Stable Isotope Labeling Research Articles

Spliceosomal vulnerability of MYCN-amplified neuroblastoma is contingent on PRMT5-mediated regulation of epitranscriptomic and metabolomic pathways

Approximately 50 % of poor prognosis neuroblastomas arise due to MYCN over-expression. We previously demonstrated that MYCN and PRMT5 proteins interact and PRMT5 knockdown led to apoptosis of MYCN-amplified (MNA) neuroblastoma. Here we evaluate the highly selective first-in-class PRMT5 inhibitor GSK3203591 and its in vivo analogue GSK3326593 as targeted therapeutics for MNA neuroblastoma. Cell-line analyses show MYCN-dependent growth inhibition and apoptosis, with approximately 200-fold greater sensitivity of MNA neuroblastoma lines. RNA sequencing of three MNA neuroblastoma lines treated with GSK3203591 reveal deregulated MYCN transcriptional programmes and altered mRNA splicing, converging on key regulatory pathways such as DNA damage response, epitranscriptomics and cellular metabolism. Stable isotope labelling experiments in the same cell lines demonstrate that glutamine metabolism is impeded following GSK3203591 treatment, linking with disruption of the MLX/Mondo nutrient sensors via intron retention of MLX mRNA. Interestingly, glutaminase (GLS) protein decreases after GSK3203591 treatment despite unchanged transcript levels. We demonstrate that the RNA methyltransferase METTL3 and cognate reader YTHDF3 proteins are lowered following their mRNAs undergoing GSK3203591-induced splicing alterations, indicating epitranscriptomic regulation of GLS; accordingly, we observe decreases of GLS mRNA m6A methylation following GSK3203591 treatment, and decreased GLS protein following YTHDF3 knockdown. In vivo efficacy of GSK3326593 is confirmed by increased survival of Th-MYCN mice, with drug treatment triggering splicing events and protein decreases consistent with in vitro data. Together our study demonstrates the PRMT5-dependent spliceosomal vulnerability of MNA neuroblastoma and identifies the epitranscriptome and glutamine metabolism as critical determinants of this sensitivity.

Enhancing solution structural analysis of large molecular proteins through optimal stereo array isotope labeling of aromatic amino acids

The observation of side-chain peaks of aromatic amino acids is the prerequisite for a high-resolution three-dimensional structure determination of proteins by NMR. However, it becomes difficult with increasing molecular size due to an increased transverse relaxation and the control of the relaxation pathway is needed to achieve the observation. We demonstrated that even for the large molecular size of 82 kDa Malate synthase G (MSG), the aromatic 13C-1H (CH) peaks of Tryptophan (Trp) and Phenylalanine (Phe) residues can be observed with high quality using a systematic stable isotope labeling scheme, Stereo-Array Isotope Labeling (SAIL) method. However, the sequence specific assignments of these peaks relied on the use of amino acid substitutions, employing an inefficient method that required many isotopes labeled samples. In this study, we developed novel SAIL amino acids that allow for the observation of the aromatic ring δ,ζ and the aliphatic β position peak of Phe residues. The application of TROSY-based experiment to the isolated CH moieties resulted in the successful observation of discernible and resolved CH peaks in Phe residues in MSG. In MSG, the sequence-specific assignments of the backbone and Cβ positions have already been confirmed. Therefore, using this labeling method, the δ and β position peaks of Phe residues can be clearly assigned in a sequence-specific and stereospecific manner through experiments based on intra-residue NOE. Furthermore, the NOESY experiment also allows for the acquisition of information pertaining to the conformation of Phe residues, such as the χ1 dihedral angle, providing valuable insights for the determination of accurate protein structures and in dynamic analysis. This new SAIL amino acids open an avenue to achieve a variety of NMR analysis of large molecular proteins, including a high-resolution structure determination and dynamics and interaction analysis.

