European populations but was higher than in Siberian populations. The sensitivity was notably high for brown-eyed individuals (0.99), but further research is needed for blue and intermediate eye colors. This study establishes IrisPlex as a useful predictive tool in the Kazakh population and provides a basis for future investigations into the genetic basis of phenotypic variations in this diverse population.

Skin colour: A window into human phenotypic evolution and environmental adaptation

As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.

Genomic insights into shank and eggshell color in Italian local chickens

Eggshell and shank color in poultry is an intriguing topic of research due to the roles in selection, breed recognition, and environmental adaptation. This study delves into the genomics foundations of shank and eggshell pigmentation in Italian local chickens through genome-wide association studies analysis to uncover the mechanisms governing these phenotypes. To this purpose, 483 animals from 20 local breeds (n = 466) and 2 commercial lines (n = 17) were considered and evaluated for shank and eggshell color. All animals were genotyped using the Affymetrix Axiom 600 K Chicken Genotyping Array. As regards shank color, the most interesting locus was detected on chromosome Z, close to the TYRP1 gene, known to play a key role in avian pigmentation. Additionally, several novel loci and genes associated with shank pigmentation, skin pigmentation, UV protection, and melanocyte regulation were identified (e.g., MTAP, CDKN2A, CDKN2B). In eggshell, fewer significant loci were identified, including SLC7A11 and MITF on chromosomes 4 and 12, respectively, associated with melanocyte processes and pigment synthesis. This comprehensive study shed light on the genetic architecture underlying shank and eggshell color in Italian native chicken breeds, contributing to a better understanding of this phenomenon which plays a role in breed identification and conservation, and has ecological and economic implications.

Resequencing Analyses Revealed Genetic Diversity and Selection Signatures during Rabbit Breeding and Improvement

Domestication has shaped the diverse characteristics of rabbits, including coat color, fur structure, body size, and various physiological traits. Utilizing whole-genome resequencing (DNBSEQ-T7), we analyzed the genetic diversity, population structure, and genomic selection across 180 rabbits from 17 distinct breeds to uncover the genetic basis of these traits. We conducted whole-genome sequencing on 17 rabbit breeds, identifying 17,430,184 high-quality SNPs and analyzing genomic diversity, patterns of genomic variation, population structure, and selection signatures related to coat color, coat structure, long hair, body size, reproductive capacity, and disease resistance. Through PCA and NJ tree analyses, distinct clusters emerged among Chinese indigenous rabbits, suggesting varied origins and domestication histories. Selective sweep testing pinpointed regions and genes linked to domestication and key morphological and economic traits, including those affecting coat color (TYR, ASIP), structure (LIPH), body size (INSIG2, GLI3), fertility (EDNRA, SRD5A2), heat stress adaptation (PLCB1), and immune response (SEC31A, CD86, LAP3). Our study identified key genomic signatures of selection related to traits such as coat color, fur structure, body size, and fertility; these findings highlight the genetic basis underlying phenotypic diversification in rabbits and have implications for breeding programs aiming to improve productive, reproductive, and adaptive traits. The detected genomic signatures of selection also provide insights into rabbit domestication and can aid conservation efforts for indigenous breeds.

Epigenetics insights from perceived facial aging

Facial aging is the most visible manifestation of aging. People desire to look younger than others of the same chronological age. Hence, perceived age is often used as a visible marker of aging, while biological age, often estimated by methylation markers, is used as an objective measure of age. Multiple epigenetics-based clocks have been developed for accurate estimation of general biological age and the age of specific organs, including the skin. However, it is not clear whether the epigenetic biomarkers (CpGs) used in these clocks are drivers of aging processes or consequences of aging. In this proof-of-concept study, we integrate data from GWAS on perceived facial aging and EWAS on CpGs measured in blood. By running EW Mendelian randomization, we identify hundreds of putative CpGs that are potentially causal to perceived facial aging with similar numbers of damaging markers that causally drive or accelerate facial aging and protective methylation markers that causally slow down or protect from aging. We further demonstrate that while candidate causal CpGs have little overlap with known epigenetics-based clocks, they affect genes or proteins with known functions in skin aging, such as skin pigmentation, elastin, and collagen levels. Overall, our results suggest that blood methylation markers reflect facial aging processes, and thus can be used to quantify skin aging and develop anti-aging solutions that target the root causes of aging.

Basonuclin-2 regulates extracellular matrix production and degradation

Epithelial-mesenchymal transition is essential for tissue patterning and organization. It involves both regulation of cell motility and alterations in the composition and organization of the ECM-a complex environment of proteoglycans and fibrous proteins essential for tissue homeostasis, signaling in response to chemical and biomechanical stimuli, and is often dysregulated under conditions such as cancer, fibrosis, and chronic wounds. Here, we demonstrate that basonuclin-2 (BNC2), a mesenchymal-expressed gene, that is, strongly associated with cancer and developmental defects across genome-wide association studies, is a novel regulator of ECM composition and degradation. We find that at endogenous levels, BNC2 controls the expression of specific collagens, matrix metalloproteases, and other matrisomal components in breast cancer cells, and in fibroblasts that are primarily responsible for the production and processing of the ECM within the tumour microenvironment. In so doing, BNC2 modulates the motile and invasive properties of cancers, which likely explains the association of high BNC2 expression with increasing cancer grade and poor patient prognosis.

Identifying signatures of positive selection in human populations from North Africa

Because of its location, North Africa (NA) has witnessed continuous demographic movements with an impact on the genomes of present-day human populations. Genomic data describe a complex scenario with varying proportions of at least four main ancestry components: Maghrebi, Middle Eastern-, European-, and West-and-East-African-like. However, the footprint of positive selection in NA has not been studied. Here, we compile genome-wide genotyping data from 190 North Africans and individuals from surrounding populations, investigate for signatures of positive selection using allele frequencies and linkage disequilibrium-based methods and infer ancestry proportions to discern adaptive admixture from post-admixture selection events. Our results show private candidate genes for selection in NA involved in insulin processing (KIF5A), immune function (KIF5A, IL1RN, TLR3), and haemoglobin phenotypes (BCL11A). We also detect signatures of positive selection related to skin pigmentation (SLC24A5, KITLG), and immunity function (IL1R1, CD44, JAK1) shared with European populations and candidate genes associated with haemoglobin phenotypes (HPSE2, HBE1, HBG2), other immune-related (DOCK2) traits, and insulin processing (GLIS3) traits shared with West and East African populations. Finally, the SLC8A1 gene, which codifies for a sodium-calcium exchanger, was the only candidate identified under post-admixture selection in Western NA.

Additional predictions for forensic DNA phenotyping of externally visible characteristics using the ForenSeq and Imagen kits

Multiplex DNA typing methods using massively parallel sequencing can be used to predict externally visible characteristics (EVCs) in forensic DNA phenotyping through the analysis of single-nucleotide polymorphisms. The focus of EVC determination has focused on hair color, eye color, and skin tone as well as visible biogeographical ancestry features. In this study, we researched off-label applications beyond what is currently marketed by the manufacturer of the Verogen ForenSeq kit primer set B and Imagen primer set E SNP loci. We investigated additional EVC predictions by examining published genome wide sequencing studies and reported allele-specific gene expression and predictive values. We have identified 15 SNPs included in the ForenSeq kit panel and Imagen kits that have additional EVC prediction capabilities beyond what is published in the Verogen manuals. The additional EVCs that can be predicted include hair graying, ephelides hyperpigmented spots, dermatoheliosis, facial pigmented spots, standing height, pattern balding, helix-rolling ear morphology, hair shape, hair thickness, facial morphology, eyebrow thickness, sarcoidosis, obesity, vitiligo, and tanning propensity. The loci can be used to augment and refine phenotype predictions with software such as MetaHuman for missing persons, cold case, and historic case investigations.

