Sarcoidosis: proteomics and new perspectives for improving personalized medicine

Systematic and Comprehensive Analysis of tRNA-Derived Small RNAs Reveals Their Potential Regulatory Roles and Clinical Relevance in Sarcoidosis

Introduction

The pathogenesis of sarcoidosis, which involves several systems, is unclear, and its pathological type is non-caseating epithelioid granulomas. tRNA-derived small RNA (tsRNA) is a novel class of short non-coding RNAs with potential regulatory functions. However, whether tsRNA contributes to sarcoidosis pathogenesis remains unclear.

Methods

Deep sequencing technology was used to identify alterations in tsRNA relative abundance profiles between patients with sarcoidosis and healthy controls and quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate. The clinical parameters were analysis to evaluate the clinical feature correlations initially. Target prediction and bioinformatics analysis of validated tsRNA were conducted to explore the mechanisms of tsRNAs in sarcoidosis pathogenesis.

Results

A total of 360 tsRNAs were identified for exact matches. Among them, the relative abundance of three tRNAs (tiRNA-Glu-TTC-001, tiRNA-Lys-CTT-003, and tRF-Ser-TGA-007) was markedly regulated in sarcoidosis. The levels of various tsRNAs were significantly correlated with age, the number of affected systems, and calcium levels in the blood. Additionally, target prediction and bioinformatics analyses revealed that these tsRNAs may play roles in chemokine, cAMP, cGMP-PKG, retrograde endorphin, and FoxO signalling pathways. The related genes, APP, PRKACB, ARRB2, and NR5A1 finding may participate in the occurrence and development of sarcoidosis through immune inflammation.

Conclusion

This study provides novel insights to explore tsRNA as a novel and efficacious pathogenic target of sarcoidosis.

Novel insights in fibrotic pulmonary sarcoidosis

PURPOSE OF REVIEW

In chronic pulmonary sarcoidosis, the transition from the inflammatory to the fibrotic stage of the lungs occurs in about 10-20% of cases, eventually causing end-stage fibrotic disease. To date, pathogenetic mechanisms and clinical management remain challenging; thus, we highlight the recent evidence in pulmonary fibrotic processes, clinical signs for an early detection and the potential role of the current investigated antifibrotic agents and promising targeted therapies.

RECENT FINDINGS

Recent findings of relevant key cellular pathways can be considered as a glimmer of light in the complexity of sarcoidosis. In some patients, granulomas persist and serve as a nidus for fibrosis growth, sustained by several fibrosis-stimulating cytokines. Preclinical studies have detected profibrotic, antifibrotic and pleiotropic T cells as promoters of fibrosis. Epigenetics, genetics and transcriptomics research can lead to new target therapies. Antifibrotic drug nintedanib has shown a positive effect on non-idiopathic pulmonary fibrosis fibrotic lung diseases including fibrotic sarcoidosis; other antifibrotic drugs are under investigation.

SUMMARY

Pulmonary fibrosis strongly impacts the outcome of sarcoidosis, and a better understanding of the underlying pathogenic mechanisms can facilitate the development of novel treatments, improving clinical care and life expectancy of these patients. The greatest challenge is to investigate effective antifibrotic therapies once fibrosis develops. The role of these findings in fibrotic sarcoidosis can be translated into other interstitial lung diseases characterized by the coexistence of inflammatory and fibrotic processes.

Multi-omics strategies for personalized and predictive medicine: past, current, and future translational opportunities

Precision medicine is driven by the paradigm shift of empowering clinicians to predict the most appropriate course of action for patients with complex diseases and improve routine medical and public health practice. It promotes integrating collective and individualized clinical data with patient specific multi-omics data to develop therapeutic strategies, and knowledgebase for predictive and personalized medicine in diverse populations. This study is based on the hypothesis that understanding patient's metabolomics and genetic make-up in conjunction with clinical data will significantly lead to determining predisposition, diagnostic, prognostic and predictive biomarkers and optimal paths providing personalized care for diverse and targeted chronic, acute, and infectious diseases. This study briefs emerging significant, and recently reported multi-omics and translational approaches aimed to facilitate implementation of precision medicine. Furthermore, it discusses current grand challenges, and the future need of Findable, Accessible, Intelligent, and Reproducible (FAIR) approach to accelerate diagnostic and preventive care delivery strategies beyond traditional symptom-driven, disease-causal medical practice.