Temperature differentially regulates estuarine microbial N2O production along a salinity gradient

Nitrous oxide (N2O) is atmospheric trace gas that contributes to climate change and affects stratospheric and ground-level ozone concentrations. Ammonia oxidizers and denitrifiers contribute to N2O emissions in estuarine waters. However, as an important climate factor, how temperature regulates microbial N2O production in estuarine water remains unclear. Here, we have employed stable isotope labeling techniques to demonstrate that the N2O production in estuarine waters exhibited differential thermal response patterns between nearshore and offshore regions. The optimal temperatures (Topt) for N2O production rates (N2OR) were higher at nearshore than offshore sites. 15N-labeled nitrite (15NO2-) experiments revealed that at the nearshore sites dominated by ammonia-oxidizing bacteria (AOB), the thermal tolerance of 15N-N2OR increases with increasing salinity, suggesting that N2O production by AOB-driven nitrifier denitrification may be co-regulated by temperature and salinity. Metatranscriptomic and metagenomic analyses of enriched water samples revealed that the denitrification pathway of AOB is the primary source of N2O, while clade II N2O-reducers dominated N2O consumption. Temperature regulated the expression patterns of nitrite reductase (nirK) and nitrous oxide reductase (nosZ) genes from different sources, thereby influencing N2O emissions in the system. Our findings contribute to understanding the sources of N2O in estuarine waters and their response to global warming.

Use of stable isotope labeled (SIL) antibodies in cassette dosing to improve pharmacokinetics screening efficiency of ADCs with novel cytotoxic payloads

Stable isotope labelling by amino acids in cell culture (SILAC) is an established technique used in quantitative mass spectrometry (MS)-based proteomics. SILAC is also used to generate stable isotope labelled (SIL) antibodies for internal standards (IS) used in LC-MS/MS bioassays to improve quantitative robustness. Total antibody (TAb) is measured to evaluate pharmacokinetics (PK) of antibody drug conjugate (ADC) candidates measured by either ligand binding (LBA) or LC-MS/MS. Herein, we describe an application of SILAC, where multiple SIL combinations of an antibody are used for cassette dosing and PK evaluation. Our preclinical studies demonstrate SILAC-labelled ADC therapeutics did not alter antibody PK. Furthermore, with cassette dosing SIL antibodies exhibited comparable exposure to discretely administered unlabelled test articles in rats. In addition, SIL antibodies were conjugated to cytotoxic payloads to create SIL ADCs and cassette dosed in a cynomolgus monkey PK study and SIL ADCs yielded comparable PK results to discrete dosed unlabelled ADCs. In conclusion, SIL antibodies used with a cassette dosing strategy increases PK screening throughput of ADC candidates in preclinical species. Additionally, cassette dosing strategy further facilitates the responsible use of laboratory animals to achieve the three-Rs (Replacement, Reduction, and Refinement).

Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification

Data-independent acquisition (DIA) is increasingly preferred over data-dependent acquisition due to its higher throughput and fewer missing values. Whereas data-dependent acquisition often uses stable isotope labeling to improve quantification, DIA mostly relies on label-free approaches. Efforts to integrate DIA with isotope labeling include chemical methods like mass differential tags for relative and absolute quantification and dimethyl labeling, which, while effective, complicate sample preparation. Stable isotope labeling by amino acids in cell culture (SILAC) achieves high labeling efficiency through the metabolic incorporation of heavy labels into proteins invivo. However, the need for metabolic incorporation limits the direct use in clinical scenarios and certain high-throughput experiments. Spike-in SILAC (SiS) methods use an externally generated heavy sample as an internal reference, enabling SILAC-based quantification even for samples that cannot be directly labeled. Here, we combine DIA-SiS, leveraging the robust quantification of SILAC without the complexities associated with chemical labeling. We developed DIA-SiS and rigorously assessed its performance with mixed-species benchmark samples on bulk and single cell-like amount level. We demonstrate that DIA-SiS substantially improves proteome coverage and quantification compared to label-free approaches and reduces incorrectly quantified proteins. Additionally, DIA-SiS proves effective in analyzing proteins in low-input formalin-fixed paraffin-embedded tissue sections. DIA-SiS combines the precision of stable isotope-based quantification with the simplicity of label-free sample preparation, facilitating simple, accurate, and comprehensive proteome profiling.

