Previous proteomic studies in IBD patients have revealed specific protein expression profiles that correlate with either Crohn's disease (CD) or ulcerative colitis (UC). Four potential protein markers, PF4, MRP8, FIBA ​​and Hpalpha2, have been found, which appear to be characteristic of IBD and therefore can be used to screen for IBD in undiagnosed populations. In addition, a frequent problem of IBD is the difficulty of diagnosis between CD and UC, which may present similar symptoms and clinical picture and make it difficult for the attending physician to diagnose them and, consequently, to choose the appropriate treatment. Proteome analysis between these two groups has revealed specific expression profiles that correlate with either CD or UC and therefore, can be used as specific biomarkers. Corresponding proteomic analyzes with the aim of a better and more accurate diagnosis are also carried out in other diseases, such as neurological diseases (Parkinson's), leukemias, spondyloarthritis, psoriasis, etc.

Due to the great heterogeneity among patients with IBD, choosing the appropriate treatment is often a challenge. Literature indicates that there are groups of patients who will either not respond at all to the respective biological treatment or will lose their response to it after a short period of time. In a first pilot proteomic study in CD patients, the PF4 index was found to be associated with a good response to an anti-TNF biologic agent. Therefore, the identification of biomarkers that demonstrate a possible response or not to a biological agent is of major importance, not only in the case of IBD, but also for other diseases, such as cancer, rheumatoid arthritis, spondyloarthritis, etc.

In the case of chronic autoimmune diseases and cancer, knowing their evolution plays an important role, both to avoid possible complications and to choose the best therapeutic strategy. In an earlier study in patients with IBD, the analysis of the expression of CD8+ T lymphocytes at the RNA level, highlighted important indicators of the prognosis of the disease, which if confirmed at the protein level with proteomic analysis, would be decisive indicators for Precision Medicine. Similar proteomic studies with the aim of identifying prognostic biomarkers are also carried out in other diseases, such as leukemia, spondyloarthritis, multiple sclerosis, etc.

Similar to proteomic analyses, mass spectrometry is a sensitive method capable of detecting metabolites with extremely high sensitivity. Its applications in IBD have already been carried out with quite encouraging results. One of them is the metabolomic analysis of samples from twin patients with Crohn's Disease (CD), which showed differences in the metabolic profile between patients and healthy individuals. In fact, differences were also found between patients who showed diversity in terms of the location of the disease. It is assumed that the use of Metabolomics can be used as a tool to diagnose the disease, but also to characterize its phenotype. Accordingly, a metabolomics study was also done in patients with Ulcerative Colitis (UC), which also showed differences in the metabolites of patients and healthy controls, demonstrating the role of metabolomics in the prognosis of the disease. Of course, the applications of Metabolomics have expanded and are expanding to several serious and incurable diseases with promising results. Characteristic examples are cancer, Alzheimer's disease, etc.

Regarding IBD, previous studies from our laboratory and others have shown that specific metabolites of the organism or the microbiome are associated with specific manifestations of CD and UC and therefore, could perform as specialized biomarkers for categorizing the subphenotypes of IBD and help the attending physicians in the selection of the appropriate treatment, but also in the better management of the symptoms and the clinical course of these patients. 

Similarly, to proteomic analysis, metabolome analysis can reveal biomarkers to predict response to treatment. Such analyses have been carried out in various diseases such as cancer, metabolic syndrome, cardiovascular, psychiatric etc., highlighting the effect of various pathological and pharmacological processes on metabolism and thus determining the response to treatment. A study has been done on the role of aspirin and the response to it in patients with thromboembolic diseases. A similar study has been done in patients with high cholesterol which found that the metabolic profile between patients who responded to statin therapy was different from those who did not. But in addition to human metabolism, microbial metabolism seems to play an important role in such cases. Indicatively, it is worth mentioning that in a pilot study on kidney transplant patients, it was found that those who required a 50% increase in the dose of the immunosuppressant drug tacrolimus also had high levels of the microbe Faecalibacterium prausnitzii, whose metabolism appears to affect the metabolism of this drug. From the above examples, it appears that the analysis of the metabolomic profile of both the human organism and the microbiome can help predict response to the treatment of various diseases and is therefore a field whose applications have a great impact on Precision Medicine.

The applications of Metabolomics also extend to the study of disease progression and the identification of characteristic prognostic biomarkers, with numerous publications regarding various diseases such as dementia, chronic kidney disease, non-alcoholic liver disease, etc.