Genome-wide association study of psoriasis in an Egyptian population

Sex-dependent association of central circadian clock gene polymorphisms with clinical risk markers for noncommunicable diseases in the young population

BACKGROUND

The circadian clock, which governs periodic physiological changes, is influenced by various environmental factors, and its disruptions can lead to non-communicable chronic diseases (NCDs). Among the genes that control the circadian clock are ARNTL, CLOCK, CRY1, PER1, PER2, NR1D2, and MTNR1B, with several polymorphisms associated with diseases such as diabetes and hypertension. Therefore, this study aimed to determine the association between SNPs in the aforementioned genes and markers of non-communicable chronic diseases (NCDs) in a young population, stratified by gender.

METHODS

A sample of 346 individuals of both sexes aged 18 to 27 underwent clinical and nutritional evaluations to determine clinical markers associated with NCDs. Using isothermal PCR, 119 polymorphisms in the ARNTL, CLOCK, CRY1, PER1, PER2, NR1D2, and MTNR1B genes were determined. Subsequently, binary logistic regression analyses and mean comparisons using Student's t-test and one-way ANOVA with Bonferroni adjustment were performed.

RESULTS

Polymorphisms were associated with risk factors such as elevated waist circumference, BMI, insulin, and lipid imbalances, while some acted protectively. Notable SNPs included rs6486122, rs77486964, rs11022756, rs72869158 from ARNTL; rs7309618, rs10778528 from CRY1; rs2304911 from PER1; rs72620839, rs58574366 from PER2; rs6832769, rs1056547 from CLOCK; and rs4858095, rs11922577 from NR1D2, providing insights into the associations of genetic markers with clinically relevant markers for NCDs.

CONCLUSION

Clock gene polymorphisms exhibit associations with clinical markers of NCDs, emphasizing the intricate interaction between the biological clock and risk factors. This underscores the importance of genetic testing and personalized clinical approaches for prevention and treatment. Further research is needed to understand the underlying mechanisms and long-term health impacts of these genetic variations.

The Role of Genetics on Psoriasis Susceptibility, Comorbidities, and Treatment Response

This review highlights advances made in psoriasis genetics, including findings from genome-wide association studies, exome-sequencing studies, and copy number variant studies. The impact of genetic variants on various comorbidities and therapeutic responses is discussed.

Genome-wide association study for systemic lupus erythematosus in an egyptian population

Systemic lupus erythematosus (SLE) susceptibility has a strong genetic component. Genome-wide association studies (GWAS) across trans-ancestral populations show both common and distinct genetic variants of susceptibility across European and Asian ancestries, while many other ethnic populations remain underexplored. We conducted the first SLE GWAS on Egyptians-an admixed North African/Middle Eastern population-using 537 patients and 883 controls. To identify novel susceptibility loci and replicate previously known loci, we performed imputation-based association analysis with 6,382,276 SNPs while accounting for individual admixture. We validated the association analysis using adaptive permutation tests (n = 109). We identified a novel genome-wide significant locus near IRS1/miR-5702 (Pcorrected = 1.98 × 10-8) and eight novel suggestive loci (Pcorrected < 1.0 × 10-5). We also replicated (Pperm < 0.01) 97 previously known loci with at least one associated nearby SNP, with ITGAM, DEF6-PPARD and IRF5 the top three replicated loci. SNPs correlated (r 2 > 0.8) with lead SNPs from four suggestive loci (ARMC9, DIAPH3, IFLDT1, and ENTPD3) were associated with differential gene expression (3.5 × 10-95 < p < 1.0 × 10-2) across diverse tissues. These loci are involved in cellular proliferation and invasion-pathways prominent in lupus and nephritis. Our study highlights the utility of GWAS in an admixed Egyptian population for delineating new genetic associations and for understanding SLE pathogenesis.

Variants in PRKCE and KLC1, Potential Regulators of Type I Psoriasis

Purpose

Psoriasis is a multifactorial disease with a complex genetic predisposition. The pathophysiology of psoriasis is associated with genetic variants. To better characterize gene variants in psoriasis and identify the relationship between clinical characteristics and variant genes in its pathogenesis.

Patients and Methods

DNA was extracted and purified from eight pairs of monozygotic twins with psoriasis discordance and 282 type I psoriasis patients. Thirteen variable genes were amplified and sequenced using the Sanger method after whole genome sequencing.

