Structural Basis of Feedback Control of Oncogenic Signaling in B-Lymphoid Malignancies

Introduction: Multiple structural elements are known that recruit kinases to sites of active signal transduction (e.g. lipid rafts) within the plasma membrane. For instance, pleckstrin homology (PH) domains and the conserved intracellular loop (CIL) motifs recently discovered by us (Lee et al., Nature 2021) direct kinase molecules (Src, BTK, AKT and PI3K) to large signaling clusters in lipid rafts to amplify normal or oncogenic B-cell signaling. While concepts of site-specific recruitment of kinases to initiate signaling are well established, little is known about spatial control of inhibitory phosphatases and how they are directed to sites of maximal signaling strength. Results: Here we discovered the cytoplasmic tail of CD25 as an essential structural element for site-specific recruitment of inhibitory phosphatases. CD25-mediated shuttling of inhibitory phosphatases balances oncogenic signaling strength and is essential for cell-survival in B-cell malignancies, including B-ALL, CLL and mantle cell lymphoma. This was unexpected because CD25 (IL2RA) is known as one of three chains of the Interleukin-2 (IL2) receptor on T- and NK-cells. Studying clinical outcome and gene expression in multiple clinical cohorts, we found CD25 as a top-ranking predictor of poor clinical outcome in patients with B-ALL, mantle cell lymphoma and CLL. Our mechanistic experiments revealed that CD25 expressed on B-cells is monomeric. Unlike T- and NK-cells, CD25 expressed on activated or transformed B-cells does not form a heterotrimeric IL2 receptor with the IL2Rb and common g-chain. Instead of contributing to IL2-signaling, CD25 showed dynamic recruitment either to the B-cell receptor (BCR) or transforming oncogenes within lipid rafts. Conditional deletion of CD25 at earliest stages of B-cell development in mice resulted in profound B-cell defects. However, these defects were not replicated by IL2-deficiency and B-cell development in Il2-/- mice was normal. Inducible deletion of CD25 in genetic models for B-ALL and mantle cell lymphoma revealed an essential function of CD25 in maintaining homeostasis of signaling strength. In the absence of CD25, B-ALL and mantle cell lymphoma cells showed autonomous Ca 2+ oscillations, constitutive activation of Src-family kinases, BTK and ERK as well as the AMPK energy-stress sensor. CD25-deficient B-ALL and mantle cell lymphoma cells initially showed increased proliferation but rapidly died from exhaustion. Consistent with massive accumulation of p53, CD25-deficient B-ALL cells failed to form colonies and to initiate leukemia in transplant-recipient mice. Our mechanistic studies focused on the short (13 residues) cytoplasmic tale of CD25, which features a prominent serine/threonine kinase substrate motif. In vitro kinase assays for 62 candidate serine/threonine kinases revealed PKCd as top-ranking kinase and the serine residue 268 in the tail of CD25 as its principal substrate. The proximity-based labeling assays (BioID) revealed that the CD25 tail recruits PKCd and its adapter RACK1, which scaffold the inhibitory phosphatases SHIP1 and SHP1 for site-specific activation in lipid rafts (see Schematic). Consistent with these results, phospho-proteomic studies revealed that inducible deletion of CD25 resulted in acute inactivation of SHIP1 and SHP1 as well as the inhibitory RACK1 scaffold. Multiscale molecular dynamics (MD) simulations revealed that PKCd-mediated phosphorylation of the CD25-tail (S268) tightened interactions with RACK1 and SHIP1 and SHP1 phosphatases, whereas these interactions were destabilized when the CD25-tail was mutated (S268A). Conclusions: Mechanisms of site-specific recruitment of kinases for signal amplification have been extensively studied. However, structural elements that direct inhibitory phosphatases to sites of maximal signaling activity for feedback control remained largely unknown. Here we discovered a PKCd substrate motif in the cytoplasmic tail of CD25 (S268) as a central element to recruit inhibitory phosphatases, scaffolded by RACK1, to curb excessive signaling activity and energy expenditure. High expression levels of CD25 enable higher baseline activity of oncogenic signaling and are associated with poor patient-outcome. Our preclinical studies based on CD25-antibody-drug-conjugates (ADC) revealed that CD25 as a novel target in refractory B-ALL and mantle cell lymphoma. Figure 1 Figure 1. Disclosures Weinstock: SecuraBio: Consultancy; ASELL: Consultancy; Bantam: Consultancy; Abcuro: Research Funding; Verastem: Research Funding; Daiichi Sankyo: Consultancy, Research Funding; AstraZeneca: Consultancy; Travera: Other: Founder/Equity; Ajax: Other: Founder/Equity.

