The role protein phosphorylation and ubiquitylation in human health and disease
The ADP-heptose-ALPK1-TIFA signalling system in immunity and human disease
Five years ago, Feng Shao’s lab in China discovered a previously unrecognised innate immune signalling pathway in which the bacterial metabolites ADP-D,D-heptose and ADP-L,D heptose activate an atypical human protein kinase ALPK1, which is a member of the small alpha protein kinase subfamily whose amino acid sequences are unrelated to any of the other 500+ protein kinases encoded by the human genome. ADP-heptose binds to an N-terminal domain in ALPK1 initiating a conformational change that activates the kinase and permits it to phosphorylate TIFA. This induces the polymerisation of TIFA and subsequent recruitment of the E3 ligases TRAF6, TRAF2-cIAP1 and LUBAC. TRAF6 and TRAF2-cIAP1 generate Lys63-linked and LUBAC generates Met1-linked ubiquitin chains that activate the TAK1 and canonical IKK complexes, respectively, the master kinases of the innate immune system . The TAK1 and IKK complexes switch on other protein kinases triggering a myriad of phosphorylation events that control the production of inflammatory mediators to combat bacterial infection
Mutations in ALPK1 have recently been shown to cause two human diseases. The mutation of Thr237 to Met, which has so far been identified in 60 patients from 29 unrelated families causes an autosomal dominant disease termed ROSAH syndrome (Retinal dystrophy, Optic nerve oedema, Splenomegaly, Anhidrosis (the inability to sweat) and migraine Headache). These patients usually present in the clinic with failing eyesight or severe abdominal pain caused by a massive increase in spleen size. Interestingly, Thr237 lies within the ADP-heptose binding site, where it forms a hydrogen bond with the adenine ring of ADP-heptose.
Spiradenomas are a group of predominantly benign neoplasms, usually observed as abnormal growths on the head, neck and upper body, but they can undergo malignant transformation to Spiradenocarcinomas, which have high rates of mortality. Remarkably, in a cohort of 30 unrelated patients with Spiradenoma or Spiradenocarcinoma, 7 of the 16 Spirademona patients and 4 of the 14 Spiradenocarcinoma patients were found to have the same Val1092 to Ala mutation located in the protein kinase domain of ALPK1.
We are now investigating the mechanisms by which these mutations cause ROSAH and spiradenoma, respectively.
Sugar ubiquitylation; a new surveillance mechanism for the recognition and elimination of misfolded macromolecules?
Ubiquitylation was discovered over 40 years ago as a mechanism that marks proteins for destruction. Since then, ubiquitylation has been found to regulate the functions of proteins in other ways, but the concept that proteins are the sole targets for ubiquitylation has never altered. Now our lab has found that sugars can also be ubiquitylated.
In 2022, we discovered that mice in which the E3 ubiquitin ligase HOIL-1 is replaced by an E3-ligase inactive mutant accumulate insoluble deposits, termed Polyglucosan Bodies (PB), in the brain, heart and other tissues . PB consist of unbranched glucosaccharides that lack the α1:6 branch points found in normally branched glycogen. HOIL-1 deficiency in humans also leads to the accumulation of PB, causing cardiomyopathy and heart failure in young adults. PB can also cause neurodegeneration and epilepsy.
Several years ago we discovered that the HOIL-1 E3 ligase catalyses the formation of ester bonds between the C-terminal carboxylate of ubiquitin and the hydroxyl side chains of serine and threonine residues in proteins . This finding, together with the observation that PB are formed in the tissues of mice expressing an E3 ligase-inactive mutant of HOIL-1, led us to discover that HOIL-1 can ubiquitylate the C6 hydroxyl group of glucose in unbranched glucosaccharides and to propose a new idea for how HOIL-1 detects unbranched glycogen molecules and initiates glycophagy, the process that destroys these abnormal molecules before they precipitate as PB and cause disease .
We are now investigating whether our hypothesis is correct and our goal is to elucidate how ubiquitylation of unbranched glycogen molecules triggers their uptake into lysosomes where they are destroyed by the lysosomal α1:4 glucosidase. We are also investigating whether sugar ubiquitylation has other roles in human health and disease. Our research is opening up new aspects of ubiquitin biology.
 Snelling, T., Shpiro, N., Gourlay, R., Lamoliatte, F. andCohen, P. (2022)“Coordinated control of the ADP-heptose/ALPK1 signalling network by the E3 ligases TRAF6,
TRAF2/c-IAP1 and LUBAC” Biochem J. 479, 2195-2216. https://doi.org/10.1042/BCJ20220401
 Kelsall, I.R., McCrory, E.H., Xu, Y., Scudamore, C.L., Nanda S.K., Mancebo-Gamella, P., WoodN.T., Knebel, A., Matthews, S.J. and Cohen, P. (2022) “HOIL-1 ubiquitin ligase activity targets unbranched unbranched glucosaccharides and is required to prevent polyglucosan accumulation”EMBO Journal 41:e109700 https://www.embopress.org/doi/pdf/10.15252/embj.2021109700
 Kelsall, I.R., Zhang, J., Knebel, A., Arthur, J.S.C. and Cohen, P. (2019) ‘The E3 ligase HOIL-1 catalyses ester bond formation between ubiquitin and components of the myddosome in mammalian cells.” Proc. Nat. Acad. Sci. USA 116, 13293-13298 https://doi.org/10.1073/pnas.1905873116
 McCrory, E., Akimov, V., Cohen, P.* and Blagoev, B.* (2022) “ Identification of ester-linked ubiquitylation sites during TLR7 signalling increases the number of inter-ubiquitin linkages from 8 to 12” Biochem J. 479, 2419-2431 * joint corresponding authors. https://doi.org/10.1042/BCJ20220510
Other recent papers from the Cohen lab
Petrova1, T., Nanda, S., Vadillo, C.F., Scudamore, T., and Cohen, P. (2023) “Effect of pacritinib on the lupus phenotype of ABIN1[D485N] mice” Lupus Science & Medicine 10:e000822 http://dx.doi.org/10.1136/lupus-2022-000822
Petrova T, Nanda, S.K., Scudamore, C., Lee, K.L., Wright, S.W., Rao, V.R. and Cohen, P. (2021) “Prevention and partial reversal of the lupus phenotype in ABIN1[D485N] mice by an IRAK4 inhibitor”. Lupus Science and Medicine 8:e000573 https://lupus.bmj.com/content/lupusscimed/8/1/e000573.full.pdf
Cohen, P., Cross, D. and Janne, P.A. (2021) “Kinase Drug Discovery 20 years after Imatinib: progress and future directions. Nat. Rev. Drug Disc. 20, 551-569 10.1038/s41573-021-00195-4