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Viral CD8+ epitopes are generated by the cellular turnover of viral proteins, predominantly by the proteasome. Mutations located within viral epitopes can result in escape from memory T cells but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two of the most dominant SARS-CoV-2 nucleoprotein CD8+ epitopes, we identified mutations in epitope flanking regions and investigated the contribution of these mutations to antigen processing and T cell activation using SARS-CoV-2 nucleoprotein transduced B cell lines and in vitro proteasomal processing of peptides. We found that decreased NP9-17-B*27:05 CD8+ T cell responses to the NP-Q7K mutation correlated with lower epitope surface expression, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+ T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on antigen processing and presentation, thereby contributing to escape from immunodominant T cell responses. Alternatively, mutations could enhance antigen processing and efficacy of T cell recognition, opening new avenues for improving future vaccine designs.One Sentence SummaryNatural mutations in the flanking regions of known immunodominant SARS-CoV-2 nucleoprotein epitopes can decrease CD8+ T cell responses leading to partial escape.

Arginine deprivation therapy (ADT) is a new metabolic targeting approach with high therapeutic potential for various solid cancers. Combination of ADT with low doses of the natural arginine analog canavanine effectively sensitizes malignant cells to irradiation. However, the molecular mechanisms determining the sensitivity of intrinsically non-auxotrophic cancers to arginine deficiency are still poorly understood. We here show for the first time that arginine deficiency is accompanied by global metabolic changes and protein/membrane breakdown, and results in the induction of specific, more or less pronounced (severe vs. mild) ER stress responses in head and neck squamous cell carcinoma (HNSCC) cells that differ in their intrinsic ADT sensitivity. Combination of ADT with canavanine triggered catastrophic ER stress via the eIF2α-ATF4(GADD34)-CHOP pathway, thereby inducing apoptosis; the same signaling arm was irrelevant in ADT-related radiosensitization. The particular strong supra-additive effect of ADT, canavanine and irradiation in both intrinsically more and less sensitive cancer cells supports the rational of ER stress pathways as novel target for improving multi-modal metabolic anti-cancer therapy. Electronic supplementary material The online version of this article (10.1007/s00018-020-03704-7) contains supplementary material, which is available to authorized users.

Lipid metabolism plays a key role in many cellular processes. We show here that regulatory T cells have enhanced lipid storage within subcellular lipid droplets (LD). They also express elevated amounts of both isoforms of diacylglycerol acyl transferase (DGAT1 & 2), enzymes required for the terminal step of triacylglycerol synthesis. In regulatory T-cells (Tregs), the conversion of diacylglycerols to triacylglycerols serves two additional purposes other than lipid storage. First, we demonstrate that it protects T cells from the toxic effects of saturated long chain fatty acids. Second, we show that Triglyceride formation is essential for limiting activation of protein kinase C via free diacyl glycerol moieties. Inhibition of DGAT1 resulted in elevated active PKC and nuclear NFKB, as well as impaired Foxp3 induction in response to TGFβ. Thus, Tregs utilize a positive feedback mechanism to promote sustained expression of Foxp3 associated with control of LD formation.

Remodeling of cellular metabolism is a genuine feature of rapidly growing cells. Herein we report that mouse embryonic fibroblasts, lacking the Cathepsin L (Cts L) gene, proliferate faster than wild-types and display a noticeable glycolytic shift to satisfy their ever-growing metabolic needs. Mass spectrometry analyses identified LDHA as an essential metabolic junction in these cells, and downstream biochemical studies suggested that Cts L regulates LDHA expression and function. Together, these data uncover an unprecedented role for Cathepsin L in cell metabolism., Graphical Abstract Highlights Cts L−/− cells proliferate faster than wild types and shift to aerobic glycolysis. LDHA is a key glycolytic enzyme controlling Cts L−/− cell proliferation. Cts L regulates LDHA expression and function., Rapidly proliferating cells reshape their metabolism to satisfy their ever-lasting need for cellular building blocks. This phenomenon is exemplified in certain malignant conditions such as cancer but also during embryonic development when cells rely heavily on glycolytic metabolism to exploit its metabolic intermediates for biosynthetic processes. How cells reshape their metabolism is not fully understood. Here we report that loss of cathepsin L (Cts L) is associated with a fast proliferation rate and enhanced glycolytic metabolism that depend on lactate dehydrogenase A (LDHA) activity. Using mass spectrometry analysis of cells treated with a pan cathepsin inhibitor, we observed an increased abundance of proteins involved in central carbon metabolism. Further inspection of putative Cts L targets revealed an enrichment for glycolytic metabolism that was independently confirmed by metabolomic and biochemical analyses. Moreover, proteomic analysis of Cts L-knockout cells identified LDHA overexpression that was demonstrated to be a key metabolic junction in these cells. Lastly, we show that Cts L inhibition led to increased LDHA protein expression, suggesting a causal relationship between LDHA expression and function. In conclusion, we propose that Cts L regulates this metabolic circuit to keep cell division under control, suggesting the therapeutic potential of targeting this protein and its networks in cancer.

