Henk Hilkmann

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

The evidence for T-cell–mediated regression of human cancers such as non–small-cell lung carcinoma, renal cell carcinoma, and—in particular—melanoma after immunotherapy is strong. Anti-CTLA4 (ipilimumab) treatment has been approved for treatment of meta-static melanoma,1 and antibody-mediated blockade of PD-1, a second inhibitory receptor on T cells, has shown highly encouraging results in early clinical trials.2,3 Although the clinical activity of these treatments is apparent, it is still unknown which T-cell reactivities are involved in immunotherapy-induced cancer regression.4 T-cell reactivity against nonmutated tumor-associated self-antigens has been analyzed in patients treated with ipilimumab or with autologous tumor-infiltrating T cells, but the magnitude of the T-cell responses observed has been relatively modest.5,6 In part on the basis of such data, recognition of patient-specific mutant epitopes (hereafter referred to as neoantigens) has been suggested to be a potentially important component.7 A potential involvement of mutated epitopes in T-cell control would also fit well with the observation that the mutation load in sun-exposed melanomas is particularly high.8-10 Intriguingly, on the basis of animal model data, it has recently been suggested that (therapy-induced) analysis of T-cell reactivity against patient-specific neoantigens may be feasible through exploitation of cancer genome data.11,12 However, human data have thus far been lacking. Here we report a case of a patient with stage IV melanoma who exhibited a clinical response to ipilimumab treatment. Cancer exome–guided analysis of T-cell reactivity in this patient revealed reactivity against two neoantigens, including a dominant T-cell response against a mutant epitope of the ATR (ataxia telangiectasia and Rad3 related) gene product that increased strongly after ipilimumab treatment. These data provide the first demonstration (to our knowledge) of cancer exome–guided analysis to dissect the effects of melanoma immunotherapy.

High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4 + T cells in human melanoma

Tumor-specific neo-antigens that arise as a consequence of mutations are thought to be important for the therapeutic efficacy of cancer immunotherapies. Accumulating evidence suggests that neo-antigens may be commonly recognized by intratumoral CD8+ T cells, but it is unclear whether neo-antigen–specific CD4+ T cells also frequently reside within human tumors. In view of the accepted role of tumor-specific CD4+ T-cell responses in tumor control, we addressed whether neo-antigen–specific CD4+ T-cell reactivity is a common property in human melanoma.

Chemical Synthesis of Ubiquitin, Ubiquitin-Based Probes, and Diubiquitin

Post-translational modification of proteins with ubiquitin (Ub) and Ub chains controls protein breakdown by the proteasome, cellular localization of proteins, transcriptional activity, and DNA repair.[1] Ubiquitin is a highly conserved 76 amino acid protein that can be linked to target proteins through an isopeptide bond between the C-terminal carboxylate of Ub and the ɛ-amine of a lysine residue or N terminus of the target protein. Ubiquitin is able to form chains by self-conjugation onto any of its seven lysine residues (namely, K6, K11, K33, K27, K29, K48, and K63). Although all the linkages have been identified in cells,[2] only K48 and K63 linkages have been thoroughly studied so far. The conjugation of ubiquitin requires the concerted action of E1, E2, and E3 enzymes, defined combinations of which provide specificity for the protein target and the nature of the Ub chain topoisomers. The E1 enzyme initiates the cascade by activating Ub at the expense of ATP to form an E1-Ub thioester between the cysteine residue of the E1 active site and the C-terminal carboxylate of Ub. This E1-Ub thioester serves as a donor of activated Ub that then enters the complex enzymatic conjugation cascade.

Accumulation of an alkyl lysophospholipid in tumor cell membranes affects membrane fluidity and tumor cell invasion

Tumor cells grown in the presence of 1-O-alkyl-2-O-methylglycero-3-phosphocholine (AMG-PC) accumulated this ether lipid in their membranes. Depending on the cell type and the dose of the compound, up to 17% of the total phospholipids of the purified plasma membranes consisted of authentic AMG-PC. Extensive incorporation of the agent resulted in a decrease in plasma membrane fluidity and inhibition of tumor cell invasiveness in embryonic chick heart fragments. The extent of AMG-PC incorporation and fluidity change was not strictly correlated with the degree to which tumor cell invasion was inhibited.