Younger facial looks are associate with a lower likelihood of several age-related morbidities in the middle-aged to elderly

BACKGROUND

Looking older for one's chronological age is associated with a higher mortality rate. Yet it remains unclear how perceived facial age relates to morbidity and the degree to which facial ageing reflects systemic ageing of the human body.

OBJECTIVES

To investigate the association between ΔPA and age-related morbidities of different organ systems, where ΔPA represents the difference between perceived age (PA) and chronological age.

METHODS

We performed a cross-sectional analysis on data from the Rotterdam Study, a population-based cohort study in the Netherlands. High-resolution facial photographs of 2679 men and women aged 51.5-87.8 years of European descent were used to assess PA. PA was estimated and scored in 5-year categories using these photographs by a panel of men and women who were blinded for chronological age and medical history. A linear mixed model was used to generate the mean PAs. The difference between the mean PA and chronological age was calculated (ΔPA), where a higher (positive) ΔPA means that the person looks younger for their age and a lower (negative) ΔPA that the person looks older. ΔPA was tested as a continuous variable for association with ageing-related morbidities including cardiovascular, pulmonary, ophthalmological, neurocognitive, renal, skeletal and auditory morbidities in separate regression analyses, adjusted for age and sex (model 1) and additionally for body mass index, smoking and sun exposure (model 2).

RESULTS

We observed 5-year higher ΔPA (i.e. looking younger by 5 years for one's age) to be associated with less osteoporosis [odds ratio (OR) 0.76, 95% confidence interval (CI) 0.62-0.93], less chronic obstructive pulmonary disease (OR 0.85, 95% CI 0.77-0.95), less age-related hearing loss (model 2; B = -0.76, 95% CI -1.35 to -0.17) and fewer cataracts (OR 0.84, 95% CI 0.73-0.97), but with better global cognitive functioning (g-factor; model 2; B = 0.07, 95% CI 0.04-0.10).

CONCLUSIONS

PA is associated with multiple morbidities and better cognitive function, suggesting that systemic ageing and cognitive ageing are, to an extent, externally visible in the human face.

Prediction and association analyses of skin phenotypes in Japanese females using genetic, environmental, and physical features

BACKGROUND

Skin characteristics show great variation from person to person and are affected by multiple factors, including genetic, environmental, and physical factors, but details of the involvement and contributions of these factors remain unclear.

OBJECTIVES

We aimed to characterize genetic, environmental, and physical factors affecting 16 skin features by developing models to predict personal skin characteristics.

METHODS

We analyzed the associations of skin phenotypes with genetic, environmental, and physical features in 1472 Japanese females aged 20-80 years. We focused on 16 skin characteristics, including melanin, brightness/lightness, yellowness, pigmented spots, wrinkles, resilience, moisture, barrier function, texture, and sebum amount. As genetic factors, we selected 74 single-nucleotide polymorphisms of genes related to skin color, vitamin level, hormones, circulation, extracellular matrix (ECM) components and ECM-degrading enzymes, inflammation, and antioxidants. Histories of ultraviolet (UV) exposure and smoking as environmental factors and age, height, and weight as physical factors were acquired by means of a questionnaire.

RESULTS

A linear association with age was prominent for increase in the area of crow's feet, increase in number of pigmented spots, decrease in forehead sebum, and increase in VISIA wrinkle parameters. Associations were analyzed by constructing linear regression models for skin feature changes and logistic regression models to predict whether subjects show lower or higher skin measurement values in the same age groups. Multiple genetic factors, history of UV exposure and smoking, and body mass index were statistically selected for each skin characteristic. The most important association found for skin spots, such as lentigines and wrinkles, was adolescent sun exposure.

CONCLUSION

Genetic, environmental, and physical factors associated with interindividual differences of the selected skin features were identified. The developed models should be useful to predict the skin characteristics of individuals and their age-related changes.

Genetic Variants in Telomerase Reverse Transcriptase Contribute to Solar Lentigines

Solar lentigines (SLs) are a hallmark of human skin aging. They result from chronic exposure to sunlight and other environmental stressors. Recent studies also imply genetic factors, but findings are partially conflicting and lack of replication. Through a multi-trait based analysis strategy, we discovered that genetic variants in telomerase reverse transcriptase were significantly associated with non-facial SL in two East Asian (Taizhou longitudinal cohort, n = 2,964 and National Survey of Physical Traits, n = 2,954) and one Caucasian population (SALIA, n = 462), top SNP rs2853672 (P-value for Taizhou longitudinal cohort = 1.32 × 10^‒28 and P-value for National Survey of Physical Traits = 3.66 × 10^‒17 and P-value for SALIA = 0.0007 and P_meta = 4.93 × 10^‒44). The same variants were nominally associated with facial SL but not with other skin aging or skin pigmentation traits. The SL-enhanced allele/haplotype upregulated the transcription of the telomerase reverse transcriptase gene. Of note, well-known telomerase reverse transcriptase‒related aging markers such as leukocyte telomere length and intrinsic epigenetic age acceleration were not associated with SL. Our results indicate a previously unrecognized role of telomerase reverse transcriptase in skin aging‒related lentigines formation.

Estimating the Relative Contribution of Environmental and Genetic Risk Factors to Different Aging Traits by Combining Correlated Variables into Weighted Risk Scores

Genetic and exposomal factors contribute to the development of human aging. For example, genetic polymorphisms and exposure to environmental factors (air pollution, tobacco smoke, etc.) influence lung and skin aging traits. For prevention purposes it is highly desirable to know the extent to which each category of the exposome and genetic factors contribute to their development. Estimating such extents, however, is methodologically challenging, mainly because the predictors are often highly correlated. Tackling this challenge, this article proposes to use weighted risk scores to assess combined effects of categories of such predictors, and a measure of relative importance to quantify their relative contribution. The risk score weights are determined via regularized regression and the relative contributions are estimated by the proportion of explained variance in linear regression. This approach is applied to data from a cohort of elderly Caucasian women investigated in 2007-2010 by estimating the relative contribution of genetic and exposomal factors to skin and lung aging. Overall, the models explain 17% (95% CI: [9%, 28%]) of the outcome's variance for skin aging and 23% ([11%, 34%]) for lung function parameters. For both aging traits, genetic factors make up the largest contribution. The proposed approach enables us to quantify and rank contributions of categories of exposomal and genetic factors to human aging traits and facilitates risk assessment related to common human diseases in general. Obtained rankings can aid political decision making, for example, by prioritizing protective measures such as limit values for certain exposures.

Commentary: Facial Aesthetic Dermatological Procedures and Photoprotection in Chinese Populations

The medical literature on aesthetic dermatology has primarily focused on a light-skinned patient population, yet patients of darker skin types have different needs and priorities. In Chinese individuals, key concerns include altered pigmentation, which is perceived to age the individual, and also relates to the Chinese cultural standard of beauty of fair skin; many seek aesthetic treatment for this. Non-invasive cosmetic procedures such as lasers and injections are also gaining in popularity in the Chinese market, but this population is prone to hyperpigmentation as an adverse effect of such procedures. Considered and tailored approaches, both to primary concerns of photoaging and the side effects of cosmetic treatments, are warranted.

