ALKBH7 mediates necrosis via rewiring of glyoxal metabolism

Kulkarni, Chaitanya A.; Nadtochiy, Sergiy M.; Kennedy, Leslie; Zhang, Jimmy; Chhim, Sophea; Alwaseem, Hanan; Murphy, Elizabeth; Fu, Dragony; Brookes, Paul S.

doi:10.7554/elife.58573

Cited by 16 publications

(10 citation statements)

References 80 publications

(174 reference statements)

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“…Although a natural cellular metabolite produced from both sugar and lipid oxidation, − glyoxal can be cytotoxic at higher concentrations, , and we wanted to verify that slow intracellular release of small amounts glyoxal was tolerable in cellulo . Qualitatively, we observed no differences in morphology or growth rate between any cell groups receiving differentially caged ASOs, and all treated cells displayed roughly equivalent doubling times and were confluent by end of the experiment (Figure S40).…”

Section: Resultsmentioning

confidence: 99%

Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging

et al. 2020

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Controlling the structure and activity of nucleic acids dramatically expands their potential for application in therapeutics, biosensing, nanotechnology, and biocomputing. Several methods have been developed to impart responsiveness of DNA and RNA to small-molecule and light-based stimuli. However, heat-triggered control of nucleic acids has remained largely unexplored, leaving a significant gap in responsive nucleic acid technology. Moreover, current technologies have been limited to natural nucleic acids and are often incompatible with polymerase-generated sequences. Here we show that glyoxal, a well-characterized compound that covalently attaches to the Watson–Crick–Franklin face of several nucleobases, addresses these limitations by thermoreversibly modulating the structure and activity of virtually any nucleic acid scaffold. Using a variety of DNA and RNA constructs, we demonstrate that glyoxal modification is easily installed and potently disrupts nucleic acid structure and function. We also characterize the kinetics of decaging and show that activity can be restored via tunable thermal removal of glyoxal adducts under a variety of conditions. We further illustrate the versatility of this approach by reversibly caging a 2′-O-methylated RNA aptamer as well as synthetic threose nucleic acid (TNA) and peptide nucleic acid (PNA) scaffolds. Glyoxal caging can also be used to reversibly disrupt enzyme–nucleic acid interactions, and we show that caging of guide RNA allows for tunable and reversible control over CRISPR-Cas9 activity. We also demonstrate glyoxal caging as an effective method for enhancing PCR specificity, and we cage a biostable antisense oligonucleotide for time-release activation and titration of gene expression in living cells. Together, glyoxalation is a straightforward and scarless method for imparting reversible thermal responsiveness to theoretically any nucleic acid architecture, addressing a significant need in synthetic biology and offering a versatile new tool for constructing programmable nucleic acid components in medicine, nanotechnology, and biocomputing.

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Section: Resultsmentioning

confidence: 99%

Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging

et al. 2020

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“…Through Ingenuity Pathway Analysis (IPA), genes regulated by TANC1 were enriched in hepatic inflammation and HCC ( Wu et al, 2021 ). ALKBH7, a mitochondrial ketoglutarate dioxygenase, decreases ROS formation to regulate programmed necrosis ( Meng et al, 2019 ; Kulkarni et al, 2020 ). A single-nucleotide polymorphism (SNP) of ALKBH7 was clarified as a new prostate cancer biomarker in 2017 ( Walker et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Association of a Novel DOCK2 Mutation-Related Gene Signature With Immune in Hepatocellular Carcinoma