Exogenous phospholipase D generates Iysophosphatidic acid and activates Ras, Rho and Ca2+ signaling pathways

BACKGROUND Phospholipase D (PLD) hydrolyzes phospholipids to generate phosphatidic acid (PA) and a free headgroup. PLDs occur as both intracellular and secreted forms; the latter can act as potent virulence factors. Exogenous PLD has growth-factor-like properties, in that it induces proto-oncogene transcription, mitogenesis and cytoskeletal changes in target cells. The underlying mechanism is unknown, although it is generally assumed that PLD action is mediated by PA serving as a putative second messenger. RESULTS In quiescent fibroblasts, exogenous PLD (from Streptomyces chromofuscus) stimulated accumulation of the GTP-bound form of Ras, activation of mitogen-activated protein (MAP) kinase and DNA synthesis, through the pertussis-toxin-sensitive inhibitory G protein Gi. Furthermore, PLD mimicked bioactive lysophospholipids (but not PA) in inducing Ca2+ mobilization, membrane depolarization and Rho-mediated neurite retraction. PLD action was mediated by Iysophosphatidic acid (LPA) derived from Iysophosphatidylcholine acting on cognate G-protein-coupled LPA receptor(s). There was no evidence for the involvement of PA in mediating the effects of exogenous PLD. CONCLUSIONS Our results provide a molecular explanation for the multiple cellular responses to exogenous PLDs. These PLDs generate bioactive LPA from pre-existing Iysophosphatidylcholine in the outer membrane leaflet, resulting in activation of G-protein-coupled LPA receptors and consequent activation of Ras, Rho and Ca2+ signaling pathways. Unscheduled activation of LPA receptors may underlie, at least in part, the known pathogenic effects of exogenous PLDs.

Involvement of Phosphatidylcholine-specific Phospholipase C in Platelet-derived Growth Factor-induced Activation of the Mitogen-activated Protein Kinase Pathway in Rat-1 Fibroblasts

The role of phosphatidylcholine (PC) hydrolysis in activation of the mitogen-activated protein kinase (MAPK) pathway by platelet-derived growth factor (PDGF) was studied in Rat-1 fibroblasts. PDGF induced the transient formation of phosphatidic acid, choline, diacylglycerol (DG), and phosphocholine, the respective products of phospholipase D (PLD) and phospholipase C (PC-PLC) activity, with peak levels at 5-10 min. PLD-catalyzed transphosphatidylation (with n-butyl alcohol) diminished DG formation at 5 min but not at later stages of PDGF stimulation. Phorbol ester-induced down-regulation of protein kinase C (PKC) completely blocked PLD activation but not the formation of DG and phosphocholine at 10 min of PDGF stimulation. Collectively, these data indicate that PDGF activates both PLD and PC-PLC. In contrast, epidermal growth factor did not activate PC-PLC in these cells, and it activated PLD only weakly. DG formation by itself, through Bacillus cereus PC-PLC treatment of cells, was sufficient to mimic PDGF in activation of MAPK independent of phorbol ester-sensitive PKC. Since PKC down-regulation blocked PDGF-induced PLD but not MAPK activation, we conclude that PLD is not involved in MAPK signaling. In contrast, MAPK activation by exogenous (bacterial) PLD was not affected by PKC down-regulation, indicating that signals evoked by exogenous PLD differ from endogenous PLD. D609 (2-10 μg/ml), an inhibitor of PC-PLC, blocked PDGF- but not epidermal growth factor-induced MAPK activation. However, D609 should be used with caution since it also affects PLD activity. The results suggest that PC-PLC rather than PLD plays a critical role in the PDGF-activated MAPK pathway.

Rapid attenuation of receptor-induced diacylglycerol and phosphatidic acid by phospholipase D-mediated transphosphatidylation: formation of bisphosphatidic acid.

Generation and attenuation of lipid second messengers are key processes in cellular signalling. Receptor‐mediated increase in 1,2‐diacylglycerol (DG) levels is attenuated by DG kinase and DG lipase. We here report a novel mechanism of DG attenuation by phospholipase D (PLD), which also precludes the production of another (putative) second messenger, phosphatidic acid (PA). In the presence of an alcohol, PLD converts phosphatidylcholine (PC) into a phosphatidylalcohol (by transphosphatidylation) rather than into PA. We found in bradykinin‐stimulated human fibroblasts that PLD mediates transphosphatidylation from PC (donor) to the endogenous ‘alcohol’ DG (acceptor), yielding bis(1,2‐diacylglycero)‐3‐sn‐phosphate (bisphosphatidic acid; bisPA). This uncommon phospholipid is thus a condensation product of the phospholipase C (PLC) and PLD signalling pathways, where PLC produces DG and PLD couples this DG to a phosphatidyl moiety. Long‐term phorbol ester treatment blocks bradykinin‐induced activation of PLD and consequent bisPA formation, thereby unveiling rapid formation of DG. BisPA formation is rapid (15 s) and transient (peaks at 2–10 min) and is also induced by other stimuli capable of raising DG and activating PLD simultaneously, e.g. endothelin, lysophosphatidic acid, fetal calf serum, phorbol ester, dioctanoylglycerol or bacterial PLC. This novel metabolic route counteracts rapid accumulation of receptor‐induced DG and PA, and assigns for the first time a physiological role to the transphosphatidylation activity of PLD, that is signal attenuation.