Results

Thirteen genes were found to be variable in eight pairs of monozygotic twins with psoriasis discordance. Among the 13 genes, the variant frequencies of protein kinase C epsilon (PRKCE) (c.240T>C, 35.9% vs 47.7%, P < 0.05) and kinesin light chain 1 (KLC1) (c.216A>G, 2.9% vs 98.1%, P< 0.01) were significantly lower in psoriasis than in normal Asian individuals. Additionally, we found considerable differences in the relationship between variants in genes CADM2, JPH2, SPTLC3 and clinical characteristics stratified by medical history and family history. Moreover, the variants in MEGF6 (39.52% vs 22.50%, χ²=3.83, p < 0.05) showed a stronger association with the mild group (PASI ≤10) than the heavy group.

Conclusion

Our results provide a comprehensive correlation analysis of regulatory genes that are regulated in psoriasis. This integrated analysis offers novel insight into the pathogenic mechanisms involved in psoriasis.

Break on through: The role of innate immunity and barrier defence in atopic dermatitis and psoriasis

The human skin can be affected by a multitude of diseases including inflammatory conditions such as atopic dermatitis and psoriasis. Here, we describe how skin barrier integrity and immunity become dysregulated during these two most common inflammatory skin conditions. We summarise recent advances made in the field of the skin innate immune system and its interaction with adaptive immunity. We review gene variants associated with atopic dermatitis and psoriasis that affect innate immune mechanisms and skin barrier integrity. Finally, we discuss how current and future therapies may affect innate immune responses and skin barrier integrity in a generalized or more targeted approach in order to ameliorate disease in patients.

Roles Played by Stress-Induced Pathways in Driving Ethnic Heterogeneity for Inflammatory Skin Diseases

Immune-mediated skin conditions (IMSCs) are a diverse group of autoimmune diseases associated with significant disease burden. Atopic dermatitis and psoriasis are among the most common IMSCs in the United States and have disproportionate impact on racial and ethnic minorities. African American patients are more likely to develop atopic dermatitis compared to their European American counterparts; and despite lower prevalence of psoriasis among this group, African American patients can suffer from more extensive disease involvement, significant post-inflammatory changes, and a decreased quality of life. While recent studies have been focused on understanding the heterogeneity underlying disease mechanisms and genetic factors at play, little emphasis has been put on the effect of psychosocial or psychological stress on immune pathways, and how these factors contribute to differences in clinical severity, prevalence, and treatment response across ethnic groups. In this review, we explore the heterogeneity of atopic dermatitis and psoriasis between African American and European American patients by summarizing epidemiological studies, addressing potential molecular and environmental factors, with a focus on the intersection between stress and inflammatory pathways.

PSORS1 Locus Genotyping Profile in Psoriasis: A Pilot Case-Control Study

(1) Background: The psoriasis susceptibility 1 (PSORS1) locus, located within the major histocompatibility complex, is one of the main genetic determinants for psoriasis, the genotyping profile for three single-nucleotide polymorphisms (SNPs) comprising the PSORS1 locus: rs1062470 within PSORS1C1/CDSN genes, rs887466 within PSORS1C3 gene, rs10484554 within LOC105375015 gene, were investigated and correlated with psoriasis risk and severity. (2) Methods: This pilot case-controlled study involved 100 psoriatic patients and 100 healthy individuals. We investigated three SNPs and assessed the relative gene expression profile for the PSORS1C1 gene. We then correlated the results with both disease risk and severity. (3) Results: The most significantly associated SNP in PSORS1 locus with psoriasis was rs10484554 with its C/T genotype 5.63 times more likely to develop psoriasis under codominant comparison. Furthermore, C/T and T/T genotypes were 5 times more likely to develop psoriasis. The T allele was 3 times more likely to develop psoriasis under allelic comparison. The relative gene expression of PSORS1C1 for psoriatic patients showed to be under-expressed compared to normal controls. (4) Conclusions: Our study revealed the association of the three studied SNPs with psoriasis risk and severity in an Egyptian cohort, indicating that rs10484554 could be the major key player in the PSORS1 locus.