Dual-species proteomics and targeted intervention of animal-pathogen interactions

IntroductionHost-microbe interactions are important to human health and ecosystems globally, so elucidating the complex host-microbe interactions and associated protein expressions drives the need to develop sensitive and accurate biochemical techniques. Current proteomics techniques reveal information from the point of view of either the host or microbe, but do not provide data on the corresponding partner. Moreover, it remains challenging to simultaneously study host-microbe proteomes that reflect the direct competition between host and microbe. This raises the need to develop a dual-species proteomics method for host-microbe interactions. ObjectivesWe aim to establish a forward + reverse Stable Isotope Labeling with Amino acids in Cell culture (SILAC) proteomics approach to simultaneously label and quantify newly-expressed proteins of host and microbe without physical isolation, for investigating mechanisms in direct host-microbe interactions. MethodsUsing Caenorhabditis elegans-Pseudomonas aeruginosa infection model as proof-of-concept, we employed SILAC proteomics and molecular pathway analysis to characterize the differentially-expressed microbial and host proteins. We then used molecular docking and chemical characterization to identify chemical inhibitors that intercept host-microbe interactions and eliminate microbial infection. ResultsBased on our proteomics results, we studied the iron competition between pathogen iron scavenger and host iron uptake protein, where P. aeruginosa upregulated pyoverdine synthesis protein (PvdA) (fold-change of 5.2313) and secreted pyoverdine, and C. elegans expressed ferritin (FTN-2) (fold-change of 3.4057). Targeted intervention of iron competition was achieved using Galangin, a ginger-derived phytochemical that inhibited pyoverdine production and biofilm formation in P. aeruginosa. The Galangin-ciprofloxacin combinatorial therapy could eliminate P. aeruginosa biofilms in a fish wound infection model, and enabled animal survival. ConclusionOur work provides a novel SILAC-based proteomics method that can simultaneously evaluate host and microbe proteomes, with future applications in higher host organisms and other microbial species. It also provides insights into the mechanisms dictating host-microbe interactions, offering novel strategies for anti-infective therapy.

Click chemistry-mediated stable isotope labeling combined with HPLC-MS/MS analysis for highly sensitive determination of steroid hormones

Steroid hormone residues in food are a significant sources of endocrine disrupting chemicals (EDCs) that can adversely affect public health. However, the current analytical methods for determining steroid hormones using liquid chromatography-tandem mass spectrometry (LC-MS/MS) can be challenging due to the poor ionization efficiency of steroid hormones and the matrix effect of complex food samples. Herein, based on Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and stable isotope labeling (SIL) technique, a novel pair of chemoselective probes ABI/d5-ABI was precisely designed and synthesized. This pair of probes comprises a H/D isotope tag, a linker, a reactive site azido group (N3) and a MS tag (imidazolium salt). The probe ABI was employed to label ethynyl-containing steroid hormones in real samples and d5-ABI was applied to label standards, respectively, followed by mixing the two labeled samples for high performance (HP)LC-MS/MS analysis. It was found that the ionization efficiencies of target analytes were increased by 17–4532 folds after ABI labeling. More importantly, the heavy labeled samples serving as internal standards (ISs) can effectively compensate matrix effect during HPLC-MS/MS analysis. Finally, the proposed SIL-HPLC-MS/MS method was successfully used to highly sensitive determine four synthetic steroid hormones in food samples (milk, pork and egg). Furthermore, the good detection limits (0.015–0.020 ng/mL), satisfactory recoveries (75.7–122.9 %), and precisions (RSDs less than 9.2 %) were obtained. Hence, the established method not only provides new insights in designing SIL probes for determination of ethynyl-containing analytes within complex matrix, but also extends the application of CuAAC reaction in the field of food chemistry.

Tracing de novo Lipids using Stable Isotope Labeling LC-TIMS-TOF MS/MS.

Lipids are highly diverse, and small changes in lipid structures and composition can have profound effects on critical biological functions. Stable isotope labeling (SIL) offers several advantages for the study of lipid distribution, mobilization, and metabolism, as well as de novo lipid synthesis. The successful implementation of the SIL technique requires the removal of interferences from endogenous molecules. In the present work, we describe a high-throughput analytical protocol for the screening of SIL lipids from biological samples; examples will be shown of lipid de novo identification during mosquito ovary development. The use of complementary liquid chromatography trapped ion mobility spectrometry and mass spectrometry allows for the separation and lipids assignment from a single sample in a single scan (<1 h). The described approach takes advantage of recent developments in data-dependent acquisition and data-independent acquisition, using parallel accumulation in the mobility trap followed by sequential fragmentation and collision-induced dissociation. The measurement of SIL at the fatty acid chain level reveals changes in lipid dynamics during the ovary development of mosquitoes. The lipids de novo structures are confidently assigned based on their retention time, mobility, and fragmentation pattern.