A metabolite of an antineoplastic ether phospholipid may inhibit transmembrane signalling via protein kinase C.

In our search for the mechanisms by which the drug 1-O-alkyl-2-O-methylglycero-3-phosphocholine (AMG-PC) inhibits tumor growth and metastasis, we have detected a metabolite, 1-O-alkyl-2-O-methylglycerol (AMG), in membranes of MO4 mouse fibrosarcoma cells grown in the presence of the drug. Synthetic AMG inhibited the activation of highly purified human protein kinase C by diacylglycerol in the presence of phosphatidylserine. Furthermore, AMG also inhibited the receptor-specific binding of3H-phorbol-12,13-dibutyrate to human HL-60 promyeloid leukemia cells in a dose-dependent fashion. AMG-PC was not effective or much less so in these assays. We suggest that interaction of the metabolite AMG with protein kinase C may inhibit stimulus-response coupling in tumor cells and may thus potentially contribute to the mechanism by which AMG-PC exerts its anticancer activities.

Differences in membrane lipid composition and fluidity of transplanted grsl lymphoma cells, depending on their site of growth in the mouse

GRSL lymphoma cells were isolated from various growth sites in the host. The relative membrane lipid fluidities of these cells and of normal lymphoid cells were estimated by fluorescence polarization, using the probe diphenylhexatriene and by measuring the (free) cholesterol/phospholipid molar ratio in whole cells. The results indicate that the membrane fluidity (reciprocal of the lipid structural order) of the lymphoma cells increases in the order of their location: peripheral blood less than spleen less than mesenterial lymph node less than ascites fluid. The membrane fluidities of normal lymphocytes from thymus, mesenterial lymph node and spleen were about the same, but higher than of peripheral blood lymphocytes, and between those of the lymphoma cells from lymph node and spleen. These results are confirmed by more extensive analysis on purified plasma membranes from the splenic and ascitic GRSL lymphoma cells and from normal splenocytes and thymocytes. The significantly higher lipid order parameter found in the GRSL plasma membrane isolated from the spleen as compared to those from the ascites cells could be fully explained by the differences measured in the major chemical determinants of the fluidity, i.e., the cholesterol/phospholipid ratio, the sphingomyelin content and the degree of saturation of the fatty acyl groups of the phospholipids. It was also found that the cholesterol/phospholipid ratio in erythrocyte membranes isolated from the peripheral blood of the tumor bearers was higher than in those from normal control mice. The observed differences in membrane fluidity between distinct subsets of tumor cells may be relevant to the sensitivity of these cells to immune attack or to drugs.

Catalytic hydrogenation of fatty acyl chains in plasma membranes; effect on membrane lipid fluidity and expression of cell surface antigens

Optimal reaction conditions were established for hydrogenation of plasma membranes of living murine GRSL leukemia cells, using the water-soluble catalyst Pd(QS)2 (QS, sulphonated alizarine; C14H6O7NaS). Under these conditions more than 80% of the cells remained viable. Analysis by gas chromatography revealed that hydrogenation occurred predominantly in the 18:2, 20:4 and 22:6 fatty acyl chains of the membrane phospholipids. Under the same conditions hydrogenation was also performed in purified plasma membranes from GRSL cells and from rat liver, and in liposomes prepared from the total lipid extracts of these membranes. Hydrogenation increased the lipid structural order parameter in the membranes, as measured by fluorescence polarization. This increase was more pronounced in the liposomes (46%) than in the plasma membranes (17-25%). Hydrogenation increased the expression of a 15 kDa antigen on the surface of viable GRSL cells, as measured in a Fluorescence Activated Cell Sorter, using monoclonal antibodies. The expression of four other antigens, among which H-2k, was not or much less affected by this treatment.