Insights into interplay of immunopathophysiological events and molecular mechanistic cascades in psoriasis and its associated comorbidities

Psoriasis is an inflammatory skin disease with complex pathogenesis and multiple etiological factors. Besides the essential role of autoreactive T cells and constellation of cytokines, the discovery of IL-23/Th17 axis as a central signaling pathway has unraveled the mechanism of accelerated inflammation in psoriasis. This has provided insights into psoriasis pathogenesis and revolutionized the development of effective biological therapies. Moreover, genome-wide association studies have identified several candidate genes and susceptibility loci associated with this disease. Although involvement of cellular innate and adaptive immune responses and dysregulation of immune cells have been implicated in psoriasis initiation and maintenance, there is still a lack of unifying mechanism for understanding the pathogenesis of this disease. Emerging evidence suggests that psoriasis is a high-mortality disease with additional burden of comorbidities, which adversely affects the treatment response and overall quality of life of patients. Furthermore, changing trends of psoriasis-associated comorbidities and shared patterns of genetic susceptibility, risk factors and pathophysiological mechanisms manifest psoriasis as a multifactorial systemic disease. This review highlights the recent progress in understanding the crucial role of different immune cells, proinflammatory cytokines and microRNAs in psoriasis pathogenesis. In addition, we comprehensively discuss the involvement of various complex signaling pathways and their interplay with immune cell markers to comprehend the underlying pathophysiological mechanism, which may lead to exploration of new therapeutic targets and development of novel treatment strategies to reduce the disastrous nature of psoriasis and associated comorbidities.

Clock Regulation of Skin Regeneration in Stem Cell Aging

The circadian clockwork evolved as an adaptation to daily environmental changes and allows temporal alignment of functions between cells and organs on a systemic level in complex multicellular organisms. These clock functions are particularly important in the skin, which is directly exposed to the external environment. Recent studies have revealed the important impact of circadian rhythmicity on stem cell (SC) homeostasis and regeneration in both young and old skin. This review discusses how the circadian clock regulates tissue function in skin-resident SCs and their niche and how altered daily rhythms in aged SCs negatively affect skin regeneration.

An integrated personal and population-based Egyptian genome reference

A small number of de novo assembled human genomes have been reported to date, and few have been complemented with population-based genetic variation, which is particularly important for North Africa, a region underrepresented in current genome-wide references. Here, we combine long- and short-read whole-genome sequencing data with recent assembly approaches into a de novo assembly of an Egyptian genome. The assembly demonstrates well-balanced quality metrics and is complemented with variant phasing via linked reads into haploblocks, which we associate with gene expression changes in blood. To construct an Egyptian genome reference, we identify genome-wide genetic variation within a cohort of 110 Egyptian individuals. We show that differences in allele frequencies and linkage disequilibrium between Egyptians and Europeans may compromise the transferability of European ancestry-based genetic disease risk and polygenic scores, substantiating the need for multi-ethnic genome references. Thus, the Egyptian genome reference will be a valuable resource for precision medicine.

Variation at ACOT12 and CT62 locus represents susceptibility to psoriasis in Han population

Background

Psoriasis is a chronic inflammatory disorder of the skin, and genetic factors are reported to be involved in the disease pathogenesis. Many studies have named psoriasis candidate genes.

Objective

In this study, we determined the mutation frequency of 7 variable genes in 1,027 psoriatic patients and investigated its possible mechanism associated with psoriasis.

Method

A total of 7 variable genes from 1,027 psoriatic patients were amplified and sequenced using the Sanger method. The mutation frequency was compared to that of non‐psoriatic individuals in Asia using information from databases.

Results

Among the 7 investigated genes, the mutation frequency of ACOT12 (c.80A>G, 9.98% vs. 5.85%, p < .05) and CT62 (c.476C>T,15.8% vs. 9.93%, p < .05) was found to be significantly higher than among non‐psoriatic Asian individuals. The mutation frequencies of CASZ1(c.599T>G), SPRED1(c.155A>G), and ACOT12 (c.80A>G) differed significantly between the groups organized by medical history, PASI, and family history. SPRED1 gene variants (17.25% vs. 7.78%, p < .01) showed a stronger association with the family history group at the onset of psoriasis than with the no family history group.

Conclusions

Our results provide a comprehensive correlation analysis of susceptibility genes in psoriasis patients. Clinical characteristics of patients play important roles in the development of psoriatic skin.