Polyamines are a class of poly-cationic aliphatic amines, playing a role in different cellular processes such as maintaining intracellular pH and membrane potential that are relevant for general cellular physiology and ageing. The development of analytical methods for detection and quantitation of this class of compounds has been challenging due to the basic nature of these species. Both liquid chromatography (LC) and gas chromatography (GC) have been applied for separation, mostly coupled to mass spectrometry (MS) for detection. However, current methodologies suffer from lengthy extraction protocols and limitations in separation and detection levels. Here, we present a simplified and optimised method for straightforward extraction of polyamine metabolites including spermine, spermidine, norspermidine, cadaverine and putrescine from cellular and tissue material. We demonstrate that strong acid-based extraction and chemical derivatisation not only improves isolation, but also recovery. Combined with two-dimensional gas chromatography, this method provides clear separation and femtomole sensitivity for the profiling of polyamines.

Summary Depleting the microenvironment of important nutrients such as arginine is a key strategy for immune evasion by cancer cells. Many tumors overexpress arginase, but it is unclear how these cancers, but not T cells, tolerate arginine depletion. In this study, we show that tumor cells synthesize arginine from citrulline by upregulating argininosuccinate synthetase 1 (ASS1). Under arginine starvation, ASS1 transcription is induced by ATF4 and CEBPβ binding to an enhancer within ASS1. T cells cannot induce ASS1, despite the presence of active ATF4 and CEBPβ, as the gene is repressed. Arginine starvation drives global chromatin compaction and repressive histone methylation, which disrupts ATF4/CEBPβ binding and target gene transcription. We find that T cell activation is impaired in arginine-depleted conditions, with significant metabolic perturbation linked to incomplete chromatin remodeling and misregulation of key genes. Our results highlight a T cell behavior mediated by nutritional stress, exploited by cancer cells to enable pathological immune evasion., Graphical abstract, Highlights • Arginine starvation induces ASS1 expression in some cancers but not in T cells • ATF4 binds an internal ASS1 enhancer to drive expression in cancer but not T cells • T cell activation is disrupted by arginine starvation, with a loss of reprogramming • Arginine starvation compacts chromatin in T cells, disrupting ATF4 binding, Arginine depletion by many tumors generates an immunosuppressive microenvironment. Crump et al. show that cancer cells can tolerate this by inducing ATF4-dependent upregulation of ASS1, allowing de novo arginine synthesis. T cells are unable to synthesize arginine as ASS1 is repressed, disrupting T cell function and the chromatin remodeling associated with activation.

TNF is a primitive protein that has emerged from more than 550 million years of evolution. Our bioinformatics study of TNF from nine different taxa in vertebrates revealed several conserved regions in the TNF sequence. By screening overlapping peptides derived from human TNF to determine their role in three different TNF-induced processes – apoptosis, necrosis and NF-κB stimulation – we found that TNF conserved regions are mostly related to cell death rather than NF-κB stimulation. Among the most conserved regions, peptides (P)12, P13 and P1213 (comprising P12 and P13) induced apoptosis, whereas P14, P15, P16 and P1516 (comprising P15 and P16) induced necrosis. Cell death induced by these peptides was not through binding to the TNF receptor. P16-induced necrosis was mainly through disruption of the cell membrane, whereas P1213-induced apoptosis involved activation of TRADD followed by formation of complex II. Finally, using a monoclonal antibody and a mutant TNF protein, we show that TNF-induced apoptosis is determined by a conserved linear sequence that corresponds to that within P1213. Our results reveal the determinant sequence that is key to the TNF primitive function of inducing apoptosis.

