RNAseq-Based Prioritization Revealed COL6A5, COL8A1, COL10A1 and MIR146A as Common and Differential Susceptibility Biomarkers for Psoriasis and Psoriatic Arthritis: Confirmation from Genotyping Analysis of 1417 Italian Subjects

Exploration of Conserved Human Adipose Subpopulations Using Targeted Single-Nuclei RNA Sequencing Data Sets

BACKGROUND

Smooth-muscle cells and pericytes are mural cells. Pericytes can differentiate into myofibroblasts, chondrocytes, vascular smooth-muscle cells, and adipocytes, marking them as a distinct progenitor population. Our goal was to molecularly define the progenitor cell populations in human adipose tissues and test the adipogenic potential of human mural cells.

METHODS

We used informatic analysis of single-cell RNA sequencing data from human tissues to identify and define pericytes and adipose progenitor cells found in human adipose tissues, including perivascular, brown, and white adipose tissues.

RESULTS

We established tissue-specific patterns of gene expression in pericytes and other putative human adipocyte progenitor cells. PPARG-expressing pericytes were present in multiple human adipose depots with consistent expression of COL25A1, MYO1B, and POSTN. We also found evidence of tissue-specific pericyte markers. Although there is some conservation between human and mouse adipose tissues, human pericyte populations have unique, depot-specific gene expression signatures. Immunofluorescence staining of human adipose tissue revealed the presence of pericytes both distant from and adjacent to vasculature in human adipose tissue. Additionally, we demonstrated the potential of human brain pericytes and aortic vascular smooth-muscle cells to differentiate into adipocytes in vitro on the basis of intracellular lipid accumulation and expression of adipocyte markers.

CONCLUSIONS

Human adipose cell populations are distinct from mice, and the pericyte subpopulation in human adipose tissues are present across adipose depots. Given that vascular mural cells, including pericytes and smooth-muscle cells, can undergo adipogenesis, we postulate that they are a novel source of adipocytes in the vascular microenvironment.

Biomarkers of Extracellular Matrix Fragments in Patients with Psoriasis

Blood-based extracellular matrix (ECM) fragments have been identified as potential pharmacologic biomarkers in spondyloarthritis and diagnostic biomarkers in psoriatic arthritis and psoriasis vulgaris. This study aimed to explore whether ECM fragments can differentiate patients with psoriasis from healthy controls (HC) and determine their potential as biomarkers for response to treatment in psoriasis. The study population included 59 patients with moderate to severe psoriasis, not receiving systemic anti-psoriatic treatment at inclusion, and 52 HC matched by age, sex, and BMI. An EDTA plasma sample was taken from all subjects at inclusion. Nine patients with psoriasis who initiated treatment with adalimumab after inclusion and responded successfully had an additional EDTA plasma sample taken after three to six months. Twelve ECM fragments were measured using validated ELISAs and Immunodiagnostic Systems automated chemiluminescent assays. C4M, indicating collagen IV degradation, PRO-C3, indicating tissue fibrosis, and PRO-C4, indicating epidermal basement membrane turnover showed significantly elevated levels in psoriasis patients compared with HC (p = 0.005, p = 0.016, and p = 0.018, respectively). Despite successful treatment, adalimumab did not alter C4M, PRO-C3, or PRO-C4 levels. In conclusion, compared with controls, C4M, PRO-C3, and PRO-C4 were elevated in psoriasispatients, but treatment did not modulate these fragments.

Clinical, genetic and omics-based biomarkers that might support the identification of the development of psoriatic arthritis in individuals with psoriasis: a narrative review of the literature

It is known that 25%-30% of individuals with cutaneous psoriasis (PsC) will develop psoriatic arthritis (PsA). To date, the reasons for the development of PsA in individuals with PsC have not been identified. Furthermore, there are considerable delays in the diagnosis and treatment of PsA, which lead to joint and bone deformation and chronic pain. It is therefore important to develop more precise diagnostic and screening tools. In this narrative review of the literature, clinical risk factors and novel molecular biomarkers (genetic markers, blood and inflammatory markers, lipid, metabolite and protein biomarkers) have been evaluated. The review included 38 publications that were reported between May 2020 and May 2024. Similar to previous reviews, nail involvement was one of the strongest clinical risk factors for the development of PsA, while molecular biomarkers did not provide a clear and robust differentiation between PsC and PsA groups. The seemingly poor performance of molecular markers may be largely attributed to small study populations and heterogeneity in study designs. Data and sample sharing in large consortia such as HIPPOCRATES (Health initiatives in Psoriasis and PsOriatic arthritis ConsoRTium European States) could help to overcome the limitations of small studies and enable the development of more robust diagnostic and screening tools for PsA.

