Skin Phototype and Disease: A Comprehensive Genetic Approach to Pigmentary Traits Pleiotropy Using PRS in the GCAT Cohort

Validation of selection signatures for coat color in the Podolica Italiana gray cattle breed

Taurine and indicine gray cattle represent relevant livestock resources in many countries of the world. A gray coat color and pigmented skin, which are common in most of the gray cattle breeds, have been demonstrated to confer better adaptation to solar radiation and thermal stresses. In a previous study adopting the FST-outlier approach with BayeScan v2.0, we identified differentially selected genomic regions in a set of gray cattle breeds, including the Podolica Italiana, and contrasted these findings with four non-gray cattle breeds. More supported signals were detected on bovine chromosomes (BTAs) 2, 4, 14, and 26 that encompassed more than fifty genes known to be directly or indirectly related to one or more steps in pigment biology. In the present study, we aimed to validate the previously observed signals using the same methodological approach on three new Podolica Italiana sample sets (N = 30 animals each). These animals were selected from the ANABIC genetic station during performance tests as being representative of the Podolica Italiana population at three different timeframes separated by approximately 10 years each. We typed these samples to the loci of 23,027 quality-controlled single-nucleotide polymorphisms. We also analyzed the dataset using the haplotype-based approach available in hapFLK v1.4 software. Both the FST-outlier and hapFLK approaches validated the abovementioned signals on BTAs 2, 4, 14, and 26. Moreover, both methods detected additional supported regions on BTAs 7 and 18 that included a total of 42 genes, of which most were already known from literature to be implicated in pigmentation traits.

Genome wide association study and meta-analysis identified multiple new risk loci for freckles in 4813 Chinese individuals

Freckle is a prevalent pigmentary dermatosis with an obvious hereditary component. Dozens of freckles risk loci have been discovered through research on multiple traits or other diseases, rather than as an independent trait. To discover novel variants associated with freckles, we performed GWAS and meta-analysis in 4813 Chinese individuals. We conducted GWAS and meta-analysis of two cohorts: 197 patients and 1603 controls (Cohort I), and 336 patients and 2677 controls (Cohort II), both from China. Then we performed linkage disequilibrium (LD) analysis, eQTL study, and enrichment analysis with association results for functional implications. Finally, we discovered 59 new SNPs and 13 novel susceptibility genes associated with freckles (Pmeta <5 × 10-8), which has enriched the genetic research on freckles.

Retinoic acid, an essential component of the roof plate organizer, promotes the spatiotemporal segregation of dorsal neural fates

Dorsal neural tube-derived retinoic acid promotes the end of neural crest production and transition into a definitive roof plate. Here, we analyze how this impacts the segregation of central and peripheral lineages, a process essential for tissue patterning and function. Localized in ovo inhibition in quail embryos of retinoic acid activity followed by single-cell transcriptomics unraveled a comprehensive list of differentially expressed genes relevant to these processes. Importantly, progenitors co-expressed neural crest, roof plate and dI1 interneuron markers, indicating a failure in proper lineage segregation. Furthermore, separation between roof plate and dI1 interneurons is mediated by Notch activity downstream of retinoic acid, highlighting their crucial role in establishing the roof plate-dI1 boundary. Within the peripheral branch, where absence of retinoic acid resulted in neural crest production and emigration extending into the roof plate stage, sensory progenitors failed to separate from melanocytes, leading to formation of a common glia-melanocyte cell with aberrant migratory patterns. In summary, the implementation of single-cell RNA sequencing facilitated the discovery and characterization of a molecular mechanism responsible for the segregation of dorsal neural fates during development.

Editorial on the Special Issue "Genetic and Molecular Basis of Inherited Disorders"

This Special Issue of Genes, titled "Genetic and Molecular Basis of Inherited Disorders", presents a collection of pioneering research articles that advance our understanding of the genetic mechanisms underlying various hereditary diseases. The studies employ cutting-edge genomic techniques, including next-generation sequencing and genome-wide association studies, to elucidate novel genetic variants and their functional implications. Key investigations span a diverse range of conditions, from congenital idiopathic nystagmus and hereditary hearing loss to familial hypercholesterolemia and rare cancer predisposition syndromes. Notable findings include the identification of new gene-disease associations in congenital anomalies of the kidney and urinary tract, the discovery of large genomic rearrangements in breast cancer susceptibility, and insights into the genetic basis of pigmentary traits and associated disease risks. This Special Issue also highlights the significance of copy number variations and rare structural variants in disease pathogenesis. Collectively, these studies underscore the complexity of genetic variation in inherited disorders and demonstrate the critical role of integrating advanced genetic analyses with clinical practice to enhance diagnostic precision and develop targeted therapeutic approaches.

Childhood sunburn and risk of melanoma and non-melanoma skin cancer: a Mendelian randomization study

Previous evidence has suggested that childhood sunburn could be a risk factor for cutaneous malignant melanoma (MM) and non-melanoma skin cancer (NMSC). However, existing observational studies could not reveal the causal associations genetically. This study aimed to investigate whether there was a genetic causal relationship between childhood sunburn and skin cancers. Univariable Mendelian randomization (MR) and Causal Analysis Using Summary Effect analysis was carried out for causal estimates and evaluation for the horizontal pleiotropy. Multivariable MR and the mediation effects analysis were used to test whether the causal associations were mediated by potential confounders. A suggestively significant causal association between childhood sunburn and MM was indicated (OR = 4.74; 95% CI: 1.31-17.19; p = 1.79E-02). Genetically predicted childhood sunburn was significantly associated with increased risk of overall melanoma in situ (MIS) (OR = 4.02; 95% CI: 2.00-8.08; p = 9.40E-05), MIS of face (OR = 18.28; 95% CI: 5.28-63.35; p = 4.59E-06), and MIS of trunk (OR = 7.05; 95% CI: 2.06-24.13; p = 1.88E-03). Similar trends were found for childhood sunburn and NMSC (OR = 8.16; 95% CI: 6.07-10.99; p = 1.53E-20), including both basal cell carcinoma (BCC) (OR = 3.76; 95% CI:2.96-4.77; p = 2.19E-08) and squamous cell carcinoma (SCC) (OR = 7.44; 95% CI: 5.09-10.87; p = 2.19E-08). After adjustment for hair and skin color, facial ageing, vitamin D levels, body mass index, alcohol consumption, and smoking status, childhood sunburn showed an independent association with MIS, MIS of face, MIS of trunk, as well as NMSC, including both BCC and SCC. Mediation analysis showed no significant mediation effect. This study demonstrated a causal relationship between childhood sunburn and the risk of both MM and NMSC, which suggested that enhanced screening and prevention for childhood sunburn could contribute to the early detection and decreased risk of MM and NMSC.