Advances in proteomics: characterization of the innate immune system after birth and during inflammation

Integrating Proteomics into Personalized Medicine for Inflammatory Bowel Disease—Reality or Challenge?

Inflammatory bowel diseases (IBD) represent chronic conditions with etiopathogenic mechanisms incompletely elucidated despite extensive research efforts. Therefore, it is essential for clinical monitoring of the implementation of personalized medicine, enabling risk stratification and the selection of therapies with the highest likelihood of a favorable response. Multi-omics approaches have emerged as an excellent opportunity for the prevention, clinical phenotype differentiation, and prediction of IBD development. Proteomics has gained significant enthusiasm in medical practice, primarily due to its focus on studying the composition and dynamic expression of various cellular and tissue structures. This approach provides critical insights into their impact on signaling pathways, post-translational modifications, and the development of sequence variations. Hence, it could provide the foundation for developing biomarkers with the potential to assess mucosal healing and predict prognostic variability among patients, facilitating the implementation of a personalized therapeutic approach. This review focuses on the recent research regarding the possibility of implementing proteomics technologies into clinical practice, given the challenges and limitations, and the advantages of increasing the quality of life in patients with IBD.

Systemic Changes in Adults With a Fontan Circulation: Insights From the Plasma Proteome

BACKGROUND

Despite multiple surgeries and extensive follow-up, individuals with a univentricular heart have significant residual morbidity and mortality throughout life. By applying a state-of-the-art characterization of the plasma proteome, this study aimed at providing a comprehensive insight into the proteomic impact of living with a Fontan circulation.

METHODS AND RESULTS

This study enrolled individuals with a Fontan circulation and compared them 2:1 with healthy controls. Relative quantification of the levels of 2943 plasma proteins was performed using Olink Explorer 3072 panels. The unprecedented number of plasma proteins constitutes the most detailed characterization of the Fontan proteome to date. A total of 87 individuals, 58 with a Fontan circulation age 26 (23-38) and 29 healthy controls age 24 years (20-27) were included. Following quality control 2605 proteins were quantifiable. Of these, 513 were changed in the group with Fontan (424 increased and 89 decreased) after covariate adjustment for age, sex, and body mass index. Looking at the related biological function(s), a pathway enrichment analysis found that proteins involved in angiogenesis, bone and calcium homeostasis, metabolism, and inflammation and fibrosis increased, whereas proteins involved in cholesterol synthesis and muscle structure and function were decreased.

CONCLUSIONS

This study represents a small step in understanding the pathophysiological consequences of the Fontan circulation. Based on biological pathways and proteins displaying changes, we speculate local hypoxia to be a potential driver for multiple of the reported changes. This study provides the foundation and direction for future studies wanting to examine changes in detail or explore possible therapeutic targets.

Exhaled breath protein composition in patients hospitalised during the first wave of COVID-19

Coronavirus 2019 (COVID-19) leads to substantial morbidity and excess mortality all over the world which may be aggravated by the propensity of Severe Acute Respiratory Syndrome Coronavirus 2 to mutate. Mechanisms for development of severe COVID-19 are poorly understood. The air we exhale contains endogenous proteins and represents a highly accessible yet unexploited biological sample that can be collected without use of invasive procedures. We collected exhaled breath condensate samples from 28 patients hospitalised due to COVID-19 at admission and discharge using RTubes™. Bottom-up proteomic analysis of tandem mass-tag-labelled single exhaled breath samples was performed in 25 exhaled breath samples collected at admission and 13 samples collected at discharge using discovery-based nano-liquid chromatography-tandem mass spectrometry. In total, 232 proteins were identified in the exhaled breath samples after stringent data filtering. Most of the exhaled proteins were related to the immune systems function and regulation. The levels of four proteins, KRT77, DCD, CASP14 and SERPINB12 decreased from admission to discharge as patients generally recovered from the infection. These proteins are expressed in lung epithelium or macrophages and are associated with the regulation of inflammation drivers in COVID-19. In particular, the alarmins S100A8 and S100A9 accounted for 8% of the exhaled breath proteins. In conclusion, our study demonstrates that analysis of the exhaled breath protein composition can give insights into mechanisms related to inflammation and response to infections, and hereby also of severe COVID-19.Clinical Trial No: NCT04598620.

Multiomics analysis of human serum and animal experiments reveals the protective mechanism of Qingre Huoxue Decoction against rheumatoid arthritis

Objective

Qingre Huoxue Decoction (QRHXD) is a traditional Chinese herbal prescription widely used in clinical practice with significant therapeutic effects on RA; however, its mechanism of action remains unclear. This study aimed to investigate the efficacy and underlying mechanisms of QRHXD in treating RA through clinical research, multiomics approaches, and animal experiments.

Methods

We conducted a 24-week clinical study in which QRHXD was the primary treatment, collecting serum samples from patients before and after treatment for integrated proteomic and metabolomic analysis to identify potential therapeutic targets. Bioinformatics analysis of differentially expressed proteins (DEPs) and differential metabolites (DMs) was performed using hierarchical clustering, volcano plots, heat maps, Gene Ontology (GO), and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis. To validate the identified therapeutic targets, we constructed a collagen-induced arthritis (CIA) mouse model.

