Proteomic Studies of Psoriasis

An AI-assisted morphoproteomic approach is a supportive tool in esophagitis-related precision medicine

Esophagitis is a frequent, but at the molecular level poorly characterized condition with diverse underlying etiologies and treatments. Correct diagnosis can be challenging due to partially overlapping histological features. By proteomic profiling of routine diagnostic FFPE biopsy specimens (n = 55) representing controls, Reflux- (GERD), Eosinophilic-(EoE), Crohn's-(CD), Herpes simplex (HSV) and Candida (CA)-esophagitis by LC-MS/MS (DIA), we identified distinct signatures and functional networks (e.g. mitochondrial translation (EoE), immunoproteasome, complement and coagulations system (CD), ribosomal biogenesis (GERD)), and pathogen-specific proteins for HSV and CA. Moreover, combining these signatures with histological parameters in a machine learning model achieved high diagnostic accuracy (100% training set, 93.8% test set), and supported diagnostic decisions in borderline/challenging cases. Applied to a young patient representing a use case, the external GERD diagnosis could be revised to CD and ICAM1 was identified as highly abundant therapeutic target. This resulted in CyclosporinA as a personalized treatment recommendation by the local multidisciplinary molecular inflammation board. Our integrated AI-assisted morphoproteomic approach allows deeper insights in disease-specific molecular alterations and represents a promising tool in esophagitis-related precision medicine.

Mass Spectrometry-Based Proteomics Analysis Unveils PTPRS Inhibits Proliferation and Inflammatory Response of Keratinocytes in Psoriasis

In this study, we used data-independent acquisition-mass spectrometry (DIA-MS) to analyze the serum proteome in psoriasis vulgaris (PsO). The serum proteomes of seven healthy controls and eight patients with PsO were analyzed using DIA-MS. Weighted gene co-expression network analysis was used to identify differentially expressed proteins (DEPs) that were closely related to PsO. Hub proteins of PsO were also identified. The Proteomics Drug Atlas 2023 was used to predict candidate hub protein drugs. To confirm the expression of the candidate factor, protein tyrosine phosphatase receptor S (PTPRS), in psoriatic lesions and the psoriatic keratinocyte model, immunohistochemical staining, quantitative real-time polymerase chain reaction, and western blotting were performed. A total of 129 DEPs were found to be closely related to PsO. The hub proteins for PsO were PVRL1, FGFR1, PTPRS, CDH2, CDH1, MCAM, and THY1. Five candidate hub protein drugs were identified: encorafenib, leupeptin, fedratinib, UNC 0631, and SCH 530348. PTPRS was identified as a common pharmacological target for these five drugs. PTPRS knockdown in keratinocytes promoted the proliferation and expression of IL-1α, IL-1β, IL-23A, TNF-α, MMP9, CXCL8, and S100A9. PTPRS expression was decreased in PsO, and PTPRS negatively regulated PsO. PTPRS may be involved in PsO pathogenesis through the inhibition of keratinocyte proliferation and inflammatory responses and is a potential treatment target for PsO.

From Manifestations to Innovations: A Deep Dive into Psoriasis, its Clinical Diversity, Conventional Treatments, and Emerging Therapeutic Paradigms

Psoriasis, a persistent inflammatory dermatological illness, places a significant load on those affected, requiring ongoing investigation into innovative therapies. This review examines the significance of pre-clinical models in defining our comprehension of psoriasis, as well as the valuable insights obtained from clinical trials that aid in developing treatment approaches. The evaluation includes existing established medicines such as topicals, phototherapy, and traditional systemic drugs targeting different pathological mediators of psoriasis. Further, emerging frontiers in the treatment of psoriasis are examined, including personalized medicine, novel biologics, small molecule inhibitors, and advanced delivery methods. The objective is to identify potential advancements that can be applied in clinical practice to the patients. In light of current knowledge, this review delineates what are perceived as critical future research directions and noteworthy therapeutic and clinical developments in the domain of psoriasis.

