DeBerardinis Lab at UT Southwestern Medical Center
@rjdlab.bsky.social
I still like small data but I'm not opposed to big data. We study #metabolism, #genetics, #pediatric inborn errors & cancer. Views are my own.
19/Work from the Yang group: www.jci.org/articles/vie...
JCI -
The NUDIX hydrolase NUDT5 regulates thiopurine metabolism and cytotoxicity
www.jci.org
November 6, 2025 at 7:12 PM
19/Work from the Yang group: www.jci.org/articles/vie...
18/Work from the Jourdain group: www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
November 6, 2025 at 7:11 PM
18/Work from the Jourdain group: www.biorxiv.org/content/10.1...
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/...
www.science.org/doi/10.1126/...
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...
www.science.org
November 6, 2025 at 7:10 PM
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/...
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.
November 6, 2025 at 7:07 PM
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.
November 6, 2025 at 7:07 PM
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.
November 6, 2025 at 7:07 PM
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.
November 6, 2025 at 7:06 PM
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.
November 6, 2025 at 7:05 PM
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.
November 6, 2025 at 7:05 PM
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.
November 6, 2025 at 7:04 PM
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.
November 6, 2025 at 7:04 PM
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.
November 6, 2025 at 7:04 PM
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).
November 6, 2025 at 7:04 PM
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.
November 6, 2025 at 7:03 PM
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.
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...
pmc.ncbi.nlm.nih.gov/articles/PMC...
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 ...
pmc.ncbi.nlm.nih.gov
November 6, 2025 at 7:03 PM
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...
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.
November 6, 2025 at 7:02 PM
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.
November 6, 2025 at 7:02 PM
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.
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...
www.sciencedirect.com/science/arti...
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…
www.sciencedirect.com
November 6, 2025 at 7:02 PM
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...
www.sciencedirect.com/science/arti...
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.
November 4, 2025 at 5:06 PM
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.