Vegetation restoration limited microbial carbon sequestration in areas affected by soil erosion

The impact of vegetation restoration on soil structure, nutrients, and microorganisms in eroded areas has been extensively studied, but the effect of vegetation restoration on carbon-sequestering bacterial communities and their associated carbon fixation capacity remains largely unknown. In this study, we focused on the 0–20 cm soil layer in eroded and vegetation restoration sites in areas of southern China that have been severely affected by soil erosion and utilized 13C stable isotope labeling and high-throughput sequencing technologies to investigate the influence of vegetation restoration on carbon-sequestering bacterial communities and their carbon sequestration potential. Compared with eroded areas, vegetation restoration areas presented greater soil nutrient contents and greater diversity of bacteria with carbon sequestration functions. Vegetation restoration also altered the composition of carbon-sequestering bacterial communities by increasing the soil alkali-hydrolyzable nitrogen content, with the dominant carbon-sequestering bacteria shifting from Nocardia to Bradyrhizobium. However, the microbial carbon sequestration rate in soil erosion areas significantly increased by 2.15 times compared with that in vegetation restoration areas. Among the factors considered, pH (68.90 %, P = 0.000) was identified as the primary explanatory factor regulating changes in the microbial carbon sequestration rate. Our results are important for revealing the role of vegetation restoration in the global carbon cycle and elucidating the role of microorganisms in the soil carbon cycle.

Nickel Catalyzed Carbonylative Cross Coupling for Direct Access to Isotopically Labeled Alkyl Aryl Ketones.

Here we present an effective nickel-catalyzed carbonylative cross-coupling for direct access to alkyl aryl ketones from readily accessible redox-activated tetrachlorophthalimide esters and aryl boronic acids. The methodology, which is run employing only 2.5 equivalents of CO and simple Ni(II) salts as the metal source, exhibits a broad substrate scope under mild conditions. Furthermore, this carbonylation chemistry provides an easy switch between isotopologues for stable (13CO) and radioactive (14CO) isotope labeling, allowing its adaptation to the late-stage isotope labeling of pharmaceutically relevant compounds. Based on DFT calculations as well as experimental evidence, a catalytic cycle is proposed involving a carbon-centered radical formed via nickel(I)-induced outer-sphere decarboxylative fragmentation of the redox-active ester.

Strategies of resource sharing in clonal plants: a conceptual model and an example of contrasting strategies in two closely related species.

Clonal growth is widespread among herbaceous plants, and helps them to cope with environmental heterogeneity through resource integration via connecting clonal organs. Such integration is considered to balance heterogeneity by translocation of resources from rich to poor patches. However, such an 'equalization' strategy is only one of several possible strategies. Under certain conditions, a strategy emphasizing acropetal movement and exploration of new areas or a strategy of accumulating resources in older ramets may be preferred. The optimal strategy may be determined by environmental conditions, such as resource availability and level of light competition. We aimed to summarize possible translocation strategies in a conceptual analysis and to examine translocation in two species from different habitats. Resource translocation was compared between two closely related species from different habitats with contrasting productivity. The study examined the bidirectional translocation of carbon and nitrogen in pairs of mother and daughter ramets grown under light heterogeneity (one ramet shaded) at two developmental stages using stable-isotope labelling. At the early developmental stage, both species translocated resources towards daughters and the translocation was modified by shading. Later, the species of low-productivity habitats, Fragaria viridis, translocated carbon to shaded ramets (both mother and daughter), according to the 'equalization' strategy. In contrast, the species of high-productivity habitats, Potentilla reptans, did not support shaded mother ramets. Nitrogen translocation remained mainly acropetal in both species. The two studied species exhibited different translocation strategies, which may be linked to the habitat conditions experienced by each species. The results indicate that we need to consider different possible strategies. We emphasize the importance of bidirectional tracing in translocation studies and the need for further studies to investigate the translocation patterns in species from contrasting habitats using a comparative approach.