Stiffness-Dependent Lysyl Oxidase Regulation through Hypoxia-Inducing Factor 1 Drives Extracellular Matrix Modifications in Psoriasis

Psoriasis is a common chronic inflammatory skin disease characterized by a thickened epidermis with elongated rete ridges and massive immune cell infiltration. It is currently unclear what impact mechanoregulatory aspects may have on disease progression. Using multiphoton second harmonic generation microscopy, we found that the extracellular matrix was profoundly reorganized within psoriatic dermis. Collagen fibers were highly aligned and assembled into thick, long collagen bundles, whereas the overall fiber density was reduced. This was particularly pronounced within dermal papillae extending into the epidermis. Furthermore, the extracellular matrix-modifying enzyme lysyl oxidase was highly upregulated in the dermis of patients with psoriasis. In vitro experiments identified a previously unreported link between hypoxia-inducing factor 1 stabilization and lysyl oxidase protein regulation in mechanosensitive skin fibroblasts. Lysyl oxidase secretion and activity directly correlated with substrate stiffness and were independent of hypoxia and IL-17. Finally, single-cell RNA-sequencing analysis identified skin fibroblasts expressing high amounts of lysyl oxidase and confirmed elevated hypoxia-inducing factor 1 expression in psoriasis. Our findings suggest a potential yet undescribed mechanical aspect of psoriasis. Deregulated mechanical forces hence may be involved in initiating or maintaining of a positive feedback loop in fibroblasts and contribute to tissue stiffening and diminished skin elasticity in psoriasis, potentially exacerbating disease pathogenesis.

Risk and Resilience Variants in the Retinoic Acid Metabolic and Developmental Pathways Associated with Risk of FASD Outcomes

Fetal Alcohol Spectrum Disorder (FASD) is a common neurodevelopmental disorder that affects an estimated 2-5% of North Americans. FASD is induced by prenatal alcohol exposure (PAE) during pregnancy and while there is a clear genetic contribution, few genetic factors are currently identified or understood. In this study, using a candidate gene approach, we performed a genetic variant analysis of retinoic acid (RA) metabolic and developmental signaling pathway genes on whole exome sequencing data of 23 FASD-diagnosed individuals. We found risk and resilience alleles in ADH and ALDH genes known to normally be involved in alcohol detoxification at the expense of RA production, causing RA deficiency, following PAE. Risk and resilience variants were also identified in RA-regulated developmental pathway genes, especially in SHH and WNT pathways. Notably, we also identified significant variants in the causative genes of rare neurodevelopmental disorders sharing comorbidities with FASD, including STRA6 (Matthew-Wood), SOX9 (Campomelic Dysplasia), FDG1 (Aarskog), and 22q11.2 deletion syndrome (TBX1). Although this is a small exploratory study, the findings support PAE-induced RA deficiency as a major etiology underlying FASD and suggest risk and resilience variants may be suitable biomarkers to determine the risk of FASD outcomes following PAE.

Disentangling archaic introgression and genomic signatures of selection at human immunity genes

Pathogens and infectious diseases have imposed exceptionally strong selective pressure on ancient and modern human genomes and contributed to the current variation in many genes. There is evidence that modern humans acquired immune variants through interbreeding with ancient hominins, but the impact of such variants on human traits is not fully understood. The main objectives of this research were to infer the genetic signatures of positive selection that may be involved in adaptation to infectious diseases and to investigate the function of Neanderthal alleles identified within a set of 50 Lithuanian genomes. Introgressed regions were identified using the machine learning tool ArchIE. Recent positive selection signatures were analysed using iHS. We detected high-scoring signals of positive selection at innate immunity genes (EMB, PARP8, HLAC, and CDSN) and evaluated their interactions with the structural proteins of pathogens. Interactions with human immunodeficiency virus (HIV) 1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. Overall, genomic regions introgressed from Neanderthals were shown to be enriched in genes related to immunity, keratinocyte differentiation, and sensory perception.