Evaluation of Personalized Skincare Through in-silico Gene Interactive Networks and Cellular Responses to UVR and Oxidative Stress

Purpose

Personalized approaches in dermatology are designed to match the specific requirements based on the individual genetic makeup. One major factor accounting for the differences in skin phenotypes is single nucleotide polymorphism (SNP) within several genes with diverse roles that extend beyond skin tone and pigmentation. Therefore, the cellular sensitivities to the environmental stress and damage linked to extrinsic aging could also underlie the individual characteristics of the skin and dictate the unique skin care requirements. This study aimed to identify the likely biomarkers and molecular signatures expressed in skin cells of different ethnic backgrounds, which could aid further the design of personalized skin products based on specific demands.

Methods

Using data mining and in-silico modeling, the association of SNP-affected genes with three major skin types of European, Asian and African origin was analyzed and compared within the structure-function gene interaction networks. Cultured dermal fibroblasts were subsequently subjected to ultraviolet radiation and oxidative stress and analyzed for DNA damage and senescent markers. The protective applications of two cosmetic ingredients, Resveratrol and Quercetin, were validated in both cellular and in-silico models.

Results

Each skin type was characterized by the presence of SNPs in the genes controlling facultative and constitutive pigmentation, which could also underlie the major differences in responses to photodamage, such as oxidative stress, inflammation, and barrier homeostasis. Skin-type-specific dermal fibroblasts cultured in-vitro demonstrated distinctive sensitivities to ultraviolet radiation and oxidative stress, which could be modulated further by the bioactive compounds with the predicted capacities to interact with some of the genes in the in-silico models.

Conclusion

Evaluation of the SNP-affected gene networks and likely sensitivities of skin cells, defined as low threshold levels to extrinsic stress factors, can provide a valuable tool for the design and formulation of personalized skin products that match more accurately diverse ethnic backgrounds.

Evolutionary Origins of Metabolic Reprogramming in Cancer

Metabolic changes that facilitate tumor growth are one of the hallmarks of cancer. These changes are not specific to tumors but also take place during the physiological growth of tissues. Indeed, the cellular and tissue mechanisms present in the tumor have their physiological counterpart in the repair of tissue lesions and wound healing. These molecular mechanisms have been acquired during metazoan evolution, first to eliminate the infection of the tissue injury, then to enter an effective regenerative phase. Cancer itself could be considered a phenomenon of antagonistic pleiotropy of the genes involved in effective tissue repair. Cancer and tissue repair are complex traits that share many intermediate phenotypes at the molecular, cellular, and tissue levels, and all of these are integrated within a Systems Biology structure. Complex traits are influenced by a multitude of common genes, each with a weak effect. This polygenic component of complex traits is mainly unknown and so makes up part of the missing heritability. Here, we try to integrate these different perspectives from the point of view of the metabolic changes observed in cancer.

Ross J, Scott Herron G. Genetic and Epigenetic Influences on Cutaneous Cellular Senescence

Skin is the largest human organ system, and its protective function is critical to survival. The epithelial, dermal, and subcutaneous compartments are heterogeneous mixtures of cell types, yet they all display age-related skin dysfunction through the accumulation of an altered phenotypic cellular state called senescence. Cellular senescence is triggered by complex and dynamic genetic and epigenetic processes. A senescence steady state is achieved in different cell types under various and overlapping conditions of chronological age, toxic injury, oxidative stress, replicative exhaustion, DNA damage, metabolic dysfunction, and chromosomal structural changes. These inputs lead to outputs of cell-cycle withdrawal and the appearance of a senescence-associated secretory phenotype, both of which accumulate as tissue pathology observed clinically in aged skin. This review details the influence of genetic and epigenetic factors that converge on normal cutaneous cellular processes to create the senescent state, thereby dictating the response of the skin to the forces of both intrinsic and extrinsic aging. From this work, it is clear that no single biomarker or process leads to senescence, but that it is a convergence of factors resulting in an overt aging phenotype.

Epidemiological survey of the quantity and anatomical position of facial pigmented spots in relation to age in 454 Japanese women

Facial pigmented spots are one of the phenotypes of skin aging, but no quantitative analysis of spot features such as color intensity, size, anatomical position, and number on the cheek has yet been performed. In the current study, we conducted an epidemiological survey of 454 Japanese women in their 20s to 70s and analyzed age-related changes and site differences of facial pigmented spots. Using image analysis of high-resolution digital facial photographs, 4912 individual pigmented spots were quantified according to color, size, anatomical position, and total number on the cheek. As a result of color analysis, the color intensity of individual pigmented spots increased with aging, significantly so between ages 30s and 50s. The age-related increase in melanin index of facial spots was confirmed in all sites but did not significantly differ between facial subregions. Regarding the size of pigmented spots, the frequency of large spots increased with age, and large spots were detected in all facial sites. The total number of pigmented spots on the entire cheek increased with aging, significantly so between the 20s and 40s. The number of pigmented spots tended to increase from the region near the canthi to the lower cheeks. The number of spots was markedly increased in the buccal regions compared with the infraorbital and zygomatic regions. The data and methodology presented in the current study can link the state of facial pigmentation with the various factors involved in the histological development of pigmented spots, opening new possibilities in the fields of skin pharmacology and dermatology.

Novel genetic associations with five aesthetic facial traits: A genome-wide association study in the Chinese population

Background: The aesthetic facial traits are closely related to life quality and strongly influenced by genetic factors, but the genetic predispositions in the Chinese population remain poorly understood.

Methods: A genome-wide association studies (GWAS) and subsequent validations were performed in 26,806 Chinese on five facial traits: widow’s peak, unibrow, double eyelid, earlobe attachment, and freckles. Functional annotation was performed based on the expression quantitative trait loci (eQTL) variants, genome-wide polygenic scores (GPSs) were developed to represent the combined polygenic effects, and single nucleotide polymorphism (SNP) heritability was presented to evaluate the contributions of the variants.

Results: In total, 21 genetic associations were identified, of which ten were novel: GMDS-AS1 (rs4959669, p = 1.29 × 10⁻⁴⁹) and SPRED2 (rs13423753, p = 2.99 × 10⁻¹⁴) for widow’s peak, a previously unreported trait; FARSB (rs36015125, p = 1.96 × 10⁻²¹) for unibrow; KIF26B (rs7549180, p = 2.41 × 10⁻¹⁵), CASC2 (rs79852633, p = 4.78 × 10⁻¹¹⁾, RPGRIP1L (rs6499632, p = 9.15 × 10⁻¹¹), and PAX1 (rs147581439, p = 3.07 × 10⁻⁸) for double eyelid; ZFHX3 (rs74030209, p = 9.77 × 10⁻¹⁴) and LINC01107 (rs10211400, p = 6.25 × 10⁻¹⁰) for earlobe attachment; and SPATA33 (rs35415928, p = 1.08 × 10⁻⁸) for freckles. Functionally, seven identified SNPs tag the missense variants and six may function as eQTLs. The combined polygenic effect of the associations was represented by GPSs and contributions of the variants were evaluated using SNP heritability.

