MSC after in vivo aggregation show a favorable RNA expression profile for the treatment of colitis. MSC spheroids showed high expression of Ki-67 and low levels of apoptotic marker cleaved caspase-3. Locally applied MSC and MSC spheroids are both able to ameliorate DSS-induced colitis and show similar clinical effects, including improvement in the macro and microscopic IBD score. This evidence concerns the gene CASP3 and inflammatory bowel disease.