et al. 2022

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Hepatocellular carcinoma (HCC) is a malignant tumor with high morbidity and mortality worldwide. Many studies have shown that dedicator of cytokinesis 2 (DOCK2) has a crucial role as a prognostic factor in various cancers. However, the potentiality of DOCK2 in the diagnosis of HCC has not been fully elucidated. In this work, we aimed to investigate the prognostic role of DOCK2 mutation in HCC. The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) cohorts were utilized to identify the mutation frequency of DOCK2. Then, univariate Cox proportional hazard regression analysis, random forest (RF), and multivariate Cox regression analysis were performed to develop the risk score that was significantly related to DOCK2 mutation. Moreover, Gene Set Enrichment Analysis (GSEA), Gene Set Variation Analysis (GSVA), and immune correlation analysis were conducted for an in-depth study of the biological process of DOCK2 mutation involved in HCC. The results revealed that the mutation frequency of DOCK2 was relatively higher than that in non-cancer control subjects, and patients with DOCK2 mutations had a low survival rate and a poor prognosis compared with the DOCK2-wild group. In addition, the secretin receptor (SCTR), tetratricopeptide repeat, ankyrin repeat and coiled-coil domain-containing 1 (TANC1), Alkb homolog 7 (ALKBH7), FRAS1-related extracellular matrix 2 (FREM2), and G protein subunit gamma 4 (GNG4) were found to be the most relevant prognostic genes of DOCK2 mutation, and the risk score based on the five genes played an excellent role in predicting the status of survival, tumor mutation burden (TMB), and microsatellite instability (MSI) in DOCK2 mutant patients. In addition, DOCK2 mutation and the risk score were closely related to immune responses. In conclusion, the present study identifies a novel prognostic signature in light of DOCK2 mutation-related genes that shows great prognostic value in HCC patients; and this gene mutation might promote tumor progression by influencing immune responses. These data may provide valuable insights for future investigations into personalized forecasting methods and also shed light on stratified precision oncology treatment.

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“…Metabolites were serially extracted in 80 % methanol, evaporated under N 2 then resuspended in 50 % methanol. Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) analysis was performed as previously described [36], with reverse-phase LC on a Synergi Fusion-RP column (Phenomenex, Torrence CA) at 35 °C. Samples were analyzed by single reaction monitoring on a Thermo Quantum triple-quadrupole mass spectrometer.…”

Section: Methodsmentioning

confidence: 99%

“…Mouse liver mitochondria were isolated by differential centrifugation, and PT pore opening measured spectrophotometrically as osmotic swelling-induced decrease in light scatter/absorbance at 540 nm, both as previously described [36]. MGO or the pore inhibitor cyclosporin A (CsA) were added at concentrations indicated in figure legends, prior to triggering of PT pore opening by 100 μM Ca 2+ .…”

Section: Methodsmentioning

confidence: 99%

Distinct effects of intracellular vs. extracellular acidic pH on the cardiac metabolome during ischemia and reperfusion

Milliken

Ciesla

Nadtochiy

et al. 2022

Preprint

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Tissue ischemia results in intracellular pH (pHIN) acidification, and while accumulation of metabolites such as lactate is a known driver of acidic pHIN, less is known about how acidic pHIN regulates metabolism. Furthermore, acidic extracellular (pHEX) during early reperfusion confers cardioprotection, but how this impacts metabolism is unclear. Herein we employed LCMS based targeted metabolomics to analyze perfused mouse hearts exposed to: (i) control perfusion, (ii) hypoxia, (iii) ischemia, (iv) enforced acidic pHIN, (v) control reperfusion, and (vi) acidic pHEX (6.8) reperfusion. Surprisingly little overlap was seen between metabolic changes induced by hypoxia, ischemia, and acidic pHIN. Acidic pHIN elevated metabolites in the top half of glycolysis, and enhanced glutathione redox state. Acidic pHEX reperfusion induced substantial metabolic changes in addition to those seen in control reperfusion. This included elevated metabolites in the top half of glycolysis, prevention of purine nucleotide loss, and an enhancement in glutathione redox state. These data led to parallel hypotheses regarding potential roles for methylglyoxal inhibiting the mitochondrial permeability transition pore, and for acidic inhibition of ecto-5'-nucleotidase, as potential mediators of cardioprotection by acidic pHEX reperfusion. However, neither hypothesis was supported by subsequent experiments. In contrast, analysis of cardiac effluents revealed complex effects of pHEX on metabolite transport, suggesting that mildly acidic pHEX may protect in part by enhancing succinate release during reperfusion. Overall, each intervention had distinct and overlapping metabolic effects, suggesting acidic pH is an independent metabolic regulator regardless which side of the cell membrane it is imposed.

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ALKBH7 mediates necrosis via rewiring of glyoxal metabolism

Cited by 16 publications

References 80 publications

Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging

Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging

Association of a Novel DOCK2 Mutation-Related Gene Signature With Immune in Hepatocellular Carcinoma

Distinct effects of intracellular vs. extracellular acidic pH on the cardiac metabolome during ischemia and reperfusion

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