Conclusion: These identifications may facilitate a better understanding of the genetic basis of features in the Chinese population and hopefully inspire further genetic research on facial development.

A systematic review of skin ageing genes: gene pleiotropy and genes on the chromosomal band 16q24.3 may drive skin ageing

Skin ageing is the result of intrinsic genetic and extrinsic lifestyle factors. However, there is no consensus on skin ageing phenotypes and ways to quantify them. In this systematic review, we first carefully identified 56 skin ageing phenotypes from multiple literature sources and sought the best photo-numeric grading scales to evaluate them. Next, we conducted a systematic review on all 44 Genome-wide Association Studies (GWAS) on skin ageing published to date and identified genetic risk factors (2349 SNPs and 366 genes) associated with skin ageing. We identified 19 promising SNPs found to be significantly (p-Value < 1E-05) associated with skin ageing phenotypes in two or more independent studies. Here we show, using enrichment analyses strategies and gene expression data, that (1) pleiotropy is a recurring theme among skin ageing genes, (2) SNPs associated with skin ageing phenotypes are mostly located in a small handful of 44 pleiotropic and hub genes (mostly on the chromosome band 16q24.3) and 32 skin colour genes. Since numerous genes on the chromosome band 16q24.3 and skin colour genes show pleiotropy, we propose that (1) genes traditionally identified to contribute to skin colour have more than just skin pigmentation roles, and (2) further progress towards understand the development of skin pigmentation requires understanding the contributions of genes on the chromosomal band 16q24.3. We anticipate our systematic review to serve as a hub to locate primary literature sources pertaining to the genetics of skin ageing and to be a starting point for more sophisticated work examining pleiotropic genes, hub genes, and skin ageing phenotypes.

Focus on the Contribution of Oxidative Stress in Skin Aging

Skin aging is one of the most evident signs of human aging. Modification of the skin during the life span is characterized by fine lines and wrinkling, loss of elasticity and volume, laxity, rough-textured appearance, and pallor. In contrast, photoaged skin is associated with uneven pigmentation (age spot) and is markedly wrinkled. At the cellular and molecular level, it consists of multiple interconnected processes based on biochemical reactions, genetic programs, and occurrence of external stimulation. The principal cellular perturbation in the skin driving senescence is the alteration of oxidative balance. In chronological aging, reactive oxygen species (ROS) are produced mainly through cellular oxidative metabolism during adenosine triphosphate (ATP) generation from glucose and mitochondrial dysfunction, whereas in extrinsic aging, loss of redox equilibrium is caused by environmental factors, such as ultraviolet radiation, pollution, cigarette smoking, and inadequate nutrition. During the aging process, oxidative stress is attributed to both augmented ROS production and reduced levels of enzymatic and non-enzymatic protectors. Apart from the evident appearance of structural change, throughout aging, the skin gradually loses its natural functional characteristics and regenerative potential. With aging, the skin immune system also undergoes functional senescence manifested as a reduced ability to counteract infections and augmented frequency of autoimmune and neoplastic diseases. This review proposes an update on the role of oxidative stress in the appearance of the clinical manifestation of skin aging, as well as of the molecular mechanisms that underline this natural phenomenon sometimes accelerated by external factors.

Genome-wide association study of actinic keratosis identifies new susceptibility loci implicated in pigmentation and immune regulation pathways

Actinic keratosis (AK) is a common precancerous cutaneous neoplasm that arises on chronically sun-exposed skin. AK susceptibility has a moderate genetic component, and although a few susceptibility loci have been identified, including IRF4, TYR, and MC1R, additional loci have yet to be discovered. We conducted a genome-wide association study of AK in non-Hispanic white participants of the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort (n = 63,110, discovery cohort), with validation in the Mass-General Brigham (MGB) Biobank cohort (n = 29,130). We identified eleven loci (P < 5 × 10-8), including seven novel loci, of which four novel loci were validated. In a meta-analysis (GERA + MGB), one additional novel locus, TRPS1, was identified. Genes within the identified loci are implicated in pigmentation (SLC45A2, IRF4, BNC2, TYR, DEF8, RALY, HERC2, and TRPS1), immune regulation (FOXP1 and HLA-DQA1), and cell signaling and tissue remodeling (MMP24) pathways. Our findings provide novel insight into the genetics and pathogenesis of AK susceptibility.

Identification of New Biological Pathways Involved in Skin Aging From the Analysis of French Women Genome-Wide Data

Skin aging is an ineluctable process leading to the progressive loss of tissue integrity and is characterized by various outcomes such as wrinkling and sagging. Researchers have identified impacting environmental factors (sun exposure, smoking, etc.) and several molecular mechanisms leading to skin aging. We have previously performed genome-wide association studies (GWAS) in 502 very-well characterized French women, looking for associations with four major outcomes of skin aging, namely, photoaging, solar lentigines, wrinkling, and sagging, and this has led to new insights into the molecular mechanisms of skin aging. Since individual SNP associations in GWAS explain only a small fraction of the genetic impact in complex polygenic phenotypes, we have made the integration of these genotypes into the reference Kegg biological pathways and looked for associations by the gene set enrichment analysis (GSEA) approach. 106 pathways were tested for association with the four outcomes of skin aging. This biological pathway analysis revealed new relevant pathways and genes, some likely specific of skin aging such as the WNT7B and PRKCA genes in the “melanogenesis” pathway and some likely involved in global aging such as the DDB1 gene in the “nucleotide excision repair” pathway, not picked up in the previously published GWAS. Overall, our results suggest that the four outcomes of skin aging possess specific molecular mechanisms such as the “proteasome” and “mTOR signaling pathway” but may also share common molecular mechanisms such as “nucleotide excision repair.”

Protective Role of Melatonin and Its Metabolites in Skin Aging

The skin, being the largest organ in the human body, is exposed to the environment and suffers from both intrinsic and extrinsic aging factors. The skin aging process is characterized by several clinical features such as wrinkling, loss of elasticity, and rough-textured appearance. This complex process is accompanied with phenotypic and functional changes in cutaneous and immune cells, as well as structural and functional disturbances in extracellular matrix components such as collagens and elastin. Because skin health is considered one of the principal factors representing overall “well-being” and the perception of “health” in humans, several anti-aging strategies have recently been developed. Thus, while the fundamental mechanisms regarding skin aging are known, new substances should be considered for introduction into dermatological treatments. Herein, we describe melatonin and its metabolites as potential “aging neutralizers”. Melatonin, an evolutionarily ancient derivative of serotonin with hormonal properties, is the main neuroendocrine secretory product of the pineal gland. It regulates circadian rhythmicity and also exerts anti-oxidative, anti-inflammatory, immunomodulatory, and anti-tumor capacities. The intention of this review is to summarize changes within skin aging, research advances on the molecular mechanisms leading to these changes, and the impact of the melatoninergic anti-oxidative system controlled by melatonin and its metabolites, targeting the prevention or reversal of skin aging.

GWAS Identifies Multiple Genetic Loci for Skin Color in Korean Women

Human skin color is largely determined by genetic factors. Recent GWASs have reported several genetic variants associated with skin color, mostly in European and African populations. In this study, we performed GWAS in 17,019 Korean women to identify genetic variants associated with facial skin color, quantitatively measured as CIELAB color index. We identified variants in three, one, and six genomic loci associated with facial skin color index L∗, a∗, and b∗ values, respectively, and replicated the associations (combined analysis P-value < 5.0 × 10^-8). The significant loci included variants in known genes (OCA2 rs74653330, BNC2 rs16935073, rs72620727 near KITLG, and SLC6A17 rs6689641) and to our knowledge previously unreported genes (SCARB1 rs10846744, SYN2 rs12629034, and LINC00486 rs6543678). This is GWAS to elucidate genetic variants of facial skin color in a Korean female population. Further functional characterizations of the investigated genes are warranted to elucidate their contribution to skin pigmentation-related traits.