Selected miRNA and Psoriasis-Cardiovascular Disease (CVD)-Overweight/Obesity Network-A Pilot Study

Psoriasis is nowadays recognized as a multifactorial systemic disease with complex and not fully understood pathogenesis. In psoriatic patients, the increased cardiovascular disease (CVD) risk and frequent comorbidities like obesity are observed. The aim of this study was to investigate differences in miRNA (miR-22-3p, miR-133a-3p, miR-146a-5p, miR-369-3p, and Let-7b-5p) involved in CVD risk among psoriatic patients with overweight/obesity and with normal weight. The study comprised 28 male psoriatic patients and 16 male healthy controls. miRNA isolated from peripheral blood mononuclear cells was reverse-transcribed and RT-qPCR was performed. We have found decreased levels of miR-22, miR-133a, miR-146a, and miR-369 among the psoriatic patients. There was a statistically significant difference in miR-22 and miR-146a levels between psoriatic patients with overweight/obesity and with normal weight. There were positive correlations between miR-22 and miR-146a levels and psoriatic arthritis (PsA) in psoriatic patients with normal weight and between the miR-133a level and PsA in the overweight/obese patients. The decreased levels of selected miRNA are consistent with the levels observed in CVD indicating their impact on the CVD risk in psoriatic patients. miR-22 and miR-146 may be recognized as one of the contributing factors in the obesity-CVD-psoriasis network.

Alopecia in Patients with Collagen VI-Related Myopathies: A Novel/Unrecognized Scalp Phenotype

Collagen VI-related myopathies are characterized by severe muscle involvement and skin involvement (keratosis pilaris and impaired healing with the development of abnormal scars, especially keloids). Scalp involvement and hair loss have not been reported among cutaneous changes associated with collagen VI mutations. The aim of this study is to describe the clinical, trichoscopic, and histological findings of the scalp changes in patients affected by COL VI mutations and to estimate their prevalence. Patients with Ullrich congenital muscular dystrophy were enrolled and underwent clinical and trichoscopic examinations and a scalp biopsy for histopathology. Five patients were enrolled, and all complained of hair loss and scalp itching. One patient showed yellow interfollicular scales with erythema and dilated, branched vessels, and the histological findings were suggestive of scalp psoriasis. Two patients presented with scarring alopecia patches on the vertex area, and they were histologically diagnosed with folliculitis decalvans. The last two patients presented with scaling and hair thinning, but they were both diagnosed with folliculitis and perifolliculitis. Ten more patients answered to a "scalp involvement questionnaire", and six of them confirmed to have or have had scalp disorders and/or itching. Scalp involvement can be associated with COL VI mutations and should be investigated.

Biomarkers in psoriatic arthritis: A meta-analysis and systematic review

Introduction

Psoriatic arthritis (PsA) is a chronic inflammatory disease that frequently develops in patients with psoriasis (PsO) but can also occur spontaneously. As a result, PsA diagnosis and treatment is commonly delayed, or even missed outright due to the manifold of clinical presentations that patients often experience. This inevitably results in progressive articular damage to axial and peripheral joints and entheses. As such, patients with PsA frequently experience reduced expectancy and quality of life due to disability. More recently, research has aimed to improve PsA diagnosis and prognosis by identifying novel disease biomarkers.

Methods

Here, we conducted a systematic review of the published literature on candidate biomarkers for PsA diagnosis and prognosis in MEDLINE(Pubmed), EMBase and the Cochrane library with the goal to identify clinically applicable PsA biomarkers. Meta-analyses were performed when a diagnostic bone and cartilage turnover biomarker was reported in 2 or moredifferent cohorts of PsA and control.

Results

We identified 1444 publications and 124 studies met eligibility criteria. We highlighted bone and cartilage turnover biomarkers, genetic markers, and autoantibodies used for diagnostic purposes of PsA, as well as acute phase reactant markers and bone and cartilage turnover biomarkers for activity or prognostic severity purposes. Serum cartilage oligometrix metalloproteinase levels were significantly increased in the PsA sera compared to Healthy Control (HC) with a standardized mean difference (SMD) of 2.305 (95%CI 0.795-3.816, p=0.003) and compared to osteoarthritis (OA) with a SMD of 0.783 (95%CI 0.015-1.551, p=0.046). The pooled serum MMP-3 levels were significantly higher in PsA patients than in PsO patients with a SMD of 0.419 (95%CI 0.119-0.719; p=0.006), but no significant difference was highlighted when PsA were compared to HC. While we did not identify any new genetic biomarkers that would be useful in the diagnosis of PsA, recent data with autoantibodies appear to be promising in diagnosis, but no replication studies have been published.

