The present disclosure relates to methods of collecting exosomes and microvesicles (EMV) from urine and isolating corresponding mRNA in order to diagnose and treat acute kidney injury (AKI). In particular, certain embodiments relate to the method of capturing EMV from urine applied to a filter device that is capable of capturing EMV. Nucleic acids such as mRNA can be isolated from the EMV using an oligo(dT)-coated plate designed to accommodate the filter device and then used for further molecular analysis. Quantification of the collected nucleic acids may then be used in the diagnosis and/or treatment of IBD.