Association of pigmentation related-genes polymorphisms and geographic environmental variables in the Chinese population

Background

Human skin color is highly heritable and one of the most variable phenotypic traits. However, the genetic causes and environmental selective pressures underlying this phenotypic variation have remained largely unknown. To investigate whether the pigmentation related-genes polymorphisms are associated with the geographic environmental variables. We selected randomly 795 healthy individuals from eight ethnic groups in nine provinces in China. Six single nucleotide polymorphisms (SNPs) of SLC45A2 and TYR were genotyped using Agena MassARRAY. The Chi-square test and Spearman correlation analysis were used to compare the frequency distribution of genotypes among different ethnic groups and evaluate the relationship between SNP genetic diversity and environmental variables, respectively.

Results

The results indicated that rs28777 and rs183671 (SLC45A2) and rs1042602 (TYR) genotype frequency distributions were significantly different between the Xinjiang-Uighur and other ethnic groups (P < 0.05). Spearman correlation analysis found that rs28777-A (r = − 0.090, P = 0.011), rs183671-G (r = − 0.105, P = 0.003), rs1042602-A (r = − 0.108, P = 0.002), rs1126809-A (r = − 0.151, P < 0.001) allele frequencies were negatively correlated with the longitude; rs183671-G (r = 0.151), rs1042602-A (r = 0.157) and rs1126809-A (r = 0.138) allele frequencies were positively associated with the latitude (P < 0.001); rs183671-G (r = 0.116, P = 0.001), rs1042602-A (r = 0.105, P = 0.003) and rs1126809-A (r = 0.070, P = 0.048) allele frequencies were positively correlated with the sunshine hours; rs183671-G (r = − 0.076, P = 0.033), rs1042602-A (r = − 0.079, P = 0.027) and rs1126809-A (r = − 0.076, P = 0.031) were negatively correlated with the annual average temperature.

Conclusions

Our results confirmed the idea that environmental factors have been an important selective pressure upon pigmentation related gene polymorphisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41065-021-00189-7.

Mitochondrial Secrets of Youthfulness

SUMMARY

The genetic basis of youthfulness is poorly understood. The aging of skin depends on both intrinsic factors and extrinsic factors. Intrinsic factors include personal genetics, and extrinsic factors include environmental exposure to solar radiation and pollution. We recently reported the critical role of the mitochondria in skin aging phenotypes: wrinkle formation, hair graying, hair loss, and uneven skin pigmentation. This article focuses on molecular mechanisms, specifically mitochondrial mechanisms underlying skin aging. This contribution describes the development of an mitochondrial DNA depleter-repleter mouse model and its usefulness in developing strategies and identifying potential agents that can either prevent, slow, or mitigate skin aging, lentigines, and hair loss. The ongoing research efforts include the transplantation of young mitochondria to rejuvenate aging skin and hair to provide youthfulness in humans.

Epigenetic regulation during melanocyte development and homeostasis

Melanocytes originate in the neural crest as precursor cells which then migrate and proliferate to reach their destination where they differentiate into pigment-producing cells. Melanocytes not only determine the colour of hair, skin and eyes but also protect against the harmful effects of UV irradiation. The establishment of the melanocyte lineage is regulated by a defined set of transcription factors and signalling pathways that direct the specific gene expression programmes underpinning melanoblast specification, survival, migration, proliferation and differentiation. In addition, epigenetic modifiers and replacement histones play key roles in regulating gene expression and its timing during the different steps of this process. Here, we discuss the evidence for the role of epigenetic regulators in melanocyte development and function and how they interact with transcription factors and signalling pathways to establish and maintain this important cell lineage.

A genome-wide association study identifies novel gene associations with facial skin wrinkling and mole count in Latin Americans

BACKGROUND

Genome-wide association studies (GWASs) have identified genes influencing skin ageing and mole count in Europeans, but little is known about the relevance of these (or other genes) in non-Europeans.

OBJECTIVES

To conduct a GWAS for facial skin ageing and mole count in adults < 40 years old, of mixed European, Native American and African ancestry, recruited in Latin America.

METHODS

Skin ageing and mole count scores were obtained from facial photographs of over 6000 individuals. After quality control checks, three wrinkling traits and mole count were retained for genetic analyses. DNA samples were genotyped with Illumina's HumanOmniExpress chip. Association testing was performed on around 8 703 729 single-nucleotide polymorphisms (SNPs) across the autosomal genome.

RESULTS

Genome-wide significant association was observed at four genome regions: two were associated with wrinkling (in 1p13·3 and 21q21·2), one with mole count (in 1q32·3) and one with both wrinkling and mole count (in 5p13·2). Associated SNPs in 5p13·2 and in 1p13·3 are intronic within SLC45A2 and VAV3, respectively, while SNPs in 1q32·3 are near the SLC30A1 gene, and those in 21q21·2 occur in a gene desert. Analyses of SNPs in IRF4 and MC1R are consistent with a role of these genes in skin ageing.

CONCLUSIONS

We replicate the association of wrinkling with variants in SLC45A2, IRF4 and MC1R reported in Europeans. We identify VAV3 and SLC30A1 as two novel candidate genes impacting on wrinkling and mole count, respectively. We provide the first evidence that SLC45A2 influences mole count, in addition to variants in this gene affecting melanoma risk in Europeans.

Evolutionary genetics of skin pigmentation in African populations

Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.

Environmentally-Induced (Extrinsic) Skin Aging: Exposomal Factors and Underlying Mechanisms

As a barrier organ, the skin is an ideal model to study environmentally-induced (extrinsic) aging. In this review, we explain the development of extrinsic skin aging as a consequence of skin exposure to specific exposomal factors, their interaction with each other, and the modification of their effects on the skin by genetic factors. We also review the evidence that exposure to these exposomal factors causes extrinsic skin aging by mechanisms that critically involve the accumulation of macromolecular damage and the subsequent development of functionally altered and/or senescent fibroblasts in the dermal compartment of the skin.

An atlas of CNV maps in cattle, goat and sheep

Copy number variation (CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region (CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study (GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected (P<0.00001), and these CNVRs may be more persist than the single nucleotide polymorphisms (SNPs) shared between species. We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes. This study provides the evidence that balancing selection might be more common in mammals than previously considered, and might play an important role in the daily activities of these ruminant species.

Genome-Wide Association Study Identifies Genetic Associations with Perceived Age

Failure of dermal protection or repair mechanisms might lead to visibly aged skin. The study aimed to identify genetic associations with perceived age. A genome-wide association study was undertaken in 423,992 adult participants of UK Biobank, using questionnaire data on perceived age and genetic data imputed to the Haplotype Reference Consortium imputation panel. The study identified 74 independently associated genetic loci, to our knowledge previously unreported (P < 5 × 10-8), which were enriched for cell signaling pathways, including the NEK6 and SMAD2 subnetworks. Common genetic variation was estimated to account for 14% of variation in perceived age, and the heritability of perceived age was partially shared with that of 75 other traits, including multiple traits representing adiposity, suggesting that perceived age may be a useful proxy trait in genetic association studies.

