DeBerardinis Lab at UT Southwestern Medical Center

I have been saying this. It’s an abomination. The only thing that comes close is the Quizno’s spongmonkeys.

In Memoriam: Bert W. O'Malley, M.D. In Memoriam: Bert W. O'Malley, M.D....

A true legend.
www.bcm.edu/about-us/lea...

Regulated decay of microRNAs plays a critical role in controlling body size in mammals! Check out our new paper in @genesdev.bsky.social and see thread previously posted with our pre-print 👇 for more info. Congrats to Collette LaVigne, Jaeil Han, and all authors!
genesdev.cshlp.org/cgi/content/...

Here's the beautiful paper from @chembiohub.bsky.social reporting NUDT5's role in purine synthesis. I cannot emphasize enough how gracious and open these authors were when we all realized we were working on the same mechanism.

19/Work from the Yang group: www.jci.org/articles/vie...

Uridine-sensitized screening identifies genes and metabolic regulators of nucleotide synthesis Nucleotides are essential for nucleic acid synthesis, signaling, and metabolism, and can be synthesized de novo or through salvage. Rapidly proliferating cells require large amounts of nucleotides, ma...

18/Work from the Jourdain group: www.biorxiv.org/content/10.1...

A non-enzymatic role of Nudix hydrolase 5 in repressing purine de novo synthesis Folate metabolism is intricately linked to purine de novo synthesis through the incorporation of folate-derived one-carbon units into the purine scaffold. By investigating chemical and genetic depende...

17/NUDT5 is having a moment – see excellent work from other labs reporting roles for NUDT5 in purine metabolism. These include papers by Kilian Huber and Stefan Kubicek, also out today (see link), and work by Alexis Jourdain and Jun Yang (see next posts)
www.science.org/doi/10.1126/...

16/TL/DR: The DNPB pathway has been known since the 1950s, and thiopurines have been used almost as long. NUDT5 regulates the activity of this pathway, and sensitivity to drugs that block it.

15/A fascinating open question is exactly what induces the association between NUDT5 and PPAT, and whether/how this triggers disassembly of the purinosome.

14/When purines are abundant, the purinosome disassembles, but this requires NUDT5-PPAT binding. So NUDT5 controls both the biochemistry and cell biology of DNPB initiation.

13/Also interesting: DNPB involves a cytosolic complex called the purinosome, which colocalizes the DNPB enzymes together to channel metabolites along the pathway. NUDT5 regulates the purisonome through the same residues that bind PPAT.

12/Interestingly, NUDT5’s ability to suppress DNPB explains how it confers 6TG sensitivity. 6TG induces the same DNA damage in wild-type and NUDT5-deficient cells, but only the latter cells survive. Blocking residual DNPB kills NUDT5-deficient cells treated with 6TG.

11/The NUDT5-PPAT complex seems to hold PPAT into an inactive oligomer (likely a tetramer) that suppresses DNPB. In vitro, NUDT5 reduces PPAT enzymatic activity, much better than purine nucleotides alone. But this requires that NUDT5 associate with PPAT.

10/Mutating a single NUDT5 residue from the interface with PPAT eliminated NUDT5’s ability to bind PPAT and confer sensitivity to 6TG, both in cultured cells and xenografted tumors.

9/Zheng found that NUDT5’s catalytic activity is dispensable for its ability to confer sensitivity to 6TG. Rather, he found through interactome databases and computational analysis of coevolutionary signals that NUDT5 physically associates with PPAT.

8/NUDT5’s involvement was surprising. R5P provides the pentose for purines, but Zheng had shown that mitochondrial suppression massively increases R5P abundance by activating the pentose phosphate pathway. He thought NUDT5 might have a different role.

7/The screen identified HPRT1, the salvage enzyme that converts 6TG into toxic thiopurine nucleotides. That made sense. It also identified NUDT5, a hydrolase that cleaves ADP-ribose to produce ribose-5-phosphate (R5P).

6/Thiopurines are salvaged to produce thiopurine nucleotides, which inhibit DNPB and incorporate into DNA, resulting in DNA damage and cell death. So a screen for suppressors of 6TG toxicity could identify genes required to activate salvage or suppress DNPB.

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 CRISPR-Cas9-based genetic screens are a powerful new tool in biology. By simply altering the sequence of the single-guide RNA (sgRNA), Cas9 can be reprogrammed to target different sites in the genome with relative ease, but the on-target activity ...

5/Zheng first examined data from a CRISPR screen performed by John Doench and David Root, designed to identify genes required for sensitivity to thiopurine chemotherapeutics like 6-thioguanine (6TG).
pmc.ncbi.nlm.nih.gov/articles/PMC...

4/Indeed, PPAT’s enzymatic activity is blocked by purine nucleotides in vitro, but typically this requires very high levels of purines. It seemed as if something was missing.

3/The textbook answer is that when salvage is active and purines are abundant, DNPB is suppressed through feedback inhibition at the level of the initiating enzymes, including the amidotransferase PPAT.

Electron transport chain inhibition increases cellular dependence on purine transport and salvage Mitochondria house many metabolic pathways required for homeostasis and growth. To explore how human cells respond to mitochondrial dysfunction, we pe…

2/The project arose from Zheng’s previous work reporting that mitochondrial dysfunction suppresses DNPB and induces salvage. Because salvage is required for growth of cells with mitochondrial defects, Zheng asked how cells switch off DNPB during salvage.
www.sciencedirect.com/science/arti...

NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT Cells generate purine nucleotides through de novo purine biosynthesis (DNPB) and purine salvage. Purine salvage represses DNPB to prevent excessive purine nucleotide synthesis through mechanisms that ...

1/New paper from Zheng Wu, Phong Nguyen et al. @cri-utsw.bsky.social shows how cells balance the two pathways that produce purine nucleotides: de novo purine biosynthesis (DNPB) and purine salvage. The surprising mechanism involves NUDT5, a Nudix hydrolase

www.science.org/doi/10.1126/...

Excited to share our work @nature.com! Postdoc @mariopalma.bsky.social, with major contributions from @retickerflynn.bsky.social and collaborators, discovered melanoma cells in lymph nodes gain a targetable FSP1 dependency that limits progression. #TeamFSP1

www.nature.com/articles/s41...

For context, very few inborn errors of metabolism are inherited in a dominant fashion. These are zebras among zebras. Abhimanyu and colleagues report a new one.

Identification of a new, autosomal dominant form of familial partial lipodystrophy from Abhimanyu Garg and team. This disease is caused by a recurrent variant in ACAA2, which encodes an enzyme in mitochondrial fatty acid oxidation.

www.jci.org/articles/vie...

We moved the RJDLab potluck to Halloween this year. Thanks to Gaby Cano for organizing! (And decorating).

Many thanks also to @cri-utsw.bsky.social for providing such an excellent environment for training and discovery.

Congrats to all Damon Runyon's SPARK Scholars, including our own scholar Imani Williams who is studying cancer metabolism. Thank you Damon Runyon Cancer Research Foundation @damonrunyon.org for supporting this great initiative.
www.damonrunyon.org/news/entries...

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