In 1989, Patrick Baeuerle started an independent research group at Klinikum Großhadern in Martinsried, Germany. In 1993, he became Chair of Biochemistry and Molecular Biology at the medical school of University of Freiburg. Three years later, he joined the start-up company Tularik in South San Francisco as its Director of Drug Discovery. In 1998, he moved back to Germany to head research and development of Micromet AG, a Munich-based biopharmaceutical company. By acquisition of CancerVax in 2006, Patrick Baeuerle became Chief Scientific Officer of NASDAQ -listed Micromet now headquartered in Bethesda, Maryland, with a research centre in Munich, Germany.
As a student, Patrick Baeuerle showed that tyrosine sulfation is a trans-Golgi-specific modification of secretory proteins. As a postdoctoral fellow, he discovered the inhibitory subunit I-kappa B of transcription factor NF-kappa B, and became inventor of the controversial NF-kappa B patent ‘516. His own research group studied the function of purified I-kappaB proteins, supported cloning of NF-kappa B subunits p50 and p65/RelA, identified NF-kappa as a redox-controlled transcription factor demonstrated the trans-activating potential of p65/RelA, showed that NF-kappa B is binding to DNA as a heterodimer, studied how I-kappa B proteins control nuclear translocation of NF-kappaB, and unravelled the basic mechanism of NF-kappa B activation, involving phosphorylation of I-kappa B and its subsequent degradation by the proteasome. His group was also first to show that NF-kappa B plays a functional role in the nervous system. Patrick Baeuerle authored more than 150 publications on NF-kappa B and related research.
Since 1998, Patrick Baeuerle investigates the therapeutic potential of T cell-engaging BiTE antibodies for therapy of cancer, and has been responsible at Micromet for the development of blinatumomab and several other antibody therapies. He authored more than 210 publications (Search in PubMed with author name “baeuerle p”).
^Baeuerle, Patrick A.; Baltimore, David (1988). "Activation of DNA-binding activity in an apparently cytoplasmic precursor of the NF-κB transcription factor". Cell. 53 (2): 211–7. PMID3129195. doi:10.1016/0092-8674(88)90382-0.
^Baeuerle, P A; Baltimore, D (1989). "A 65-kappaD subunit of active NF-kappaB is required for inhibition of NF-kappaB by I kappaB". Genes & Development. 3 (11): 1689–98. doi:10.1101/gad.3.11.1689.
^US patent 6410516, Baltimore, David et al., "Nuclear factors associated with transcriptional regulation", issued 2002-06-25
^Zabel, Ulrike; Baeuerle, Patrick A. (1990). "Purified human IκB can rapidly dissociate the complex of the NF-κB transcription factor with its cognate DNA". Cell. 61 (2): 255–65. PMID2184941. doi:10.1016/0092-8674(90)90806-P.
^Kieran, Mark; Blank, Volker; Logeat, FrédéRique; Vandekerckhove, Joël; Lottspeich, Frledrich; Le Bail, Odile; Urban, Manuela B.; Kourilsky, Philippe; et al. (1990). "The DNA binding subunit of NF-κB is identical to factor KBF1 and homologous to the rel oncogene product". Cell. 62 (5): 1007–18. PMID2203531. doi:10.1016/0092-8674(90)90275-J.
^Ruben, S.; Dillon, P.; Schreck, R; Henkel, T; Chen, C.; Maher, M; Baeuerle, P.; Rosen, C. (1991). "Isolation of a rel-related human cDNA that potentially encodes the 65-kD subunit of NF-kappa B". Science. 254 (5028): 11. doi:10.1126/science.1925549.
^Henkel, Thomas; Zabel, Ulrike; Van Zee, Karen; Müller, Judith M.; Fanning, Ellen; Baeuerle, Patrick A. (1992). "Intramolecular masking of the nuclear location signal and dimerization domain in the precursor for the p50 NF-κB subunit". Cell. 68 (6): 1121–33. PMID1547506. doi:10.1016/0092-8674(92)90083-O.
^Bargou, R.; Leo, E.; Zugmaier, G.; Klinger, M.; Goebeler, M.; Knop, S.; Noppeney, R.; Viardot, A.; et al. (2008). "Tumor Regression in Cancer Patients by Very Low Doses of a T Cell-Engaging Antibody". Science. 321 (5891): 974–7. PMID18703743. doi:10.1126/science.1158545.
^Baeuerle, PA; Kufer, P; Bargou, R (2009). "BiTE: Teaching antibodies to engage T-cells for cancer therapy". Current opinion in molecular therapeutics. 11 (1): 22–30. PMID19169956.