Genetics of facial telangiectasia in the Rotterdam Study: a genome-wide association study and candidate gene approach

BACKGROUND

The severity of facial telangiectasia or red veins is associated with many lifestyle factors. However, the genetic predisposition remains unclear.

OBJECTIVES

We performed a genome-wide association study (GWAS) on facial telangiectasia in the Rotterdam Study (RS) and tested for replication in two independent cohorts. Additionally, a candidate gene approach with known pigmentation genes was performed.

METHODS

Facial telangiectasia were extracted from standardized facial photographs (collected from 2010-2013) of 2842 northwestern European participants (median age 66.9, 56.8% female) from the RS. Our GWAS top hits (P-value <10^-6 ) were tested for replication in 460 elderly women of the SALIA cohort and in 576 additional men and women of the RS. Associations of top single nucleotide polymorphisms (SNPs) with expression quantitative trait loci (eQTL) in various tissues were reviewed (GTEx database) alongside phenotype associations in the UK biobank database. SNP-based associations between known pigmentation genes and facial telangiectasia were tested. Conditional analysis on skin colour was additionally performed.

RESULTS

Our most significant GWAS signal was rs4417318 (P-value 5.38*10^-7 ), an intergenic SNP on chromosome 12 mapping to the SLC16A7 gene. Other suggestive SNPs tagged genes ZNF211, ZSCAN4, ICOS and KCNN3; SNP eQTLs and phenotype associations tagged links to the vascular system. However, the top signals did not pass significance in the two replication cohorts. The pigmentation genes KIAA0930, SLCA45A2 and MC1R, were significantly associated with telangiectasia in a candidate gene approach but not independently of skin colour.

CONCLUSION

In this GWAS on telangiectasia in a northwestern European population, no genome-wide significant SNPs were found, although suggestive signals indicate genes involved in the vascular system might be involved in telangiectasia. Significantly associated pigmentation genes underline the link between skin colour and telangiectasia.

Optimizing the genetic prediction of the eye and hair color for North Eurasian populations

Background

Predicting the eye and hair color from genotype became an established and widely used tool in forensic genetics, as well as in studies of ancient human populations. However, the accuracy of this tool has been verified on the West and Central Europeans only, while populations from border regions between Europe and Asia (like Caucasus and Ural) also carry the light pigmentation phenotypes.

Results

We phenotyped 286 samples collected across North Eurasia, genotyped them by the standard HIrisPlex-S markers and found that predictive power in Caucasus/Ural/West Siberian populations is reasonable but lower than that in West Europeans. As these populations have genetic ancestries different from that of West Europeans, we hypothesized they may carry a somewhat different allele spectrum. Thus, for all samples we performed the exome sequencing additionally enriched with the 53 genes and intergenic regions known to be associated with the eye/hair color. Our association analysis replicated the importance of the key previously known SNPs but also identified five new markers whose eye color prediction power for the studied populations is compatible with the two major previously well-known SNPs. Four out of these five SNPs lie within the HERС2 gene and the fifth in the intergenic region. These SNPs are found at high frequencies in most studied populations. The released dataset of exomes from Russian populations can be further used for population genetic and medical genetic studies.

Conclusions

This study demonstrated that precision of the established systems for eye/hair color prediction from a genotype is slightly lower for the populations from the border regions between Europe and Asia that for the West Europeans. However, this precision can be improved if some newly revealed predictive SNPs are added into the panel. We discuss that the replication of these pigmentation-associated SNPs on the independent North Eurasian sample is needed in the future studies.

GWAS Analysis of 17,019 Korean Women Identifies the Variants Associated with Facial Pigmented Spots

Variation in skin pigmentation can be affected by both environmental factors and intrinsic factors such as age, gender, and genetic variation. Recent GWASs revealed that genetic variants of genes functionally related to a pigmentation pathway were associated with skin pigmentary traits. However, these GWASs focused on populations with European ancestry, and only a few studies have been performed on Asian populations, limiting our understanding of the genetic basis of skin pigmentary traits in Asians. To evaluate the genetic variants associated with facial pigmented spots, we conducted a GWAS analysis of objectively measured facial pigmented spots in 17,019 Korean women. This large-scale GWAS identified several genomic loci that were significantly associated with facial pigmented spots (five previously reported loci and two previously unreported loci, to our knowledge), which were detected by UV light: BNC2 at 9p22 (rs16935073; P-value = 2.11 × 10^-46), PPARGC1B at 5q32 (rs32579; P-value = 9.04 × 10^-42), 10q26 (rs11198112; P-value = 9.66 × 10^-38), MC1R at 16q24 (rs2228479; P-value = 6.62 × 10^-21), lnc01877 at 2q33 (rs12693889; P-value = 1.59 × 10^-11), CDKN2B-AS1 at 9p21 (rs643319; P-value = 7.76 × 10^-9), and MFSD12 at 19p13 (rs2240751; P-value = 9.70 × 10^-9). Further functional characterization of the candidate genes needs to be done to fully evaluate their contribution to facial pigmented spots.

Predicting target genes of non-coding regulatory variants with IRT

SUMMARY

Interpreting genetic variants of unknown significance (VUS) is essential in clinical applications of genome sequencing for diagnosis and personalized care. Non-coding variants remain particularly difficult to interpret, despite making up a large majority of trait associations identified in genome-wide association studies (GWAS) analyses. Predicting the regulatory effects of non-coding variants on candidate genes is a key step in evaluating their clinical significance. Here, we develop a machine-learning algorithm, Inference of Connected expression quantitative trait loci (eQTLs) (IRT), to predict the regulatory targets of non-coding variants identified in studies of eQTLs. We assemble datasets using eQTL results from the Genotype-Tissue Expression (GTEx) project and learn to separate positive and negative pairs based on annotations characterizing the variant, gene and the intermediate sequence. IRT achieves an area under the receiver operating characteristic curve (ROC-AUC) of 0.799 using random cross-validation, and 0.700 for a more stringent position-based cross-validation. Further evaluation on rare variants and experimentally validated regulatory variants shows a significant enrichment in IRT identifying the true target genes versus negative controls. In gene-ranking experiments, IRT achieves a top-1 accuracy of 50% and top-3 accuracy of 90%. Salient features, including GC-content, histone modifications and Hi-C interactions are further analyzed and visualized to illustrate their influences on predictions. IRT can be applied to any VUS of interest and each candidate nearby gene to output a score reflecting the likelihood of regulatory effect on the expression level. These scores can be used to prioritize variants and genes to assist in patient diagnosis and GWAS follow-up studies.

AVAILABILITY AND IMPLEMENTATION

Codes and data used in this work are available at https://github.com/miaecle/eQTL_Trees.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Performance analysis of melanoma classifier using electrical modeling technique

An efficient and novel modeling approach is proposed in this paper for identifying proteins or genes involved in melanoma skin cancer. Two types of classifiers are modeled, based on the chemical structure and hydropathy property of amino acids. These classifiers are further implemented using NI LabVIEW-based hardware kit to observe the real-time response for proper diagnosis. The phase responses, pole-zero diagrams, and transient responses are examined to screen out the genes related to melanoma from healthy genes. The performance of the proposed classifier is measured using various performance measurement metrics in terms of accuracy, sensitivity, specificity, etc. The classifier is experimented along with a color code scheme on skin genes and illustrates the superiority in comparison with traditional methods by achieving 94% of classification accuracy with 96% of sensitivity.Graphical abstract An equivalent electrical model is developed for designing melanoma classifier. Initially, each amino acid is modeled using the RC passive circuit depending on their physicochemical structure and hydropathy nature, to form a gene structure model. The melanoma-related genes are detected by phase, transient, and color code analysis.