Failure to make adaptive immune responses is a hallmark of aging. Reduced B cell function leads to poor vaccination efficacy and a high prevalence of infections in the elderly. Here we show that reduced autophagy is a central molecular mechanism underlying immune senescence. Autophagy levels are specifically reduced in mature lymphocytes, leading to compromised memory B cell responses in old individuals. Spermidine, an endogenous polyamine metabolite, induces autophagy in vivo and rejuvenates memory B cell responses. Mechanistically, spermidine post-translationally modifies the translation factor eIF5A, which is essential for the synthesis of the autophagy transcription factor TFEB. Spermidine is depleted in the elderly, leading to reduced TFEB expression and autophagy. Spermidine supplementation restored this pathway and improved the responses of old human B cells. Taken together, our results reveal an unexpected autophagy regulatory mechanism mediated by eIF5A at the translational level, which can be harnessed to reverse immune senescence in humans.

SUMMARYFailure to make adaptive immune responses is a hallmark of aging. In particular reduced B cell function leads to poor vaccination efficacy and a high prevalence of infections in the elderly. However, the molecular mechanism underlying immune senescence is largely unknown. Here we show that autophagy levels are specifically reduced in mature lymphoid cells, leading to compromised memory B cell responses in old individuals. Spermidine, a naturally occurring polyamine metabolite, induces autophagyin vivoand rejuvenates memory B cell responses in an autophagy-dependent manner. Mechanistically, spermidine post-translationally modifies the translation factor eIF5A, which assists the synthesis of TFEB, a key transcription factor of autophagy. Spermidine is depleted in the elderly, leading to reduced TFEB expression and autophagy. Replenishing spermidine restored this pathway and improved the responses of old human B cells. Taken together, our results reveal an unexpected autophagy regulatory mechanism mediated by eIF5A at the translational level, and this pathway can be harnessed to rejuvenate immune senescence in humans.

Ischaemia and reperfusion injury (IRI) is the leading cause of acute kidney injury (AKI), which contributes to high morbidity and mortality rates in a wide range of injuries as well as the development of chronic kidney disease. The cellular and molecular responses of the kidney to IRI are complex and not fully understood. Here, we used an integrated proteomic and metabolomic approach to investigate the effects of IRI on protein abundance and metabolite levels. Rat kidneys were subjected to 45 min of warm ischaemia followed by 4 h and 24 h reperfusion, with contralateral and separate healthy kidneys serving as controls. Kidney tissue proteomics after IRI revealed elevated proteins belonging to the acute phase response, coagulation and complement pathways, and fatty acid (FA) signalling. Metabolic changes were already evident after 4 h reperfusion and showed increased level of glycolysis, lipids and FAs, whilst mitochondrial function and ATP production was impaired after 24 h. This deficit was partially compensated for by the contralateral kidney. Such a metabolic balance counteracts for the developing energy deficit due to reduced mitochondrial function in the injured kidney.

Neutrophils are critical and short-lived mediators of innate immunity that require constant replenishment. Their differentiation in the bone marrow requires extensive cytoplasmic and nuclear remodeling, but the processes governing these energy-consuming changes are unknown. While previous studies show that autophagy is required for differentiation of other blood cell lineages, its function during granulopoiesis has remained elusive. Here, we have shown that metabolism and autophagy are developmentally programmed and essential for neutrophil differentiation in vivo. Atg7-deficient neutrophil precursors had increased glycolytic activity but impaired mitochondrial respiration, decreased ATP production, and accumulated lipid droplets. Inhibiting autophagy-mediated lipid degradation or fatty acid oxidation alone was sufficient to cause defective differentiation, while administration of fatty acids or pyruvate for mitochondrial respiration rescued differentiation in autophagy-deficient neutrophil precursors. Together, we show that autophagy-mediated lipolysis provides free fatty acids to support a mitochondrial respiration pathway essential to neutrophil differentiation.

