IgG Galactosylation status combined with MYOM2-rs2294066 precisely predicts anti-TNF response in ankylosing spondylitis

The role of antibody glycosylation in autoimmune and alloimmune kidney diseases

Immunoglobulin glycosylation is a pivotal mechanism that drives the diversification of antibody functions. The composition of the IgG glycome is influenced by environmental factors, genetic traits and inflammatory contexts. Differential IgG glycosylation has been shown to intricately modulate IgG effector functions and has a role in the initiation and progression of various diseases. Analysis of IgG glycosylation is therefore a promising tool for predicting disease severity. Several autoimmune and alloimmune disorders, including critical and potentially life-threatening conditions such as systemic lupus erythematosus, anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis and antibody-mediated kidney graft rejection, are driven by immunoglobulin. In certain IgG-driven kidney diseases, including primary membranous nephropathy, IgA nephropathy and lupus nephritis, particular glycome characteristics can enhance in situ complement activation and the recruitment of innate immune cells, resulting in more severe kidney damage. Hypofucosylation, hypogalactosylation and hyposialylation are the most common IgG glycosylation traits identified in these diseases. Modulating IgG glycosylation could therefore be a promising therapeutic strategy for regulating the immune mechanisms that underlie IgG-driven kidney diseases and potentially reduce the burden of immunosuppressive drugs in affected patients.

Machine learning and deep learning for the diagnosis and treatment of ankylosing spondylitis- a scoping review

Background and objectives

Machine Learning (ML) and Deep Learning (DL) are novel technologies that can facilitate early diagnosis of Ankylosing Spondylitis (AS) and predict better patient-specific treatments. We aim to provide the current update on their use at different stages of AS diagnosis and treatment, describe different types of techniques used, dataset descriptions, contributions and limitations of existing work and ed to identify gaps in current knowledge for future works.

Methods

We curated the data of this review from the PubMed database. We searched the full-text articles related to the use of ML/DL in the diagnosis and treatment of AS, for the period 2013-2023. Each article was manually scrutinized to be included or excluded for this review as per its relevance.

Results

This review revealed that ML/DL technology is useful to assist and promote early diagnosis through AS patient characteristic profile creation, and identification of new AS-related biomarkers. They can help in forecasting the progression of AS and predict treatment responses to aid patient-specific treatment planning. However, there was a lack of sufficient-sized datasets sourced from multi-centres containing different types of diagnostic parameters. Also, there is less research on ML/DL-based AS treatment as compared to ML/DL-based AS diagnosis.

Conclusion

ML/DL can facilitate an early diagnosis and patient-tailored treatment for effective handling of AS. Benefits are especially higher in places with a lack of diagnostic resources and human experts. The use of ML/DL-trained models for AS diagnosis and treatment can provide the necessary support to the otherwise overwhelming healthcare systems in a cost-effective and timely way.

Understanding the role and adoption of artificial intelligence techniques in rheumatology research: An in-depth review of the literature

The major and upward trend in the number of published research related to rheumatic and musculoskeletal diseases, in which artificial intelligence plays a key role, has exhibited the interest of rheumatology researchers in using these techniques to answer their research questions. In this review, we analyse the original research articles that combine both worlds in a five- year period (2017-2021). In contrast to other published papers on the same topic, we first studied the review and recommendation articles that were published during that period, including up to October 2022, as well as the publication trends. Secondly, we review the published research articles and classify them into one of the following categories: disease identification and prediction, disease classification, patient stratification and disease subtype identification, disease progression and activity, treatment response, and predictors of outcomes. Thirdly, we provide a table with illustrative studies in which artificial intelligence techniques have played a central role in more than twenty rheumatic and musculoskeletal diseases. Finally, the findings of the research articles, in terms of disease and/or data science techniques employed, are highlighted in a discussion. Therefore, the present review aims to characterise how researchers are applying data science techniques in the rheumatology medical field. The most immediate conclusions that can be drawn from this work are: multiple and novel data science techniques have been used in a wide range of rheumatic and musculoskeletal diseases including rare diseases; the sample size and the data type used are heterogeneous, and new technical approaches are expected to arrive in the short-middle term.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020

This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.