The Expression of Cytokines and Chemokines Potentially Distinguishes Mild and Severe Psoriatic Non-Lesional and Resolved Skin from Healthy Skin and Indicates Different Stages of Inflammation

In the psoriatic non-lesional (PS-NL) skin, the tissue environment potentially influences the development and recurrence of lesions. Therefore, we aimed to investigate mechanisms involved in regulating tissue organization in PS-NL skin. Cytokine, chemokine, protease, and protease inhibitor levels were compared between PS-NL skin of patients with mild and severe symptoms and healthy skin. By comparing mild and severe PS-NL vs. healthy skin, differentially expressed cytokines and chemokines suggested alterations in hemostasis-related processes, while protease inhibitors showed no psoriasis severity-related changes. Comparing severe and mild PS-NL skin revealed disease severity-related changes in the expression of proteases, cytokines, and chemokines primarily involving methyl-CpG binding protein 2 (MECP2) and extracellular matrix organization-related mechanisms. Cytokine and chemokine expression in clinically resolved versus healthy skin showed slight interleukin activity, differing from patterns in mild and severe PS-NL skin. Immunofluorescence analysis revealed the severity-dependent nuclear expression pattern of MECP2 and decreased expression of 5-methylcytosine and 5-hydroxymethylcytosine in the PS-NL vs. healthy skin, and in resolved vs. healthy skin. Our results suggest distinct cytokine-chemokine signaling between the resolved and PS-NL skin of untreated patients with varying severities. These results highlight an altered inflammatory response, epigenetic regulation, and tissue organization in different types of PS-NL skin with possibly distinct, severity-dependent para-inflammatory states.

Non-invasive epidermal proteome assessment-based diagnosis and molecular subclassification of psoriasis and eczematous dermatitis

Background

Immunologic heterogeneity is known to exist within both eczematous dermatitis and psoriasis; however, selection of molecularly targeted therapies for individual patients generally does assess for or incorporate such information about patient-specific immune changes.

Objective

We sought to develop a rapid, non-invasive method for obtaining and analyzing epidermal protein biomarkers from skin and utilize this methodology to dissect immunologic heterogeneity in both psoriasis and eczematous dermatitis.

Methods

We optimize and evaluate detergent-based immune profiling system (DIPS) which utilizes a combination of two detergents to solubilize full-thickness epidermis when applied to the skin with an applicator. Downstream proteomic profiling of this material allows high-throughput immunologic characterization of immune biomarkers.

Results

DIPS was performed on 43 patients with psoriasis and 27 patients with eczematous dermatitis. This approach was found to be painless, nonscarring, and enabled rapid turnaround from sample collection to data output. We used this approach to accurately differentiate psoriasis and eczema using a limited set of proteins and to identify cases of eczema/psoriasis overlap with non-canonical molecular profiles. Additionally, we measured patient-specific cytokine profiles in eczema that correlated with response to IL-4Rα blockade.

Conclusion

DIPS is a promising new non-invasive cutaneous immune profiling approach that can deconvolute immune heterogeneity amongst patients with both psoriasis and eczematous dermatitis.

Clinical Implication

DIPS has potential applications in both research and day-to-day dermatologic practice and may help personalize diagnosis and medication selection in patients with inflammatory skin diseases.

Capsule summary

Detergent-based immune profiling system (DIPS), a novel non-invasive approach for molecular evaluation of skin disease, is described and evaluated in psoriasis and eczematous dermatitis.