Pathological alterations in cell functions are frequently accompanied by metabolic reprogramming including modifications in amino acid metabolism. Amino acid detection is thus integral to the diagnosis of many hereditary metabolic diseases. The development of malignant diseases as metabolic disorders comes along with a complex dysregulation of genetic and epigenetic factors affecting metabolic enzymes. Cancer cells might transiently or permanently become auxotrophic for non-essential or semi-essential amino acids such as asparagine or arginine. Also, transformed cells are often more susceptible to local shortage of essential amino acids such as methionine than normal tissues. This offers new points of attacking unique metabolic features in cancer cells. To better understand these processes, highly sensitive methods for amino acid detection and quantification are required. Our review summarizes the main methodologies for amino acid detection with a particular focus on applications in biomedicine and cancer, provides a historical overview of the methodological pre-requisites in amino acid analytics. We compare classical and modern approaches such as the combination of gas chromatography and liquid chromatography with mass spectrometry (GC-MS/LC-MS). The latter is increasingly applied in clinical routine. We therefore illustrate an LC-MS workflow for analyzing arginine and methionine as well as their precursors and analogs in biological material. Pitfalls during protocol development are discussed, but LC-MS emerges as a reliable and sensitive tool for the detection of amino acids in biological matrices. Quantification is challenging, but of particular interest in cancer research as targeting arginine and methionine turnover in cancer cells represent novel treatment strategies.

Two-dimensional gas chromatography mass spectrometry (GCxGC-MS) is utilized to an increasing extent in biomedical metabolomics. Here, we established and adapted metabolite extraction and derivatization protocols for cell/tissue biopsy, serum and urine samples according to their individual properties. GCxGC-MS analysis revealed detection of ~600 molecular features from which 165 were characterized representing different classes such as amino acids, fatty acids, lipids, carbohydrates, nucleotides and small polar components of glycolysis and the Krebs cycle using electron impact (EI) spectrum matching and validation using external standard compounds. Advantages of two-dimensional gas chromatography based resolution were demonstrated by optimizing gradient length and separation through modulation between the first and second column, leading to a marked increase in metabolite identification due to improved separation as exemplified for lactate versus pyruvate, talopyranose versus methyl palmitate and inosine versus docosahexaenoic acid. Our results demonstrate that GCxGC-MS represents a robust metabolomics platform for discovery and targeted studies that can be used with samples derived from the clinic., Graphical abstract fx1, Highlights • GCxGC-MS detected ~600 features;165 represented metabolites of different classes. • Optimizing gradient length and separation through modulation improved metabolite ID. • improved separation of lactate/pyruvate, talopyranose/palmitate and inosine/docosahexaenoate.

Interleukin (IL)-23 mediated signal transduction represents a major molecular mechanism underlying the pathology of inflammatory bowel disease, Crohn’s disease and ulcerative colitis. In addition, emerging evidence supports the role of IL-23-driven Th17 cells in inflammation. Components of the IL-23 signaling pathway, such as IL-23R, JAK2 and STAT3, have been characterized, but elements unique to this network as compared to other interleukins have not been readily explored. In this study, we have undertaken an integrative phosphoproteomics approach to better characterise downstream signaling events. To this end, we performed and compared phosphopeptide and phosphoprotein enrichment methodologies after activation of T lymphocytes by IL-23. We demonstrate the complementary nature of the two phosphoenrichment approaches by maximizing the capture of phosphorylation events. A total of 8202 unique phosphopeptides, and 4317 unique proteins were identified, amongst which STAT3, PKM2, CDK6 and LASP-1 showed induction of specific phosphorylation not readily observed after IL-2 stimulation. Interestingly, quantitative analysis revealed predominant phosphorylation of pre-existing STAT3 nuclear subsets in addition to translocation of phosphorylated STAT3 within 30 min after IL-23 stimulation. After IL-23R activation, a small subset of PKM2 also translocates to the nucleus and may contribute to STAT3 phosphorylation, suggesting multiple cellular responses including metabolic adaptation.

A new ligand, methyl 2,3,5,6-tetrafluoro-4-oxybenzoate (C8H3F4O3), combining an electron withdrawing group (C6F4) to tune the reactivity with an anchor group (CO2Me) for immobilization on supports, was used to prepare four new ruthenium initiators, viz. Ru(C8H3F4O3)2( CHPh)(3-Br–C5H5N)(H2IMes) and Ru(C8H3F4O3)2XL, where X = C,N-( CHCH2CH2-2-C5H4N) and L = PiPr3, PCy3 or H2IMes. The new ligand greatly reduced the reactivity of the ruthenium centre at room temperature. The 1H NMR and DSC investigation for the ROMP of norbornene dicarboximide monomers clearly demonstrated that the Ru(C8H3F4O3)2XL initiators were inactive at room temperature and required elevated temperatures for their activation.