XCP1 is a caspase that proteolyzes Pathogenesis-related protein 1 to produce the cytokine CAPE9 for systemic immunity in Arabidopsis

Proteolytic activation of cytokines regulates immunity in diverse organisms. In animals, cysteine-dependent aspartate-specific proteases (caspases) play central roles in cytokine maturation. Although the proteolytic production of peptide cytokines is also essential for plant immunity, evidence for a plant caspase is still lacking. In this study, we discovered that proteolysis of a caspase-like substrate motif “CNYD” within Pathogenesis-related protein 1 (AtPR1) in Arabidopsis generates an immunomodulatory cytokine (AtCAPE9). Salicylic acid enhances CNYD-targeted protease activity and the proteolytic release of AtCAPE9 from AtPR1 in Arabidopsis. We show that this process involves a caspase, identified as Xylem cysteine peptidase 1 (XCP1). XCP1 exhibits a calcium-modulated pH-activity profile and a comparable activity to human caspases. XCP1 is required to induce systemic immunity triggered by pathogen-associated molecular patterns. This work reveals XCP1 as the first known plant caspase, which produces the cytokine AtCAPE9 from the canonical salicylic acid signaling marker PR1 to activate systemic immunity.

Cohesin cleavage by separase is enhanced by a substrate motif distinct from the cleavage site

Chromosome segregation begins when the cysteine protease, separase, cleaves the Scc1 subunit of cohesin at the metaphase-to-anaphase transition. Separase is inhibited prior to metaphase by the tightly bound securin protein, which contains a pseudosubstrate motif that blocks the separase active site. To investigate separase substrate specificity and regulation, here we develop a system for producing recombinant, securin-free human separase. Using this enzyme, we identify an LPE motif on the Scc1 substrate that is distinct from the cleavage site and is required for rapid and specific substrate cleavage. Securin also contains a conserved LPE motif, and we provide evidence that this sequence blocks separase engagement of the Scc1 LPE motif. Our results suggest that rapid cohesin cleavage by separase requires a substrate docking interaction outside the active site. This interaction is blocked by securin, providing a second mechanism by which securin inhibits cohesin cleavage.

Evolution of protein kinase substrate recognition at the active site

Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase substrate motif. Kinases have been extensively duplicated throughout evolution but little is known about when in time new target motifs have arisen. Here we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired soon after the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.

CARM1 methylates MED12 to regulate its RNA-binding ability

The coactivator-associated arginine methyltransferase (CARM1) functions as a regulator of transcription by methylating a diverse array of substrates. To broaden our understanding of CARM1's mechanistic actions, we sought to identify additional substrates for this enzyme. To do this, we generated CARM1 substrate motif antibodies, and used immunoprecipitation coupled with mass spectrometry to identify cellular targets of CARM1, including mediator complex subunit 12 (MED12) and the lysine methyltransferase KMT2D. Both of these proteins are implicated in enhancer function. We identified the major CARM1-mediated MED12 methylation site as arginine 1899 (R1899), which interacts with the Tudor domain–containing effector molecule, TDRD3. Chromatin immunoprecipitation–seq studies revealed that CARM1 and the methyl mark it deposits are tightly associated with ERα-specific enhancers and positively modulate transcription of estrogen-regulated genes. In addition, we showed that the methylation of MED12, at the R1899 site, and the recruitment of TDRD3 by this methylated motif are critical for the ability of MED12 to interact with activating noncoding RNAs.

Enhancing the efficiency of sortase–mediated ligations through nickel–peptide complex formation

A modified sortase substrate motif allows for control of reaction equilibrium through the use of a simple Ni2+ additive.

Myelin protein zero/P0 phosphorylation and function require an adaptor protein linking it to RACK1 and PKCα

Point mutations in the cytoplasmic domain of myelin protein zero (P0; the major myelin protein in the peripheral nervous system) that alter a protein kinase Cα (PKCα) substrate motif (198HRSTK201) or alter serines 199 and/or 204 eliminate P0-mediated adhesion. Mutation in the PKCα substrate motif (R198S) also causes a form of inherited peripheral neuropathy (Charcot Marie Tooth disease [CMT] 1B), indicating that PKCα-mediated phosphorylation of P0 is important for myelination. We have now identified a 65-kD adaptor protein that links P0 with the receptor for activated C kinase 1 (RACK1). The interaction of p65 with P0 maps to residues 179–197 within the cytoplasmic tail of P0. Mutations or deletions that abolish p65 binding reduce P0 phosphorylation and adhesion, which can be rescued by the substitution of serines 199 and 204 with glutamic acid. A mutation in the p65-binding sequence G184R occurs in two families with CMT, and mutation of this residue results in the loss of both p65 binding and adhesion function.