Identification of key regulators in Sarcoidosis through multidimensional systems biological approach

Sarcoidosis is a multi-organ disorder where immunology, genetic and environmental factors play a key role in causing Sarcoidosis, but its molecular mechanism remains unclear. Identification of its genetics profiling that regulates the Sarcoidosis network will be one of the main challenges to understand its aetiology. We have identified differentially expressed genes (DEGs) by analyzing the gene expression profiling of Sarcoidosis and compared it with healthy control. Gene set enrichment analysis showed that these DEGs were mainly enriched in the inflammatory response, immune system, and pathways in cancer. Sarcoidosis protein interaction network was constructed by a total of 877 DEGs (up-down) and calculated its network topological properties, which follow hierarchical scale-free fractal nature up to six levels of the organization. We identified a large number of leading hubs that contain six key regulators (KRs) including ICOS, CTLA4, FLT3LG, CD33, GPR29 and ITGA4 are deeply rooted in the network from top to bottom, considering a backbone of the network. We identified the transcriptional factors (TFs) which are closely interacted with KRs. These genes and their TFs regulating the Sarcoidosis network are expected to be the main target for the therapeutic approaches and potential biomarkers. However, experimental validations of KRs needed to confirm their efficacy.

Non-neoplastic respiratory fluid cytology including cell differential counts for interstitial lung disease

Bronchioloalveolar lavage (BAL) is a non-invasive and well-tolerated procedure that plays a key role in the diagnosis of a variety of non-neoplastic pulmonary diseases, including acute respiratory failure, infection, diffuse parenchymal lung disease (DLPD), paediatric and occupational lung disease, and in the evaluation of the lung allograft. A variety of analytic techniques are commonly performed on BAL fluid, including cytology, cell differential count, microbiology and virology, as well as a number of additional techniques in specific circumstances.

Potential use of biomarkers for the clinical evaluation of sarcoidosis

Sarcoidosis is a systemic granulomatous disease of unknown etiology and pathogenesis with a heterogeneous clinical presentation. In the appropriate clinical and radiological context and with the exclusion of other diagnoses, the disease is characterized by the pathological presence of non-caseating epithelioid cell granulomas. Sarcoidosis is postulated to be a multifactorial disease caused by chronic antigenic stimulation. The immunopathogenesis of sarcoidosis encompasses a complex interaction between the host, genetic factors and postulated environmental and infectious triggers, which result in granuloma development.The exact pathogenesis of the disease has yet to be elucidated, but some of the inflammatory pathways that play a key role in disease progression and outcomes are becoming apparent, and these may form the logical basis for selecting potential biomarkers.Biomarkers are biological molecules that are altered pathologically. To date, there exists no single reliable biomarker for the evaluation of sarcoidosis, either diagnostically or prognostically but new candidates are emerging. A diagnosis of sarcoidosis ideally requires a biopsy confirming non-caseating granulomas, but the likelihood of progression that requires intervention remains unpredictable. These challenging aspects could be potentially resolved by incorporating biomarkers into clinical practice for both diagnosis and monitoring disease activity.This review outlines the current knowledge on sarcoidosis with an emphasis on pulmonary sarcoidosis, and delineates the understanding surrounding the implication of biomarkers for the clinical evaluation of sarcoidosis.

Application of Proteomics in Sarcoidosis

Sarcoidosis is a multisystem disease with heterogeneity in manifestations and outcomes. System-level studies leveraging "omics" technologies are expected to define mechanisms contributing to sarcoidosis heterogeneous manifestations and course. With improvements in mass spectrometry (MS) and bioinformatics, it is possible to study protein abundance for a large number of proteins simultaneously. Contemporary fast-scanning MS enables the acquisition of spectral data for deep coverage of the proteins with data-dependent or data-independent acquisition MS modes. Studies leveraging MS-based proteomics in sarcoidosis have characterized BAL fluid (BALF), alveolar macrophages, plasma, and exosomes. These studies identified several differentially expressed proteins, including protocadherin-2 precursor, annexin A2, pulmonary surfactant A2, complement factors C3, vitamin-D-binding protein, cystatin B, and amyloid P, comparing subjects with sarcoidosis with control subjects. Other studies identified ceruloplasmin, complement factors B, C3, and 1, and others with differential abundance in sarcoidosis compared with other interstitial lung diseases. Using quantitative proteomics, most recent studies found differences in PI3K/Akt/mTOR, MAP kinase, pluripotency-associated transcriptional factor, and hypoxia response pathways. Other studies identified increased clathrin-mediated endocytosis and Fcγ receptor-mediated phagocytosis pathways in sarcoidosis alveolar macrophages. Although studies in mixed BAL and blood cells or plasma are limited, some of the changes in lung compartment are detected in the blood cells and plasma. We review proteomics for sarcoidosis with a focus on the existing MS data acquisition strategies, bioinformatics for spectral data analysis to infer protein identity and quantity, unique aspects about biospecimen collection and processing for lung-related proteomics, and proteomics studies conducted to date in sarcoidosis.

