Lessons From Transcriptome Analysis of Autoimmune Diseases

T cell and autoantibody profiling for primary immune regulatory disorders

Background

Limited clinical tools exist for characterizing primary immune regulatory disorders (PIRD), which are often diagnoses of exclusion. Increased CD4 + CXCR5 + PD1 + circulating T follicular helper (cTfh) cell percentages have been identified as a marker of active disease in some, but not all, autoimmune disorders.

Objective

To develop a diagnostic approach that combines measurements of cellular and serologic autoimmunity.

Methods

We recruited 71 controls and 101 pediatric patients with PIRD with autoimmunity. Flow cytometry was used to measure CD4 + CXCR5 + T cells expressing the chemokine receptors CXCR3 and/or CCR6. IgG and IgA autoantibodies were quantified in 56 patients and 20 controls using a microarray featuring 1616 full-length, conformationally intact protein antigens. The 97.5 th percentile in the controls serves as the upper limit of normal for percentages of cTfh cells, CD4 + CXCR5 + T cells expressing CXCR3 and/or CCR6, and autoantibody intensity and number.

Results

We found that 27.7% of patients had increased percentages of CD4 + CXCR5 + PD1 + cTfh cells and 42.5% had increased percentages of CD4 + CXCR5 + cells expressing CXCR3 and/or CCR6. Patients had significantly more diverse IgG and IgA autoantibodies than controls and 37.5% had increased numbers of high-titer autoantibodies. Integrating measurements of cTfh cells, CD4 + CXCR5 + T cells with CXCR3 and/or CCR6, and numbers of high-titer autoantibodies had 71.4% sensitivity (95% CI: 0.5852 - 0.8158) and 85% specificity (95% CI: 0.6396 - 0.9476) for patients with PIRD compared to controls.

Conclusion

By integrating CD4 + T cell phenotyping and total burden of autoantibodies, this approach provides additional tools for the diagnosis of PIRD lacking clinical diagnostic criteria.

Highlights Box

Primary immune regulatory disorders (PIRD) are heterogenous and often diagnoses of exclusion if no genetic cause is identified. Current diagnostic tools do not combine cellular and serologic measures of autoimmunity. Measuring activated CD4 + T cells expressing the chemokine receptors CXCR3 and/or CCR6 and the total number of circulating autoantibodies can enhance detection of autoimmunity in PIRD beyond the capabilities of currently used tools. This study identifies new indicators of autoimmunity that can be feasibly implemented and leveraged for improving the diagnosis of PIRD.

A comprehensive review of the applications of RNA sequencing in celiac disease research

RNA sequencing (RNA-seq) has undergone substantial advancements in recent decades and has emerged as a vital technique for profiling the transcriptome. The transition from bulk sequencing to single-cell and spatial approaches has facilitated the achievement of higher precision at cell resolution. It provides valuable biological knowledge about individual immune cells and aids in the discovery of the molecular mechanisms that contribute to the development of autoimmune diseases. Celiac disease (CeD) is an autoimmune disorder characterized by a strong immune response to gluten consumption. RNA-seq has led to significantly advanced research in multiple fields, particularly in CeD research. It has been instrumental in studies involving comparative transcriptomics, nutritional genomics and wheat research, cancer research in the context of CeD, genetic and noncoding RNA-mediated epigenetic insights, disease monitoring and biomarker discovery, regulation of mitochondrial functions, therapeutic target identification and drug mechanism of action, dietary factors, immune cell profiling and the immune landscape. This review offers a comprehensive examination of recent RNA-seq technology research in the field of CeD, highlighting future challenges and opportunities for its application.

Unique transcriptomic profile of peripheral blood monocytes in rheumatoid arthritis-associated interstitial lung disease

OBJECTIVES

Though interstitial lung disease (ILD) contributes to excess morbidity and mortality in rheumatoid arthritis (RA), RA-ILD pathogenesis remains incompletely defined. As intermediate, non-classical and suppressed CD14+ monocytes are expanded in RA-ILD, this study sought to characterize gene expression profiles of circulating monocytes in RA-ILD.