Lipogenesis in Nasonia vitripennis: Influence of sugar chemistry, preferential production of triacylglycerides, and comparison of fatty acid biosynthetic capacity with Drosophilamelanogaster

Sugar consumption increases the fecundity and longevity in many species of parasitic wasps (parasitoids) but whether these insects use sugars to synthesize significant amounts of fatty acids and storage fat de novo (lipogenesis) is discussed controversially. It has long been assumed that parasitic wasps lost this ability during evolution, mainly because in several species wasps with ad libitum access to sugar did not increase teneral lipid levels. Recent studies demonstrated that many species are nonetheless capable of synthesizing fatty acids de novo from glucose. It is unclear, however, whether also other sugars are used for fatty acid biosynthesis and whether an increase of sugar concentration to levels occurring in natural sugar sources translates into higher fatty acid production. Furthermore, it has been suggested that fatty acid production in parasitoids is negligible compared to species increasing teneral fat reserves such as Drosophila melanogaster. Here we show by stable isotope labeling experiments that females of Nasonia vitripennis convert D-glucose, D-fructose, sucrose, and α,α-trehalose, major sugars consumed by adult parasitoids in nature, equally well to palmitic, stearic, oleic, and linoleic acid. Lipogenesis from D-galactose occurs as well albeit to a lesser extent. Sugar concentration is crucial for lipogenic activity, and almost 80% of de novo synthesized fatty acids were incorporated into storage fat (triacylglycerides). Comparison of fatty acid biosynthesis within a 48-h feeding period with D. melanogaster revealed that N. vitripennis produced approximately half as many fatty acids per body mass unit. Both species fed equal amounts of the glucose offered. We conclude that lipogenesis is far from negligible in N. vitripennis and plays an important role for the energy balance when teneral lipid reserves deplete.

Stable isotope labeling and functional gene prediction elucidate the carbon metabolism in fermentative bacteria and microalgae coupling system

The application of the fermentative bacteria and microalgae coupling system in the wastewater treatment has been studied, but there remains few knowledge regarding the organic and inorganic carbon metabolism within this system. In this study, the carbon metabolism of microalgae and fermentative bacteria was elucidated by 13C stable isotope labeling and functional gene prediction, respectively. The 13C glucose and 13C NaHCO3 were used as stable isotope tracers to clarify the organic and inorganic carbon metabolism of microalgae, indicating that approximately 71.5 % of the Acetyl-CoA in microalgae was synthesized from organic carbon sources, while 26.8 % was synthesized through the utilization of inorganic carbon sources. Inorganic carbon sources can enhance the activity of photosynthetic system and facilitate the Calvin cycle. Considering the adequate organic carbon sources and insufficient inorganic carbon sources in the fermentative bacteria and microalgae coupling system, NaHCO3 was added to improve carbon utilization of microalgae. The maximum microalgal lipid yield reached 1130.37 mg/L with 1000 mg/L NaHCO3 supplementation. Functional gene prediction was used to analysis the effect of various carbon composition on the bacterial carbon metabolism. Notably, the additional inorganic carbon sources increased the abundance of bacterial functional genes associated with the fermentation and acetic acids synthesis, which was advantageous for VFAs production and further promoted microalgae growth. This study can gain a deeper understanding of microbial metabolic mechanisms during the operation of fermentative bacteria and microalgae system, and improve its sustained operational stability.

Berberine alleviates ulcerative colitis by inhibiting inflammation through targeting IRGM1

BackgroundBerberine (BBR), the main active component of Coptis chinensis Franch., has a variety of pharmacological effects, notably anti-inflammatory, which make it a potential treatment for ulcerative colitis (UC). Nevertheless, the specific target and the mode of action of BBR against UC are still unclear. PurposeHere, we aim to identify BBR's anti-inflammatory target and its mode of action in UC treatment. MethodsThe therapeutic effects of BBR and Coptis chinensis Franch. extract were first assessed in UC mice. Then, stable isotope labeling using amino acids in cell culture-activity-based protein profiling (SILAC-ABPP) was applied to identify the anti-inflammatory target proteins of BBR in an inflammation model of RAW264.7 cells stimulated by LPS. Molecular docking, drug affinity responsive target stability (DARTS), molecular dynamics simulation, cellular thermal shift assay (CETSA), and biological layer interference (BLI) measurement were employed to study the interaction between BBR and its targets. Lentiviral transfection was used to knock down the target protein and investigate BBR's anti-inflammatory mechanism. ResultsBBR and Coptis chinensis Franch. extracts both significantly alleviated UC in mice. SILAC-ABPP identified IRGM1 as BBR's anti-inflammatory target, with its overexpression reduced by BBR treatment in both RAW264.7 cell inflammation models stimulated by LPS and UC mice. BBR significantly reduced inflammatory cytokines in LPS-induced RAW264.7 cells by blocking the PI3K/AKT/mTOR pathway. Knockdown of IRGM1 weakened BBR's effects on cytokine expression and pathway regulation. ConclusionFor the first time, IRGM1 was identified as the direct anti-inflammatory target of BBR. BBR has the potential to inhibit IRGM1 expression in vitro as well as in vivo. The molecular mechanism of BBR's anti-inflammatory activity was inhibiting the PI3K/AKT/mTOR pathway by targeting IRGM1.