Identification of Biomarkers for Sarcoidosis and Tuberculosis of the Lung Using Systematic and Integrated Analysis

Background

Sarcoidosis (SARC) is a multisystem inflammatory disease of unknown etiology and pulmonary tuberculosis (PTB) is caused by Mycobacterium tuberculosis. Both of these diseases affect lungs and lymph nodes and share similar clinical manifestations. However, the underlying mechanisms for the similarities and differences in genetic characteristics of SARC and PTB remain unclear.

Material/Methods

Three datasets (GSE16538, GSE20050, and GSE19314) were retrieved from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in SARC and PTB were identified using GEO2R online analyzer and Venn diagram software. Functional enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) and R packages. Two protein–protein interaction (PPI) networks were constructed using Search Tool for the Retrieval of Interacting Genes database, and module analysis was performed using Cytoscape. Hub genes were identified using area under the receiver operating characteristic curve analysis.

Results

We identified 228 DEGs, including 56 common SARC-PTB DEGs (enriched in interferon-gamma-mediated signaling, response to gamma radiation, and immune response) and 172 SARC-only DEGs (enriched in immune response, cellular calcium ion homeostasis, and dendritic cell chemotaxis). Potential biomarkers for SARC included CBX5, BCL11B, and GPR18.

Conclusions

We identified potential biomarkers that can be used as candidates for diagnosis and/or treatment of patients with SARC.

Sarcoidosis: Causes, Diagnosis, Clinical Features, and Treatments

Sarcoidosis is a multisystem granulomatous disease with nonspecific clinical manifestations that commonly affects the pulmonary system and other organs including the eyes, skin, liver, spleen, and lymph nodes. Sarcoidosis usually presents with persistent dry cough, eye and skin manifestations, weight loss, fatigue, night sweats, and erythema nodosum. Sarcoidosis is not influenced by sex or age, although it is more common in adults (< 50 years) of African-American or Scandinavians decent. Diagnosis can be difficult because of nonspecific symptoms and can only be verified following histopathological examination. Various factors, including infection, genetic predisposition, and environmental factors, are involved in the pathology of sarcoidosis. Exposures to insecticides, herbicides, bioaerosols, and agricultural employment are also associated with an increased risk for sarcoidosis. Due to its unknown etiology, early diagnosis and detection are difficult; however, the advent of advanced technologies, such as endobronchial ultrasound-guided biopsy, high-resolution computed tomography, magnetic resonance imaging, and 18F-fluorodeoxyglucose positron emission tomography has improved our ability to reliably diagnose this condition and accurately forecast its prognosis. This review discusses the causes and clinical features of sarcoidosis, and the improvements made in its prognosis, therapeutic management, and the recent discovery of potential biomarkers associated with the diagnostic assay used for sarcoidosis confirmation.

Serum amyloid A: A potential biomarker of lung disorders

Serum amyloid A is an acute-phase protein with multiple immunological functions. Serum amyloid A is involved in lipid metabolism, inflammatory reactions, granuloma formation, and cancerogenesis. Additionally, serum amyloid A is involved in the pathogenesis of different autoimmune lung diseases. The levels of serum amyloid A has been evaluated in biological fluids of patients with different lung diseases, including autoimmune disorders, chronic obstructive pulmonary diseases, obstructive sleep apnea syndrome, sarcoidosis, asthma, lung cancer, and other lung disorders, such as idiopathic pulmonary fibrosis, tuberculosis, radiation pneumonitis, and cystic fibrosis. This review focuses on the cellular and molecular interactions of serum amyloid A in different lung diseases and suggests this acute-phase protein as a prognostic marker.

Feasibility of a Comprehensive Home Monitoring Program for Sarcoidosis

Sarcoidosis is a chronic, heterogeneous disease which most commonly affects the lungs. Currently, evidence-based and individually tailored treatment options in sarcoidosis are lacking. We aimed to evaluate patient experiences with a home monitoring program for sarcoidosis and assess whether home monitoring is a feasible tool to enhance personalized treatment. Outpatients with pulmonary sarcoidosis tested the home monitoring program “Sarconline” for one month. This is a secured personal platform which consists of online patient-reported outcomes, real-time wireless home spirometry, an activity tracker, an information library, and an eContact option. Patients wore an activity tracker, performed daily home spirometry, and completed patient-reported outcomes at baseline and after one month. Patient experiences were evaluated during a phone interview. Ten patients were included in the study. Experiences with the home monitoring program were positive; 90% of patients considered the application easy to use, none of the patients found daily measurements burdensome, and all patients wished to continue the home monitoring program after the study. Mean adherence to daily spirometry and activity tracking was, respectively, 94.6% and 91.3%. In conclusion, a comprehensive home monitoring program for sarcoidosis is feasible and can be used in future research and clinical practice.