METHODS

Peripheral blood mononuclear cells were collected from patients with RA without lung disease (N = 5), RA-ILD (N = 5), idiopathic pulmonary fibrosis (IPF; N = 5), and controls without lung and autoimmune disease (N = 4). RNA was extracted from CD14+ isolated monocytes and subjected to transcriptional analysis of 1365 genes. Gene enrichment and pathway analyses were performed.

RESULTS

Unsupervised clustering grouped patients with RA-ILD together with IPF for myeloid innate genes. For fibrosis genes, patients with RA-ILD clustered independent of comparator groups. There were 103, 66, and 64 upregulated and 66, 14, and 25 downregulated genes for RA-ILD, RA, and IPF, vs controls, respectively. For RA-ILD, there was increased expression of genes involved in regulating inflammation and fibrosis (SOCS3, CECAM1, LTB4R2, CLEC7A, IRF7, PHYKPL, GBP5, RAPGEF), epigenetic modification (KDM5D, KMT2D, OGT), and macrophage activation. Top canonical pathways included macrophage differentiation-activation, IL-12, neuroinflammatory, glucocorticoid receptor, and IL-27 signalling.

CONCLUSIONS

Circulating monocytes in RA-ILD patients demonstrate unique gene expression profiles with innate immune gene features more aligned with IPF as opposed to RA in the absence of clinical lung disease with fibrosis gene expression that was distinct from RA and IPF. These studies are important for understanding disease pathogenesis and may provide information for future therapeutic targets in RA-ILD.

Sappanone A ameliorated imiquimod-induced psoriasis-like dermatitis in BALB/c mice via suppressing Mmp8 expression and IL-17 signaling pathway

Psoriasis is a prevalent immune-mediated inflammatory skin disease characterized by excessive abnormal proliferation of keratinocytes and infiltration of immune cells, which have significant impact on the life quality of individuals. Although biological agents and small molecule targeted drugs have brought significant clinical benefits to psoriasis patients, adverse reactions and high prices remains key issues in clinical medication of psoriasis, while natural product monomers possess high efficiency, low toxicity, anti-inflammatory and immunomodulatory properties, and bring new hope for the clinical treatment of psoriasis. Sappanone A (SA), a small molecule compound isolated from Caesalpinia sappan L, exhibits significant anti-inflammatory properties in various models, such as kidney inflammation and LPS-induced mice inflammation. Among these effects, the anti-inflammatory property of SA has received significant attention. In our study, we found that SA exhibited anti-proliferation and anti-inflammatory effects in HaCaT cells, and significantly alleviated imiquimod-induced psoriasis-like skin lesions via the inhibition of the excessive proliferation of keratinocytes and the infiltration of lymphocytes. Furthermore, the combinational analysis of network pharmacology and transcriptome sequencing revealed that SA exerted anti-psoriasis effects by inhibiting the matrix metalloproteinase 8 (Mmp8) expression and IL-17 pathway activation. In summary, we have first demonstrated that SA can be used as a novel anti-psoriasis drug, which may provide a novel strategy for the clinical treatment of psoriasis.

Advanced methods and novel biomarkers in autoimmune diseases ‑ a review of the recent years progress in systemic lupus erythematosus

There are several autoimmune and rheumatic diseases affecting different organs of the human body. Multiple sclerosis (MS) mainly affects brain, rheumatoid arthritis (RA) mainly affects joints, Type 1 diabetes (T1D) mainly affects pancreas, Sjogren's syndrome (SS) mainly affects salivary glands, while systemic lupus erythematosus (SLE) affects almost every organ of the body. Autoimmune diseases are characterized by production of autoantibodies, activation of immune cells, increased expression of pro-inflammatory cytokines, and activation of type I interferons. Despite improvements in treatments and diagnostic tools, the time it takes for the patients to be diagnosed is too long, and the main treatment for these diseases is still non-specific anti-inflammatory drugs. Thus, there is an urgent need for better biomarkers, as well as tailored, personalized treatment. This review focus on SLE and the organs affected in this disease. We have used the results from various rheumatic and autoimmune diseases and the organs involved with an aim to identify advanced methods and possible biomarkers to be utilized in the diagnosis of SLE, disease monitoring, and response to treatment.