Exploring formation of turanose in honey via stable isotope labelling and high-resolution mass spectrometry analysis

Turanose, an isomer of sucrose, naturally exists in honey. Previous study indicated that turanose content increased gradually in acacia honey as honeybees brewed honey in the hive. However, it is unclear how turanose is generated in honey. We hypothesised that turanose was produced by enzymes from honeybees and performed a series of simulation experiments to prove this hypothesis. We found turanose in honey was produced by honeybees processing sucrose. Furthermore, we determined that sugar composition of simulated nectar influenced the turanose concentration in honey: when sucrose concentration was below 5%, turanose was difficult to form, whereas high concentration of fructose and limited glucose were beneficial in producing turanose. Using 13C-labelled sucrose tests combined with proteomics analysis, we identified that α-glucosidase converted sucrose to turanose through an intermolecular isomerisation process. This study reveals the formation mechanism of turanose in honey and assists in the scientific control and improvement of honey quality.

Water residence time controls seasonal nitrous oxide budget in a semi-enclosed bay: Insights from an improvement estimation method

This study developed an estimation method for the N2O budget using 15N stable isotope labeling techniques, a dual-layer model and a box model, which was used to elucidate the underlying dynamics of N2O accumulation in Zhanjiang Bay. The results showed that although the net input of N2O during the rainy season was 2.36 times higher than that during the dry season, the overall N2O concentration was only 66.6 % of that during the dry season due to the extended water residence time in the dry season. Our findings highlighted that water residence time was the key factor for the N2O emission, and a longer water residence time was unfavorable for the efflux of N2O through hydrodynamic processes and was more conducive to the production and accumulation of N2O within the bay. This research enhanced our comprehension of N2O dynamics and provided crucial insights for refining nitrogen management strategies and mitigation efforts.

Isotopologues of potassium 2,2,2-trifluoroethoxide for applications in positron emission tomography and beyond

The 2,2,2-trifluoroethoxy group increasingly features in drugs and potential tracers for biomedical imaging with positron emission tomography (PET). Herein, we describe a rapid and transition metal-free conversion of fluoroform with paraformaldehyde into highly reactive potassium 2,2,2-trifluoroethoxide (CF3CH2OK) and demonstrate robust applications of this synthon in one-pot, two-stage 2,2,2-trifluoroethoxylations of both aromatic and aliphatic precursors. Moreover, we show that these transformations translate easily to fluoroform that has been labeled with either carbon-11 (t1/2 = 20.4 min) or fluorine-18 (t1/2 = 109.8 min), so allowing the appendage of complex molecules with a no-carrier-added 11C- or 18F- 2,2,2-trifluoroethoxy group. This provides scope to create candidate PET tracers with radioactive and metabolically stable 2,2,2-trifluoroethoxy moieties. We also exemplify syntheses of isotopologues of potassium 2,2,2-trifluoroethoxide and show their utility for stable isotopic labeling which can be of further benefit for drug discovery and development.