An in silico comparative transcriptome analysis identifying hub lncRNAs and mRNAs in brain metastatic small cell lung cancer (SCLC)

Small cell lung cancer (SCLC) is a particularly lethal subtype of lung cancer. Metastatic lung tumours lead to most deaths from lung cancer. Predicting and preventing tumour metastasis is crucially essential for patient survivability. Hence, in the current study, we focused on a comprehensive analysis of lung cancer patients' differentially expressed genes (DEGs) on brain metastasis cell lines. DEGs are analysed through KEGG and GO databases for the most critical biological processes and pathways for enriched DEGs. Additionally, we performed protein-protein interaction (PPI), GeneMANIA, and Kaplan-Meier survival analyses on our DEGs. This article focused on mRNA and lncRNA DEGs for LC patients with brain metastasis and underlying molecular mechanisms. The expression data was gathered from the Gene Expression Omnibus database (GSE161968). We demonstrate that 30 distinct genes are up-expressed in brain metastatic SCLC patients, and 31 genes are down-expressed. All our analyses show that these genes are involved in metastatic SCLC. PPI analysis revealed two hub genes (CAT and APP). The results of this article present three lncRNAs, Including XLOC_l2_000941, LOC100507481, and XLOC_l2_007062, also notable mRNAs, have a close relation with brain metastasis in lung cancer and may have a role in the epithelial-mesenchymal transition (EMT) in tumour cells.

Machine Learning in Rheumatic Diseases

With advances in information technology, the demand for using data science to enhance healthcare and disease management is rapidly increasing. Among these technologies, machine learning (ML) has become ubiquitous and indispensable for solving complex problems in many scientific fields, including medical science. ML allows the development of guidelines and framing of the evaluation system for complex diseases based on massive data. In the analysis of rheumatic diseases, which are chronic and remarkably heterogeneous, ML can be anticipated to be extremely helpful in deciphering and revealing the inherent interrelationships in disease development and progression, which can further enhance the overall understanding of the disease, optimize patients' stratification, calibrate therapeutic strategies, and predict prognosis and outcomes. In this review, the basics of ML, its potential clinical applications in rheumatology, together with its strengths and limitations are summarized.

The Genetic Contribution to Drug Response in Spondyloarthritis: A Systematic Literature Review

Objective: Spondyloarthritis (SpA) are a group of diseases with a high heritability, whose pathogenesis is strongly determined by an interplay between genetic and environmental factor. Therefore, the aim of our study was to determine whether genetic variants could also influence response to therapy in SpA. Methods: A systematic literature review (SLR) was conducted in PubMed and Web of Science core collection, without publication-year restrictions (Last search 8th April 2021). The search strategy was formulated according to the PEO format (Population, Exposure, Outcome) for observational studies. The population was adult (≥18 years) patients with SpA. The exposure was inheritable genetic variations of any gene involved in the disease pathogenesis/drug metabolism. The outcome was response to the drug, both as dichotomous (response yes/no) and as continuous outcomes. Exclusion criteria were: (1) languages other than English, (2) case series, case reports, editorials, and reviews, (3) studies reporting genetic contribution to drug response only limited to extra-musculoskeletal features of SpA, (4) epigenetic modifications. Quality of the included study was independently assessed by two authors. Results: After deduplication, 393 references were screened by two authors, which led to the final inclusion of 26 articles, pertinent with the research question, that were considered for qualitative synthesis. Among these, 10 cohort, one cross-sectional, and five case-control studies were considered of at least good quality according to Newcastle-Ottawa Scale (NOS). In studies about TNF-blockers therapy: (1) polymorphisms of the TNF receptor superfamily 1A/1B (TNFRSF1A/1B) genes were most frequently able to predict response, (2) -238 and -308 polymorphisms of TNFα gene were studied with conflicting results, (3) TNFα polymorphism rs1799724, rs1799964, -857, -1,013, +489 predicted drug response in non-adjusted analysis, (4) PDE3A rs3794271 had a linear relationship with DAS28 reduction after anti-TNFα therapy. DHFR polymorphism +35,289 was able to predict response to methotrexate. Conclusions: Our SLR highlighted the existence of a genetic component in determining drug response. However, further studies are warranted to better define quantify it.

Novel approaches to develop biomarkers predicting treatment responses to TNF-blockers

Introduction: Chronic inflammatory diseases (CIDs) cause significant morbidity and are a considerable burden for the patients in terms of pain, impaired function, and diminished quality of life. Important progress in CID treatment has been obtained with biological therapies, such as tumor-necrosis-factor blockers. However, more than a third of the patients fail to respond to these inhibitors and are exposed to the side effects of treatment, without the benefits. Therefore, there is a strong interest in developing tools to predict response of patients to biologics. Areas covered: The authors searched PubMed for recent studies on biomarkers for disease assessment and prediction of therapeutic responses, focusing on the effect of TNF blockers on immune responses in spondyloarthritis (SpA), and other CID, in particular rheumatoid arthritis and inflammatory bowel disease. Conclusions will be drawn about the possible development of predictive biomarkers for response to treatment. Expert opinion: No validated biomarker is currently available to predict treatment response in CID. New insight could be generated through the development of new bioinformatic modeling approaches to combine multidimensional biomarkers that explain the different genetic, immunological and environmental determinants of therapeutic responses.