In solid-phase combinatorial chemistry, analyses are performed using a wide range of analytical techniques ranging from gel-phase nuclear magnetic resonance (NMR) to colorimetric tests to elemental analysis. However, these techniques cannot be used to interrogate functional group distribution at the single-bead level. This paper explores the feasibility of using Fourier transform infrared (FT-IR) microscopy to examine site distribution on chloromethylated polystyrene resin beads and to quantify the loading after coupling with 4-cyanophenol, an IR tagging agent. FT-IR microscopy also provides a unique opportunity to better understand the reactivity of highly cross-linked polymer beads under a range of chemical conditions.

The preparation, characterisation and application of a series of non-grafted polystyrene (PS) resins containing a styrenic methoxypoly(ethylene glycol) (MPEG) derivative is presented. These novel PS-MPEG resins were designed to balance swelling and solvation with improved handling. The monomer, 1-[2-(2-methoxyethoxy)ethoxy]-4-vinyl-benzene, contained an inert phenyl ether linkage designed to provide broad chemical compatibility and stability, yet imparting all the favourable properties of the PEG group into the new resin, whilst maintaining a high loading capacity. The synthetic performance of the new resins compared very favourably to those of TentaGel™, ArgoGel™ and aminomethyl PS.

Over the past year, numerous techniques have been used to study the resins commonly utilised in solid-phase synthesis to allow a greater understanding of the chemical nature and the physical properties of the supports. In addition, to overcome some of the drawbacks of existing materials, several new resins and new methods of handling solid supports have been developed. New methodologies have also been introduced to simplify the preparation of solid supports.

Preliminary results on a new type of polymer scavenger, acetoacetoxy ethyl methacrylate (AAEM) resin, are reported. AAEM resin can selectively remove primary amines in the presence of secondary amines. Its application in a solution library synthesis is demonstrated.

The enantioselective reduction of 1-bromofluorenone by borane in the presence of different chiral amino alcohols has been studied. The alcohol obtained has the ( S ) or ( R ) configuration depending on the nature of the substitution of the amino alcohol. The experimentally determined absolute configuration can be explained when a four-center cyclic transition state consisting of the oxazaborolidine and fluorenone compound is considered.

The enantioselective reduction of substituted fluorenones by aluminium lithium hydride in the presence of different chiral amino alcohols has been investigated. The best conditions found were also assayed with a multi-substituted fluorenone achieving the corresponding fluorenol compound with high enantiomeric excess. Shorter reaction times with high conversion yields were found when compared with borane reductions.

We report a two-step synthesis of polysubstituted fluorenones by condensation of malononitrile with aromatic aldehydes and methylketones or with β-aryl-α,β-unsaturated carbonyl compounds, aldehydes or ketones. The yields of the fluorenone systems depend on the nature of the substitution on the aromatic rings.

The enantiomers of several 9-fluorenyl derivatives have been successfully resolved by HPLC on a chiral stationary phase (CSP) based on a mixed 10-undecenoate/3,5-dimethylphenylcarbamate of cellulose bonded to allylsilica gel. Previous attempts at resolution, such as NMR methods, GC and the use of a multiple interaction type chiral column for HPLC, were unsuccessful.

The higher homologues of the well-studied alkoxycarbonylmethylenetriphenylarsonium ylide (3, R=H) can be easily obtained through the sequence: a), preparation of alkyl 2-triloxyalkanoates (1); b), reaction between these trifloxyderivatives and triphenylphosphine to give 1-alkoxycarbonylalkyltriphenylarsonium triflates (2); and c), basic treatment of the triphenylarsonium triflates (2) with alumina-supported potassium fluoride to give 1-alkoxycarbonylalkyledenetriphenylarsonium ylides (3). These higher homologues of (3, R=H) react with aromatic aldehydes in good to excellent yields, and give rise to synthetically interesting “coupling” and cyclopropanation reactions.

We report a two-step synthesis of polysubstituted fluorenones by condensation of malononitrile with aromatic aldehydes and methylketones or with β-aryl-α,β-unsaturated carbonyl compounds, aldehydes or ketones. The yields of the fluorenone systems depend on the nature of the substitution on the aromatic rings.

A system for the multiparallel synthesis of polymer resins for solid-phase synthesis is presented, accelerating the preparation of new resins using standard suspension polymerization protocols. The system was evaluated by preparing a range of polystyrene resins with well-defined characteristics.

Preliminary results on a new type of polymer scavenger, acetoacetoxy ethyl methacrylate (AAEM) resin, are reported. AAEM resin can selectively remove primary amines in the presence of secondary amines. Its application in a solution library synthesis is demonstrated.