A multicenter, randomized, double-blind, placebo-controlled ascending dose study to evaluate the safety, tolerability, pharmacokinetics (PK) and pharmacodynamic (PD) effects of Posiphen in subjects with early Alzheimer’s Disease

BackgroundAmyloid beta protein (Aβ) is a treatment target in Alzheimer’s Disease (AD). Lowering production of its parent protein, APP, has benefits in preclinical models. Posiphen, an orally administered small molecule, binds to an iron-responsive element in APP mRNA and decreases translation of APP and Aβ. To augment human data for Posiphen, we evaluated safety, tolerability and pharmacokinetic and pharmacodynamic (PD) effects on Aβ metabolism using Stable Isotope Labeling Kinetic (SILK) analysis.MethodsDouble-blind phase 1b randomized ascending dose clinical trial, at five sites, under an IRB-approved protocol. Participants with mild cognitive impairment or mild AD (Early AD) confirmed by low CSF Aβ42/40 were randomized (within each dose arm) to Posiphen or placebo. Pretreatment assessment included lumbar puncture for CSF. Participants took Posiphen or placebo for 21–23 days, then underwent CSF catheter placement, intravenous infusion of 13C6-leucine, and CSF sampling for 36 h. Safety and tolerability were assessed through participant reports, EKG and laboratory tests. CSF SILK analysis measured Aβ40, 38 and 42 with immunoprecipitation-mass spectrometry. Baseline and day 21 CSF APP, Aβ and other biomarkers were measured with immunoassays. The Mini-Mental State Exam and ADAS-cog12 were given at baseline and day 21.ResultsFrom June 2017 to December 2021, 19 participants were enrolled, randomized within dose cohorts (5 active: 3 placebo) of 60 mg once/day and 60 mg twice/day; 1 participant was enrolled and completed 60 mg three times/day. 10 active drug and 5 placebo participants completed all study procedures. Posiphen was safe and well-tolerated. 8 participants had headaches related to CSF catheterization; 5 needed blood patches. Prespecified SILK analyses of Fractional Synthesis Rate (FSR) for CSF Aβ40 showed no significant overall or dose-dependent effects of Posiphen vs. placebo. Comprehensive multiparameter modeling of APP kinetics supported dose-dependent lowering of APP production by Posiphen. Cognitive measures and CSF biomarkers did not change significantly from baseline to 21 days in Posiphen vs. placebo groups.ConclusionsPosiphen was safe and well-tolerated in Early AD. A multicenter SILK study was feasible. Findings are limited by small sample size but provide additional supportive safety and PK data. Comprehensive modeling of biomarker dynamics using SILK data may reveal subtle drug effects.Trial registrationNCT02925650 on clinicaltrials.gov (registered on 10-24-2016).

Tracking DOT1L methyltransferase activity by stable isotope labelling using a selective synthetic co-factor

Epigenetic processes influence health and disease through mechanisms which alter gene expression. In contrast to genetic changes which affect DNA sequences, epigenetic marks include DNA base modifications or post-translational modification (PTM) of proteins. Histone methylation is a prominent and versatile example of an epigenetic marker: gene expression or silencing is dependent on the location and extent of the methylation. Protein methyltransferases exhibit functional redundancy and broad preferences for multiple histone residues, which presents a challenge for the study of their individual activities. We developed an isotopically labelled analogue of co-factor S-adenosyl-L-methionine (13CD3-BrSAM), with selectivity for the histone lysine methyltransferase DOT1L, permitting tracking of methylation activity by mass spectrometry (MS). This concept could be applied to other methyltransferases, linking PTM discovery to enzymatic mediators.

Comprehensive characterization of differential glycation in hepatocellular carcinoma using tissue proteomics with stable isotopic labeling.

Glycation is anon-enzymatic posttranslational modification coming from the reaction between reducing sugars and free amino groups in proteins, where early glycation products (fructosyl-lysine, FL) and advanced glycation end products (AGEs) are formed. The occurrence of glycation and accumulation of AGEs have been closely associated with hepatocellular carcinoma (HCC). Here, we reported the characterization of differential glycation in HCC using tissue proteomics with stable isotopic labeling; early glycation-modified peptides were enriched with boronate affinity chromatography (BAC), and AGEs-modified peptides were fractionated with basic reversed-phase separation. By this integrated approach, 3717 and 1137 early and advanced glycated peptides corresponding to 4007 sites on 1484 proteins were identified with afalse discovery rate (FDR) ofno more than 1%. One hundred fifty-five sites were modified with both early and advanced end glycation products. Five early and 7 advanced glycated peptides were quantified to be differentially expressed in HCC tissues relative to paired adjacent tissues. Most (8 out of 10) of the proteins corresponding to the differential glycated peptides have previously been reported with dysregulation in HCC. The results together may deepen our knowledge of glycation as well as provide insights for therapeutics.