Conclusion

In summary, no specific diagnostic biomarkers for PsA were identified and further studies are needed to assess the performance of potential biomarkers that can distinguish PsA from OA and other chronic inflammatory diseases.

Selection of Cashmere Fineness Functional Genes by Translatomics

Cashmere fineness is an important index to evaluate cashmere quality. Liaoning Cashmere Goat (LCG) has a large cashmere production and long cashmere fiber, but its fineness is not ideal. Therefore, it is important to find genes involved in cashmere fineness that can be used in future endeavors aiming to improve this phenotype. With the continuous advancement of research, the regulation of cashmere fineness has made new developments through high-throughput sequencing and genome-wide association analysis. It has been found that translatomics can identify genes associated with phenotypic traits. Through translatomic analysis, the skin tissue of LCG sample groups differing in cashmere fineness was sequenced by Ribo-seq. With these data, we identified 529 differentially expressed genes between the sample groups among the 27197 expressed genes. From these, 343 genes were upregulated in the fine LCG group in relation to the coarse LCG group, and 186 were downregulated in the same relationship. Through GO enrichment analysis and KEGG enrichment analysis of differential genes, the biological functions and pathways of differential genes can be found. In the GO enrichment analysis, 491 genes were significantly enriched, and the functional region was mainly in the extracellular region. In the KEGG enrichment analysis, the enrichment of the human papillomavirus infection pathway was seen the most. We found that the COL6A5 gene may affect cashmere fineness.

Identification of Diagnostic Biomarkers Associated with Stromal and Immune Cell Infiltration in Fatty Infiltration After Rotator Cuff Tear by Integrating Bioinformatic Analysis and Machine-Learning

Purpose

The present study aimed to explore potential diagnostic biomarkers for fatty infiltration (FI) of the rotator cuff muscles after rotator cuff tear (RCT) and investigate the influence of stromal and immune cell infiltration on this pathology.

Methods

The GSE130447 and GSE103266 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified, and gene set enrichment analyses were performed by R software. Two machine learning algorithms, random forest and multiple support vector machine recursive feature elimination (mSVM-RFE), were used to screen candidate biomarkers. The diagnostic value of the screened biomarkers was further validated by the area under the ROC curve (AUC) in the GSE103266 dataset. Murine microenvironment cell population counter (mMCP-counter) method was employed to estimate stromal and immune cell infiltration of FI. The correlation between biomarkers and infiltrated immune and stromal cell subsets was further analyzed.

Results

A total of 2123 DEGs were identified. The identified DEGs were predominantly linked to immune system process, extracellular matrix organization and PPAR signalling pathway. FABP5 (AUC = 0.958) and MGP (AUC = 1) were screened as diagnostic biomarkers of FI. Stromal and immune cell infiltration analysis showed that monocytes, mast cells, vessels, endothelial cells and fibroblasts may be related to the process of FI. FABP5 and MGP were positively correlated with vessels whereas negatively correlated with monocytes and mast cells.

Conclusion

FABP5 and MGP can serve as diagnostic biomarkers of FI after RCT, and stromal and immune cell infiltration may play a crucial role in this pathology.

Meta-Analysis of miRNA Variants Associated with Susceptibility to Autoimmune Disease

Purpose

Various studies have shown an association between miRNA polymorphisms and susceptibility to autoimmune disease (AD); however, the results are inconclusive. To evaluate whether miRNA polymorphisms account for a significant risk of AD, a total of 87 articles, including 39431 patients and 56708 controls, were identified to estimate their association with 12 AD subtypes.

Methods

Several electronic databases were searched to analyze population-based studies on the relationship between miRNA variants and AD risk. Fixed effects or random effect models were used in the meta-analysis for the risk assessment.

Results

In our meta-analysis, miR-146a rs2910164/rs57095329 conferred a marginally elevated risk for AD (allele model, OR = 1.08, 95% CI: 1.01-1.15, P = 0.019; allele model, OR = 1.09, 95 CI: 1.05-1.15, P < 0.001, respectively). Furthermore, miR-196a2 rs11614913 was also associated with AD risk (allele model, OR = 0.92, 95% CI: 0.88-0.97, P = 0.001) as well as miR-499 rs3746444 (allele model, OR = 1.16, 95% CI: 1.03-1.29, P = 0.011). In addition, associations were observed between miR-149 rs2292832/miR-27a rs895819 and AD susceptibility in the overall population (allele model, OR = 1.15, 95% CI: 1.06-1.24, P < 0.001; allele model, OR = 1.11, 95% CI:1.01-1.22, P = 0.043, respectively).

