Patients from several immune-mediated diseases experience continued trial-and-error testing of new drugs without adequate selection based on personalized molecular patterns of disease. In consequence, the patients suffer from not having an adequate response to the therapy they are given, causing perpetuation of tissue damage or even death. The main objective of 3TR is therefore to define the molecular mechanisms behind this therapeutic unresponsiveness in patients from 7 different immune-mediated diseases, systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, asthma, chronic obstructive pulmonary disease and inflammatory bowel disease - diseases that affect important portions of the European population. As secondary objectives, 3TR has as the goal to define new therapeutic targets through the molecular stratification of patients according to their tissue molecular structure and to define biomarkers that can be used in the future to design personalized therapies. Finally, 3TR will also identify the mechanisms behind the appearance of the biomarkers using novel methodologies such as tissue organoids. The results will have a major impact in the society, as it will lead to a more personalized approach towards therapy and reduce severe tissue damage and invalidation.