A Comprehensive Review of Protein Biomarkers for Invasive Lung Cancer

Invasion and metastasis are important hallmarks of lung cancer, and affect patients' survival. Early diagnostics of metastatic potential are important for treatment management. Recent findings suggest that the transition to an invasive phenotype causes changes in the expression of 700-800 genes. In this context, the biomarkers restricted to the specific type of cancer, like lung cancer, are often overlooked. Some well-known protein biomarkers correlate with the progression of the disease and the immunogenicity of the tumor. Most of these biomarkers are not exclusive to lung cancer because of their significant role in tumorigenesis. The dysregulation of others does not necessarily indicate cell invasiveness, as they play an active role in cell division. Clinical studies of lung cancer use protein biomarkers to assess the invasiveness of cancer cells for therapeutic purposes. However, there is still a need to discover new biomarkers for lung cancer. In the future, minimally invasive techniques, such as blood or saliva analyses, may be sufficient for this purpose. Many researchers suggest unconventional biomarkers, like circulating nucleic acids, exosomal proteins, and autoantibodies. This review paper aims to discuss the advantages and limitations of protein biomarkers of invasiveness in lung cancer, to assess their prognostic value, and propose novel biomarker candidates.

Assessment of Treatment-Relevant Immune Biomarkers in Psoriasis and Atopic Dermatitis: Toward Personalized Medicine in Dermatology

Immunologically targeted therapies have revolutionized the treatment of inflammatory dermatoses, including atopic dermatitis and psoriasis. Although immunologic biomarkers hold great promise for personalized classification of skin disease and tailored therapy selection, there are no approved or widely used approaches for this in dermatology. This review summarizes the translational immunologic approaches to measuring treatment-relevant biomarkers in inflammatory skin conditions. Tape strip profiling, microneedle-based biomarker patches, molecular profiling from epidermal curettage, RNA in situ hybridization tissue staining, and single-cell RNA sequencing have been described. We discuss the advantages and limitations of each and open questions for the future of personalized medicine in inflammatory skin disease.

<i>TLR9</i> gene expression in immune cells of patients with psoriasis

Background. Psoriasis (skin lesions and psoriatic arthritis PA) is a chronic inflammatory autoimmune disease that can be triggered by excessive activation of endosomal toll-like receptors (TLRs), mainly TLR9. Elevated TLR9 levels are observed in both PA and psoriasis. Therefore, studying the expression pattern of the TLR9 gene may help select therapies for patients with PA and psoriasis. Aim. To study the expression pattern of the TLR9 gene in blood mononuclear cells of PA and psoriasis patients without joint involvement for possible use in the transition to targeted therapy. Materials and methods. Mononuclear cells were isolated from the peripheral blood of 31 patients with psoriasis vulgaris without joint involvement, 45 patients with PA, and 20 healthy volunteers. TLR9 gene expression was analyzed by real-time polymerase chain reaction. Results. A comparison of expression levels in PA patients and healthy volunteers showed that the expression level of TLR9 in PA patients was 591 times higher than that in healthy volunteers. The expression level of TLR9 in psoriasis patients without joint involvement was also significantly (423-fold) higher than that in healthy subjects. Conclusion. TLR9 gene expression in mononuclear cells of psoriasis patients with severe skin lesions is similar to that in PA patients. High levels of TLR9 gene expression may be a marker of possible joint involvement in patients with psoriasis and indicate the need to reconsider the therapeutic approach to a particular patient.

DRESIS: the first comprehensive landscape of drug resistance information

Widespread drug resistance has become the key issue in global healthcare. Extensive efforts have been made to reveal not only diverse diseases experiencing drug resistance, but also the six distinct types of molecular mechanisms underlying this resistance. A database that describes a comprehensive list of diseases with drug resistance (not just cancers/infections) and all types of resistance mechanisms is now urgently needed. However, no such database has been available to date. In this study, a comprehensive database describing drug resistance information named 'DRESIS' was therefore developed. It was introduced to (i) systematically provide, for the first time, all existing types of molecular mechanisms underlying drug resistance, (ii) extensively cover the widest range of diseases among all existing databases and (iii) explicitly describe the clinically/experimentally verified resistance data for the largest number of drugs. Since drug resistance has become an ever-increasing clinical issue, DRESIS is expected to have great implications for future new drug discovery and clinical treatment optimization. It is now publicly accessible without any login requirement at: https://idrblab.org/dresis/.