Conclusions

Evidence from our systematic review suggests that miR-146a, miR-196a2, miR-499, miR-149, and miR-27a polymorphisms are associated with susceptibility to AD.

Skin Barrier Dysregulation in Psoriasis

The skin barrier is broadly composed of two elements-a physical barrier mostly localised in the epidermis, and an immune barrier localised in both the dermis and epidermis. These two systems interact cooperatively to maintain skin homeostasis and overall human health. However, if dysregulated, several skin diseases may arise. Psoriasis is one of the most prevalent skin diseases associated with disrupted barrier function. It is characterised by the formation of psoriatic lesions, the aberrant differentiation and proliferation of keratinocytes, and excessive inflammation. In this review, we summarize recent discoveries in disease pathogenesis, including the contribution of keratinocytes, immune cells, genetic and environmental factors, and how they advance current and future treatments.

Pharmacogenomics: An Update on Biologics and Small-Molecule Drugs in the Treatment of Psoriasis

Pharmacogenomic studies allowed the reasons behind the different responses to treatments to be understood. Its clinical utility, in fact, is demonstrated by the reduction in adverse drug reaction incidence and the improvement of drug efficacy. Pharmacogenomics is an important tool that is able to improve the drug therapy of different disorders. In particular, this review will highlight the current pharmacogenomics knowledge about biologics and small-molecule treatments for psoriasis. To date, studies performed on genes involved in the metabolism of biological drugs (tumor necrosis factor inhibitors and cytokines inhibitors) and small molecules (apremilast, dimethyl fumarate, and tofacitinib) have provided conflicting results, and further investigations are necessary in order to establish a set of biomarkers to be introduced into clinical practice.

The Molecular Pathophysiology of Psoriatic Arthritis-The Complex Interplay Between Genetic Predisposition, Epigenetics Factors, and the Microbiome

Psoriasis is a symmetric autoimmune/inflammatory disease that primarily affects the skin. In a significant proportion of cases, it is accompanied by arthritis that can affect any joint, the spine, and/or include enthesitis. Psoriasis and psoriatic arthritis are multifactor disorders characterized by aberrant immune responses in genetically susceptible individuals in the presence of additional (environmental) factors, including changes in microbiota and/or epigenetic marks. Epigenetic changes can be heritable or acquired (e.g., through changes in diet/microbiota or as a response to therapeutics) and, together with genetic factors, contribute to disease expression. In psoriasis, epigenetic alterations are mainly related to cell proliferation, cytokine signaling and microbial tolerance. Understanding the complex interplay between heritable and acquired pathomechanistic factors contributing to the development and maintenance of psoriasis is crucial for the identification and validation of diagnostic and predictive biomarkers, and the introduction of individualized effective and tolerable new treatments. This review summarizes the current understanding of immune activation, genetic, and environmental factors that contribute to the pathogenesis of psoriatic arthritis. Particular focus is on the interactions between these factors to propose a multifactorial disease model.

Overview of the molecular determinants contributing to the expression of Psoriasis and Psoriatic Arthritis phenotypes

Psoriasis and psoriatic arthritis are multifactorial chronic disorders whose etiopathogenesis essentially derives from the alteration of several signalling pathways and the co-occurrence of genetic, epigenetic and non-genetic susceptibility factors that altogether affect the functional and structural property of the skin. Although shared and differential susceptibility genes and molecular pathways are known to contribute to the onset of pathological phenotypes, further research is needed to dissect the molecular causes of psoriatic disease and its progression towards Psoriatic Arthritis. This review will therefore be addressed to explore differences and similarities in the etiopathogenesis and progression of both disorders, with a particular focus on genes involved in the maintenance of the skin structure and integrity (keratins and collagens), modulation of patterns of recognition (through Toll-like receptors and dectin-1) and immuno-inflammatory response (by NLRP3-dependent inflammasome) to microbial pathogens. In addition, special emphasis will be given to the contribution of epigenetic elements (methylation pattern, non-coding RNAs, chromatin modifiers and 3D genome organization) to the etiopathogenesis and progression of psoriasis and psoriatic arthritis. The evidence discussed in this review highlights how the knowledge of patients' clinical and (epi)genomic make-up could be helpful for improving the available therapeutic strategies for psoriasis and psoriatic arthritis treatment.