Immunoglobulin G Glycosylation Changes in Aging and Other Inflammatory Conditions

Among the multiple roles played by protein glycosylation, the fine regulation of biological interactions is one of the most important. The asparagine 297 (Asn₂₉₇) of IgG heavy chains is decorated by a diantennary glycan bearing a number of galactose and sialic acid residues on the branches ranging from 0 to 2. In addition, the structure can present core-linked fucose and/or a bisecting GlcNAc. In many inflammatory and autoimmune conditions, as well as in metabolic, cardiovascular, infectious, and neoplastic diseases, the IgG Asn₂₉₇-linked glycan becomes less sialylated and less galactosylated, leading to increased expression of glycans terminating with GlcNAc. These conditions alter also the presence of core-fucose and bisecting GlcNAc. Importantly, similar glycomic alterations are observed in aging. The common condition, shared by the above-mentioned pathological conditions and aging, is a low-grade, chronic, asymptomatic inflammatory state which, in the case of aging, is known as inflammaging. Glycomic alterations associated with inflammatory diseases often precede disease onset and follow remission. The aberrantly glycosylated IgG glycans associated with inflammation and aging can sustain inflammation through different mechanisms, fueling a vicious loop. These include complement activation, Fcγ receptor binding, binding to lectin receptors on antigen-presenting cells, and autoantibody reactivity. The complex molecular bases of the glycomic changes associated with inflammation and aging are still poorly understood.

A three-gene signature based on tumour microenvironment predicts overall survival of osteosarcoma in adolescents and young adults

Evidences shows that immune and stroma related genes in the tumour microenvironment (TME) play a key regulator in the prognosis of Osteosarcomas (OSs). The purpose of this study was to develop a TME-related risk model for assessing the prognosis of OSs. 82 OSs cases aged ≤25 years from TARGET were divided into two groups according to the immune/stromal scores that were analyzed by the Estimate algorithm. The differentially expressed genes (DEGs) between the two groups were analyzed and 122 DEGs were revealed. Finally, three genes (COCH, MYOM2 and PDE1B) with the minimum AIC value were derived from 122 DEGs by multivariate cox analysis. The three-gene risk model (3-GRM) could distinguish patients with high risk from the training (TARGET) and validation (GSE21257) cohort. Furthermore, a nomogram model included 3-GRM score and clinical features were developed, with the AUC values in predicting 1, 3 and 5-year survival were 0.971, 0.853 and 0.818, respectively. In addition, in the high 3-GRM score group, the enrichment degrees of infiltrating immune cells were significantly lower and immune-related pathways were markedly suppressed. In summary, this model may be used as a marker to predict survival for OSs patients in adolescent and young adults.

Early Prediction of Clinical Response to Etanercept Treatment in Juvenile Idiopathic Arthritis Using Machine Learning

Background and Aims

At present, there is a lack of simple and reliable model for early prediction of the efficacy of etanercept in the treatment of juvenile idiopathic arthritis (JIA). This study aimed to generate and validate prediction models of etanercept efficacy in patients with JIA before administration using machine learning algorithms based on electronic medical record (EMR).

Materials and Methods

EMR data of 87 JIA patients treated with etanercept between January 2011 and December 2018 were collected retrospectively. The response of etanercept was evaluated by using DAS44/ESR-3 simplified standard. The stepwise forward and backward method based on information gain was applied to select features. Five machine learning algorithms, including Extreme Gradient Boosting (XGBoost), Random Forest (RF), Gradient Boosting Decision Tree (GBDT), Extremely Random Trees (ET) and Logistic Regression (LR) were used for model generation and validation with fifty-fold stratified cross-validation. EMR data of additional 14 patients were collected for external validation of the model.

Results

Tender joint count (TJC), Time interval, Lymphocyte percentage (LYM), and Weight were screened out and included in the final model. The model generated by the XGBoost algorithm based on the above 4 features had the best predictive performance: sensitivity 75%, specificity 66.67%, accuracy 72.22%, AUC 79.17%, respectively.

Conclusion

A pre-administration model with good prediction performance for etanercept response in JIA was developed using advanced machine learning algorithms. Clinicians and pharmacists can use this simple and accurate model to predict etanercept response of JIA early and avoid treatment failure or adverse effects.