Amyloidosis and the lungs and airways

Amyloidosis can both complicate long-standing respiratory conditions and be deposited within the respiratory system itself. In acquired systemic amyloidosis, control of the underlying condition that is producing the circulating amyloid precursor protein is paramount. Systemic AA amyloidosis can result from unremitting chronic inflammation or infection such as in bronchiectasis. Control of the inflammation is paramount to amyloid regression. For systemic AL amyloidosis, treatment requires the use of chemotherapy or novel immunotherapies targeting the underlying plasma cell dyscrasia or lymphoproliferative disease that produce the abnormal amyloidogenic light chain. Localised amyloidosis can occur anywhere along the respiratory tract and can present with marked heterogeneity. In localised amyloidosis, management generally involves resection or ablation of symptomatic deposits. On occasion, localised pulmonary amyloidosis can be a manifestation of underlying Sjögren syndrome. Novel treatments are beginning to become available, including specific drug therapies to prevent translation of amyloidogenic proteins, stabilise amyloid precursor proteins and interfere with amyloid fibrillogenesis

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors

In order to fully understand protein kinase networks, new methods are needed to identify regulators and substrates of kinases, especially for weakly expressed proteins. Here we have developed a hybrid computational search algorithm that combines machine learning and expert knowledge to identify kinase docking sites, and used this algorithm to search the human genome for novel MAP kinase substrates and regulators focused on the JNK family of MAP kinases. Predictions were tested by peptide array followed by rigorous biochemical verification with in vitro binding and kinase assays on wild-type and mutant proteins. Using this procedure, we found new ‘D-site’ class docking sites in previously known JNK substrates (hnRNP-K, PPM1J/PP2Czeta), as well as new JNK-interacting proteins (MLL4, NEIL1). Finally, we identified new D-site-dependent MAPK substrates, including the hedgehog-regulated transcription factors Gli1 and Gli3, suggesting that a direct connection between MAP kinase and hedgehog signaling may occur at the level of these key regulators. These results demonstrate that a genome-wide search for MAP kinase docking sites can be used to find new docking sites and substrates