AccuCor2: isotope natural abundance correction for dual-isotope tracer experiments

Wang, Yujue; Parsons, Lance R.; Su, Xiaoyang

doi:10.1038/s41374-021-00631-4

Cited by 10 publications

(7 citation statements)

References 36 publications

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“…Fumarate/malate and other ratios were calculated by dividing peak areas. If stable isotope tracing was used in the experiment, the peak areas were additionally processed via the R package AccuCor 2 to correct for natural isotope abundance 45 . Peak areas for each sample were normalized by the measured area of the internal standard trifluoromethanesulfonate (present in the extraction buffer) and by the number of cells present in the extracted well.…”

Section: Methodsmentioning

confidence: 99%

FH variant pathogenicity promotes purine salvage pathway dependence in kidney cancer

Wilde

Chakraborty

Matulionis

et al. 2022

Preprint

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The tricarboxylic citric acid cycle enzyme fumarate hydratase (FH) is a tumor suppressor. When lost in cells, its substrate fumarate accumulates to mM levels and drives oncogenic signaling and transformation. Germline alterations lead to an autosomal dominant condition known as hereditary leiomyomatosis and renal cell cancer (HLRCC) where patients are predisposed to various benign tumors and an aggressive form of kidney cancer. FH alterations of unclear significance are frequently observed with germline testing; thus, there is an unmet need to classify FH variants by their cancer-associated risk, allowing for screening, early diagnosis and treatment. Here we quantify catalytic efficiency of 74 FH variants of uncertain significance. Over half were enzymatically inactive which is strong evidence of pathogenicity. We generated a panel of HLRCC cell lines expressing FH variants with a range of catalytic activities, then correlated fumarate levels with metabolic features. We found that fumarate accumulation blocks purine biosynthesis, rendering FH-deficient cells more sensitive to the purine salvage pathway inhibitor 6-mercaptopurine. Together, these findings suggest pathogenicity of many patient-associated FH variants and reveal nucleotide salvage as a targetable vulnerability in FH-deficient cancer cells.

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Section: Methodsmentioning

confidence: 99%

FH variant pathogenicity promotes purine salvage pathway dependence in kidney cancer

Wilde

Chakraborty

Matulionis

et al. 2022

Preprint

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show abstract

“…175, 305.171, 306.169, 307.166, 308.163, and 309.160, respectively. Successive mass shift D mass = (m/z) 0.997, which corresponds to the D mass of 14 N and 15 N. The 13 C 1 -RQ peak is not observed in this spectrum because the mass resolution is insufficient to distinguish it from the 15 N 1 peak (Wang et al, 2021).…”

Section: N Ammonia Integration Into Metabolitesmentioning

confidence: 91%

Stable isotope tracing reveals compartmentalized nitrogen assimilation in scleractinian corals

et al. 2022

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Corals form symbiotic relationships with dinoflagellate algae of the family Symbiodiniaceae, bacteria, and other microbes. Central to that relationship is the regulation of nutrition flux between the animal host and the photosynthetic Symbiodiniaceae that it is reliant on for the majority of metabolic needs. Nitrogen availability controls the growth and density of Symbiodiniaceae within coral tissues and has been proposed to play a role in host derived symbiosis regulation. Warming ocean temperatures and subsequent increases in dissolved organic carbon can potentially increase nitrogen fixation and lead to bleaching. We investigated the importance of nitrogen metabolism in vivo with LC-MS based stable isotope tracing using nubbins from three species of Hawaiian coral, the more heat tolerant Montipora capitata and Porites compressa and the more heat sensitive Pocillopora acuta, that were collected from reefs in Kāne’ohe Bay, O’ahu. In addition to 15N incorporation into nucleotides, amino acids, and urea cycle metabolites, we also observed significant isotopic labeling in dipeptides, supporting their previous identification as major heat stress response metabolites. Surprisingly, the dipeptides are highly enriched in 15N compared to free amino acids, which are the biosynthetic precursors for dipeptides. This suggests that there is a high turnover of dipeptide pools and distinct biosynthetic mechanisms that separately mediate amino acid and dipeptide production. These preliminary data show that nitrogen assimilation in the coral holobiont is likely compartmentalized, with rapid assimilation and quick dipeptide turnover occurring in one region of the holobiont and slow turnover of other nitrogen containing metabolites in other region(s).

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“…Metabolite peaks were background corrected using AccuCor2 [ 57 ], then converted to mass distribution vectors, such that each isotopologue was set as a fraction of the sum of the total isotopologues for each molecule. Pool size measurements, which reflect total molecular peak abundance, were used for calculating redox and energy status ratios.…”

Section: Methodsmentioning

confidence: 99%

Tissue-specific reprogramming of glutamine metabolism maintains tolerance to sepsis

et al. 2023

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Reprogramming metabolism is of great therapeutic interest for reducing morbidity and mortality during sepsis-induced critical illness. Disappointing results from randomized controlled trials targeting glutamine and antioxidant metabolism in patients with sepsis have begged a deeper understanding of the tissue-specific metabolic response to sepsis. The current study sought to fill this gap. We analyzed skeletal muscle transcriptomics of critically ill patients, versus elective surgical controls, which revealed reduced expression of genes involved in mitochondrial metabolism and electron transport, with increases in glutathione cycling, glutamine, branched chain, and aromatic amino acid transport. We then performed untargeted metabolomics and 13C isotope tracing to analyze systemic and tissue specific metabolic phenotyping in a murine polymicrobial sepsis model. We found an increased number of correlations between the metabolomes of liver, kidney, and spleen, with loss of correlations between the heart and quadriceps and all other organs, pointing to a shared metabolic signature within vital abdominal organs, and unique metabolic signatures for muscles during sepsis. A lowered GSH:GSSG and elevated AMP:ATP ratio in the liver underlie the significant upregulation of isotopically labeled glutamine’s contribution to TCA cycle anaplerosis and glutamine-derived glutathione biosynthesis; meanwhile, the skeletal muscle and spleen were the only organs where glutamine’s contribution to the TCA cycle was significantly suppressed. These results highlight tissue-specific mitochondrial reprogramming to support liver energetic demands and antioxidant synthesis, rather than global mitochondrial dysfunction, as a metabolic consequence of sepsis.

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AccuCor2: isotope natural abundance correction for dual-isotope tracer experiments

Cited by 10 publications

References 36 publications

FH variant pathogenicity promotes purine salvage pathway dependence in kidney cancer

FH variant pathogenicity promotes purine salvage pathway dependence in kidney cancer

Stable isotope tracing reveals compartmentalized nitrogen assimilation in scleractinian corals

Tissue-specific reprogramming of glutamine metabolism maintains tolerance to sepsis

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