Exploring the possibility of predicting human head hair greying from DNA using whole-exome and targeted NGS data

Background

Greying of the hair is an obvious sign of human aging. In addition to age, sex- and ancestry-specific patterns of hair greying are also observed and the progression of greying may be affected by environmental factors. However, little is known about the genetic control of this process. This study aimed to assess the potential of genetic data to predict hair greying in a population of nearly 1000 individuals from Poland.

Results

The study involved whole-exome sequencing followed by targeted analysis of 378 exome-wide and literature-based selected SNPs. For the selection of predictors, the minimum redundancy maximum relevance (mRMRe) method was used, and then two prediction models were developed. The models included age, sex and 13 unique SNPs. Two SNPs of the highest mRMRe score included whole-exome identified KIF1A rs59733750 and previously linked with hair loss FGF5 rs7680591. The model for greying vs. no greying prediction achieved accuracy of cross-validated AUC = 0.873. In the 3-grade classification cross-validated AUC equalled 0.864 for no greying, 0.791 for mild greying and 0.875 for severe greying. Although these values present fairly accurate prediction, most of the prediction information was brought by age alone. Genetic variants explained < 10% of hair greying variation and the impact of particular SNPs on prediction accuracy was found to be small.

Conclusions

The rate of changes in human progressive traits shows inter-individual variation, therefore they are perceived as biomarkers of the biological age of the organism. The knowledge on the mechanisms underlying phenotypic aging can be of special interest to the medicine, cosmetics industry and forensics. Our study improves the knowledge on the genetics underlying hair greying processes, presents prototype models for prediction and proves hair greying being genetically a very complex trait. Finally, we propose a four-step approach based on genetic and epigenetic data analysis allowing for i) sex determination; ii) genetic ancestry inference; iii) greying-associated SNPs assignment and iv) epigenetic age estimation, all needed for a final prediction of greying.

Transcriptome-based selection and validation of optimal house-keeping genes for skin research in goats (Capra hircus)

BACKGROUND

In quantitative real-time polymerase chain reaction (qRT-PCR) experiments, accurate and reliable target gene expression results are dependent on optimal amplification of house-keeping genes (HKGs). RNA-seq technology offers a novel approach to detect new HKGs with improved stability. Goat (Capra hircus) is an economically important livestock species and plays an indispensable role in the world animal fiber and meat industry. Unfortunately, uniform and reliable HKGs for skin research have not been identified in goat. Therefore, this study seeks to identify a set of stable HKGs for the skin tissue of C. hircus using high-throughput sequencing technology.

RESULTS

Based on the transcriptome dataset of 39 goat skin tissue samples, 8 genes (SRP68, NCBP3, RRAGA, EIF4H, CTBP2, PTPRA, CNBP, and EEF2) with relatively stable expression levels were identified and selected as new candidate HKGs. Commonly used HKGs including SDHA and YWHAZ from a previous study, and 2 conventional genes (ACTB and GAPDH) were also examined. Four different experimental variables: (1) different development stages, (2) hair follicle cycle stages, (3) breeds, and (4) sampling sites were used for determination and validation. Four algorithms (geNorm, NormFinder, BestKeeper, and ΔCt method) and a comprehensive algorithm (ComprFinder, developed in-house) were used to assess the stability of each HKG. It was shown that NCBP3 + SDHA + PTPRA were more stably expressed than previously used genes in all conditions analysis, and that this combination was effective at normalizing target gene expression. Moreover, a new algorithm for comprehensive analysis, ComprFinder, was developed and released.

CONCLUSION

This study presents the first list of candidate HKGs for C. hircus skin tissues based on an RNA-seq dataset. We propose that the NCBP3 + SDHA + PTPRA combination could be regarded as a triplet set of HKGs in skin molecular biology experiments in C. hircus and other closely related species. In addition, we also encourage researchers who perform candidate HKG evaluations and who require comprehensive analysis to adopt our new algorithm, ComprFinder.

Characterization of POU2F1 Gene and Its Potential Impact on the Expression of Genes Involved in Fur Color Formation in Rex Rabbit

The naturally colorful fur of the Rex rabbit is becoming increasingly popular in the modern textile market. Our previous study found that POU class 2 homeobox 1 gene (POU2F1) potentially affects the expression of genes involved in fur color formation in the Rex rabbit, but the function and regulation of POU2F1 has not been reported. In this study, the expression patterns of POU2F1 in Rex rabbits of various colors, as well as in different organs, were analyzed by RT-qPCR. Interference and overexpression of POU2F1 were used to identify the potential effects of POU2F1 on other genes related to fur color formation. The results show that the levels of POU2F1 expression were significantly higher in the dorsal skin of the brown and protein yellow Rex rabbits, compared with that of the black one. POU2F1 mRNAs were widespread in the tissues examined in this study and showed the highest level in the lungs. By transfecting rabbit melanocytes with an POU2F1-overexpression plasmid, we found that the POU2F1 protein was located at the nucleus, and the protein showed the classic characteristics of a transcription factor. In addition, abnormal expression of POU2F1 significantly affected the expression of pigmentation-related genes, including SLC7A11, MITF, SLC24A5, MC1R, and ASIP, revealing the regulatory roles of POU2F1 on pigmentation. The results provide the basis for further exploration of the role of POU2F1 in fur color formation of the Rex rabbit.

SDR9C7 plays an essential role in skin barrier function by dehydrogenating acylceramide for covalent attachment to proteins

Among the components of the barrier structure of the stratum corneum in human skin, the corneocyte lipid envelope (CLE) is extremely important for the skin barrier. The importance of the CLE and esterified ω-hydroxy sphingosine (CerEOS), its main precursor, has been suggested from the fact that mutations in a number of genes involved in CerEOS synthesis and CLE formation have been identified as genetic causes of congenital ichthyoses, which are severe genetic skin disorders. However, the molecule/mechanism involved in the covalent binding of CerEOS to proteins on the outer surface of the cornified cell envelope had been a missing part. Very recently, we proposed new potential modes of protein binding by covalent reactions of CerEOS-epoxy-enone. We revealed the biochemical function of short-chain dehydrogenase/reductase family 9C member 7 (SDR9C7), encoded by SDR9C7, as catalyzing the dehydrogenation of the lipoxygenase products that are esterified in CerEOS. Epoxy-enone produced by SDR9C7 covalently binds to proteins on the outer extracellular surface of the cornified cell envelope. Importantly, our recent striking findings were derived from the detailed lipid analysis of only one ARCI patient with SDR9C7 mutation. The combination of detailed analyses of precious samples from a rare patient and the establishment of corresponding animal models is an effective and powerful tool for analyzing rare inherited diseases. This review summarizes this newly revealed mechanism in skin barrier formation, describes the characteristic features of patients with SDR9C7 mutations, and introduces the clinical value of non-invasive analyses for patients with very rare intractable skin diseases.