Results

Clinical research has shown that QRHXD can improve clinical symptoms and relevant indicators in RA patients, including the disease activity score-28 (DAS28), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), tender joint count (TJC), swollen joint count (SJC), visual analogue scale (VAS), patient-reported outcome (PRO), and health assessment questionnaire (HAQ). Proteomics and metabolomics analysis identified 83 DEPs and 54 DMs, including 46 upregulated and 37 downregulated proteins, as well as 11 upregulated and 43 downregulated metabolites. KEGG enrichment analysis revealed that DEPs are primarily associated with fatty acid degradation, ferroptosis, glycerolipid metabolism, and related pathways. The identified DMs are primarily associated with the AMPK signalling pathway, FoxO signalling pathway, glycolysis/gluconeogenesis, MTOR signalling pathway, and so on. GO enrichment analysis indicated that the DEPs were mainly associated with apoptotic mitochondrial changes, protein modification processes, fatty-acyl-CoA binding, and so on. Integrated proteomics and metabolomics analyses revealed a significant increase in fructose-1,6-biphosphatase 1 (FBP1) levels and a reduction in AMP-activated protein kinase (AMPK) levels in patients with RA. QRHXD inhibited FBP1 and activated AMPK signalling. Animal experiments validated the findings from proteomics and metabolomics analyses, demonstrating that QRHXD could also delay bone destruction and reduce inflammatory factor levels in CIA mice.

Conclusion

QRHXD may reduce the disease activity of RA, attenuate the inflammatory response, and delay bone destruction by inhibiting FBP1 and activating the AMPK signalling pathway.

Mitochondrial Oxidative Stress Related Diagnostic Model Accurately Assesses Rheumatoid Arthritis Risk Stratification and Immune Infiltration Characterization

Rheumatoid arthritis (RA) is a chronic autoimmune disease that affects synovial joints, leading to joint destruction, impaired physical function, and reduced quality of life. However, no accurate method for assessing RA risk currently exists. Given the critical role of early detection and intervention in RA management, further comprehensive risk assessments are essential. Mitochondrial oxidative stress (MOS) is a key factor in the initiation and progression of RA. The bidirectional interaction between RA and MOS supports the feasibility of MOS-based risk stratification for RA. Using public databases, we first applied the weighted gene co-expression network analysis (WGCNA) model to identify key genes involved in RA among MOS-related genes. Differential expression patterns of MOS-related genes were then analyzed using various machine learning algorithms to identify potential biomarkers. A nomogram model was established using CDKN1A, GADD45B, and MAFF genes to predict RA risk, followed by an evaluation of its reliability and stability. Additionally, we analyzed MOS-associated molecular subtypes and immune infiltration characteristics. Our findings highlight the significant role of MOS in RA development and underscore the clinical value of personalized treatment strategies.

Systematic review of innate immune responses against Mycobacterium tuberculosis complex infection in animal models

Background

Mycobacterium tuberculosis (Mtb) complex (MTBC) includes ten species that affect mammals and pose a significant global health concern. Upon infection, Mtb induces various stages in the host, including early bacterial elimination, which may or may not involve memory responses. Deciphering the role of innate immune responses during MTBC infection is crucial for understanding disease progression or protection. Over the past decade, there has been growing interest in the innate immune response to Mtb, with new preclinical models emerging.

Methods

We conducted a systematic review following PRISMA guidelines, focused on innate immune mediators linked to protection or disease progression in animal models of MTBC infection. We searched two databases: National Library of Medicine and Web of Science. Two researchers independently extracted data based on specific inclusion and exclusion criteria.

Results

Eighty-three articles were reviewed. Results were categorized in four groups: MTBC species, animal models, soluble factors and innate pathways, and other molecules (metabolites and drugs). Mtb and M. bovis were the only species studied. P2X7R receptor's role in disease progression and higher macrophage recruitment were observed differentially after infection with hypervirulent Mtb strains. Mice and non-human primates (NHPs) were the most used mammals, with emerging models like Galleria mellonella and planarians also studied. NHPs provided insights into age-dependent immunity and markers for active tuberculosis (ATB). Key innate immune factors/pathways identified included TNF-α, neutrophil recruitment, ROS/RNS responses, autophagy, inflammasomes, and antimicrobial peptides, with homologous proteins identified in insects. Metabolites like vitamin B5 and prostaglandin E2 were associated with protection. Immunomodulatory drugs targeting autophagy and other mechanisms were studied, exhibiting their potential as therapeutic alternatives.

Conclusion

Simpler, physiologically relevant, and ethically sound models, such as G. mellonella, are needed for studying innate responses in MTBC infection. While insects lack adaptive immunity, they could provide insights into "pure" innate immune responses. The dissection of "pure," "sustained" (later than 7 days post-infection), and trained innate immunity presents additional challenges that require high-resolution temporospatial analytical methods. Identifying early innate immune mediators and targetable pathways in the blood and affected tissues could identify biomarkers for immunization efficiency, disease progression, and potential synergistic therapies for ATB.