Melanogenic Difference Consideration in Ethnic Skin Type: A Balance Approach Between Skin Brightening Applications and Beneficial Sun Exposure

Human skin demonstrates a striking variation in tone and color that is evident among multiple demographic populations. Such characteristics are determined predominantly by the expression of the genes controlling the quantity and quality of melanin, which can alter significantly due to the presence of small nucleotide polymorphism affecting various steps of the melanogenesis process and generally linked to the lighter skin phenotypes. Genetically determined, constitutive skin color is additionally complemented by the facultative melanogenesis and tanning responses; with high levels of melanin and melanogenic factors broadly recognized to have a protective effect against the UVR-induced molecular damage in darker skin. Long-term sun exposure, together with a genetic makeup responsible for the ability to tan or the activity of constitutive melanogenic factors, triggers defects in pigmentation across all ethnic skin types. However, sun exposure also has well documented beneficial effects that manifest at both skin homeostasis and the systemic level, such as synthesis of vitamin D, which is thought to be less efficient in the presence of high levels of melanin or potentially linked to the polymorphism in the genes responsible for skin darkening triggered by UVR. In this review, we discuss melanogenesis in a context of constitutive pigmentation, defined by gene polymorphism in ethnic skin types, and facultative pigmentation that is not only associated with the capacity to protect the skin against photo-damage but could also have an impact on vitamin D synthesis through gene polymorphism. Modulating the activities of melanogenic genes, with the focus on the markers specifically altered by polymorphism combined with differential requirements of sun exposure in ethnic skin types, could enhance the applications of already existing skin brightening factors and provide a novel approach toward improved skin tone and health in personalized skincare.

Principal component analysis of seven skin-ageing features identifies three main types of skin ageing

BACKGROUND

The underlying phenotypic correlations between wrinkles, pigmented spots (PS), telangiectasia and other related facial-ageing subphenotypes are not well understood.

OBJECTIVES

To analyse the underlying phenotypic correlation structure between seven features for facial ageing: global wrinkling, perceived age (PA), Griffiths photodamage grading, PS, telangiectasia, actinic keratosis (AK) and keratinocyte cancer (KC).

METHODS

This was a cross-sectional study. Facial photographs and a full-body skin examination were used. We used principal component analysis (PCA) to derive principal components (PCs) of common variation between the features. We performed multivariable linear regressions between age, sex, body mass index, smoking and ultraviolet radiation exposure and the PC scores derived from PCA. We also tested the association between the main PC scores and 140 single-nucleotide polymorphisms (SNPs) previously associated with skin-ageing phenotypes.

RESULTS

We analysed data from 1790 individuals with complete data on seven features of skin ageing. Three main PCs explained 73% of the total variance of the ageing phenotypes: a hypertrophic/wrinkling component (PC1: global wrinkling, PA and Griffiths grading), an atrophic/skin colour component (PC2: PS and telangiectasia) and a cancerous component (PC3: AK and KC). The associations between lifestyle and host factors differed per PC. The strength of SNP associations also differed per component with the most SNP associations found with the atrophic component [e.g. the IRF4 SNP (rs12203592); P-value = 1·84 × 10^-22 ].

CONCLUSIONS

Using a hypothesis-free approach, we identified three major underlying phenotypes associated with extrinsic ageing. Associations between determinants for skin ageing differed in magnitude and direction per component. What's already known about this topic? Facial ageing is a complex phenotype consisting of different features including wrinkles, pigmented changes, telangiectasia and cancerous-related growths; it is not clear how these phenotypes are related to each other and to other phenotypes. A few studies have described two main clinical phenotypes for photoageing, namely hypertrophic ageing and atrophic ageing, which have been based solely on the clinical assessment of photoageing characteristics. What does this study add? We are the first to use epidemiology data to identify three main components associated with photoageing, namely a hypertrophic component (global wrinkling; perceived age; Griffiths grading) and atrophic component (pigmented spots; telangiectasia) and a cancer component (actinic keratosis; keratinocyte cancer). Association analysis showed different effects and direction of environmental determinants and genetic associations with the three components, with the most significant gene variants associations found for the atrophic component.

A Combined Multi-Cohort Approach Reveals Novel and Known Genome-Wide Selection Signatures for Wool Traits in Merino and Merino-Derived Sheep Breeds

Merino sheep represents a valuable genetic resource worldwide. In this study, we investigated selection signatures in Merino (and Merino-derived) sheep breeds using genome-wide SNP data and two different approaches: a classical F_ST-outlier method and an approach based on the analysis of local ancestry in admixed populations. In order to capture the most reliable signals, we adopted a combined, multi-cohort approach. In particular, scenarios involving four Merino breeds (Spanish Merino, Australian Merino, Chinese Merino, and Sopravissana) were tested via the local ancestry approach, while nine pair-wise breed comparisons contrasting the above breeds, as well as the Gentile di Puglia breed, with non-Merino breeds from the same geographic area were tested via the F_ST-outlier method. Signals observed using both methods were compared with genome-wide patterns of distribution of runs of homozygosity (ROH) islands. Novel and known selection signatures were detected. The most reliable signals were observed on OAR 3 (MSRB3 and LEMD3), OAR10 (FRY and RXFP2), OAR 13 (RALY), OAR17 (FAM101A), and OAR18 (NFKBIA, SEC23A, and PAX9). All the above overlapped with known QTLs for wool traits, and evidences from the literature of their involvement in skin/hair/wool biology, as well as gene network analysis, further corroborated these results. The signal on OAR10 also contains well known evidence for association with horn morphology and polledness. More elusive biological evidences of association with the Merino phenotype were observed for a number of other genes, notably LOC101120019 and TMEM132B (OAR17), LOC105609948 (OAR3), LOC101110773 (OAR10), and EIF2S2 (OAR17). Taken together, the above results further contribute to decipher the genetic basis underlying the Merino phenotype.

Basal cell carcinoma genetic susceptibility increases the rate of skin ageing: a Mendelian randomization study

BACKGROUND

Onset of basal cell carcinoma (BCC) is connected to skin ageing, but it is unclear whether higher BCC genetic susceptibility drives skin ageing.

OBJECTIVES

To investigate whether loci increasing genetic susceptibility to BCC also drive multiple features of skin ageing, independently of confounding factors, using Mendelian randomization.

METHODS

A Mendelian randomization study was conducted in older adults from the Leiden Longevity Study (N = 604). A total of 25 BCC loci, selected based on a published genome-wide association study on BCC (P-value < 5 × 10^-8 ), were used as genetic instruments for the calculation of a standardized (mean = 0, SD = 1) weighted BCC genetic risk score. Based on facial photographs, we determined perceived age, and skin wrinkling and pigmented spot grading.

RESULTS

A higher BCC genetic risk score was associated with a higher perceived age (adjusted for chronological age and sex) of 0.88 years (95% CI: 0.44, 1.31; P-value = 7.1e^-5 ), greater wrinkling by 0.14 grades (95% CI: 0.05, 0.23; P-value = 2.3e^-3 ), and greater pigmented spots by 0.17 grades (95% CI: 0.08, 0.25; P-value = 1.1e^-4 ). These findings were weakened but still present after exclusion of gene variants in MC1R and IRF4 which have potential pleiotropic effects.

CONCLUSIONS

Mechanisms influenced by genetic loci increasing susceptibility to BCC also drive skin ageing suggesting shared biology and shared targets for interventions.