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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · 3d

❤️

Vikram Paralkar @paralkarlab.bsky.social · 4d

This is beautiful! 🥲

Eladio Bobadilla @eladiobobadilla.com · 4d

DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · 12d

Remarkable new human proteome-wide effort to predict protein-protein interactions using coevolutionary signals and deep learning. From Qian Cong in the Eugene McDermott Center at UT Southwestern.

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

Predicting protein-protein interactions in the human proteome

Protein-protein interactions (PPI) are essential for biological function. Coevolutionary analysis and deep learning (DL) based protein structure prediction have enabled comprehensive PPI identificatio...

www.science.org

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · 18d

Thank you @cri-utsw.bsky.social postdocs!

Children's Research Institute at UT Southwestern @cri-utsw.bsky.social · 18d

We have the best postdocs! We appreciate you being a critical part of our CRI team to help discover the treatments of tomorrow. #npaw2025 #npaw #relentlessdiscovery 🧪

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Aug 28

I do believe the part about embracing the mothers

Reposted by DeBerardinis Lab at UT Southwestern Medical Center

Zheng Wu @zhengwu1.bsky.social · Aug 19

I’m thrilled to share that I have been awarded an NIH/NIGMS K99 Pathway to Independence Award. I’m deeply grateful to everyone who has supported me along the way, especially
@rjdlab.bsky.social @cri-utsw.bsky.social

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Reposted by DeBerardinis Lab at UT Southwestern Medical Center

Nature Cell Biology @natcellbio.nature.com · Aug 14

🍹 @walterwchen.bsky.social et al show that PEX39 cooperates with PEX7 in the peroxisomal import of proteins containing a PTS2 site and uncover an (R/K)PWE motif in PEX39 and PEX13 that binds to PEX7 and facilitates the import of PTS2-containing proteins.
bit.ly/4lmjv2l

PEX39 facilitates the peroxisomal import of PTS2-containing proteins - Nature Cell Biology

Chen et al. show that PEX39 cooperates with PEX7 in the peroxisomal import of proteins containing a PTS2 site and uncover an (R/K)PWE motif in PEX39 and PEX13 that binds to PEX7 and facilitates the im...

bit.ly

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Reposted by DeBerardinis Lab at UT Southwestern Medical Center

Children's Research Institute at UT Southwestern @cri-utsw.bsky.social · Aug 12

Congrats! 👏👏👏 Two CRI scientists named 2025 Pew-Stewart & Pew Scholars — Javier Garcia-Bermudez, Ph.D. &
@hrshin.bsky.social — to advance cancer, biomedical research 🧪 Read more about their #relentlessdiscovery ⬇️ cri.utsw.edu/two-children... @pewtrusts.org

Two Children’s Research Institute scientists named 2025 Pew Scholars - Children's Medical Center Research Institute (CRI) | Dallas Texas

Javier Garcia-Bermudez, Ph.D., Hijai Regina Shin, Ph.D., selected to advance cancer, biomedical research DALLAS – Aug. 12, 2025 – Two Children’s Medical Center Research Institute at UT Southwestern fa...

cri.utsw.edu

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 31

I’ve been fortunate to have many great collaborations over the years, and I hope you will too. The best are where different scientists bring complementary skills and everyone is working towards a common goal - as we all did in this case.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

10/For more breakthroughs in peroxisomal biology, see this recent work from Michael Skowyra and Tom Rapoport: www.nature.com/articles/s41...

Import mechanism of peroxisomal proteins with an N-terminal signal sequence - Nature Cell Biology

Skowyra and Rapoport find that peroxisomal proteins with N-terminal PTS2 signals are imported through a nuclear pore-like conduit by PEX7 and a receptor. PEX7 then returns through the same conduit and...

www.nature.com

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

9/I will always be grateful for this collaboration with Daniel, Tony, Jorge and Bettina, and all the co-authors, for an experience that reinforces the value of openness in science.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

8/There was no quibbling over who would get credit for what. Everyone just wanted to make as complete a story as possible, as efficiently as possible. We agreed on an authorship structure early on and stuck to it.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

7/The collaboration allowed us to incorporate mammalian cell biology, yeast genetics and elegant biochemistry all in one paper. The end product was much greater than the sum of the parts because the technical expertise and perspectives of these different scientists all come through in the paper.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

6/So Walter reached out to them to share his work. They were receptive and generous. This led to remarkably open, productive collaboration with true experts in peroxisomal biology, including Tony Rodrigues, Daniel Wendscheck (@dwendscheck.bsky.social), Jorge Azevedo, and Bettina Warscheid.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

5/It was immediately clear to Walter that another team of scientists had found the yeast ortholog of C6ORF226 and were working on its role in peroxisome biology.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

4/Walter had worked for a couple of years on C6ORF226 in human cells and learned quite a bit about its function when he noticed that an online resource for peroxisomal biologists had provisionally identified a “PEX39” (peroxins are named in the order of their discovery).

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

3/The cell biology and biochemistry of what PEX39 does and how it works are fascinating. But I want to focus on the collaborative aspects of this study.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

2/Walter began this project by searching interactome databases for proteins of unknown function that seemed to interact with known proteins localized to metabolic organelles, like the peroxisome. That led him to C6ORF226, eventually renamed PEX39.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

1/New paper on peroxisome assembly, reporting the detailed mechanism of PEX39, a new peroxin involved in PTS2 protein transport. Fantastic work by ‪@walterwchen.bsky.social‬ and a dream team of collaborators, as explained below. www.nature.com/articles/s41...

PEX39 facilitates the peroxisomal import of PTS2-containing proteins - Nature Cell Biology

Chen et al. show that PEX39 cooperates with PEX7 in the peroxisomal import of proteins containing a PTS2 site and uncover an (R/K)PWE motif in PEX39 and PEX13 that binds to PEX7 and facilitates the im...

www.nature.com

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 30

Congrats @dwendscheck.bsky.social - what a pleasure it was to work with you on this project.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 29

4/Congrats to Jennifer Gill, Aparna Rao, Ling Cai, and the entire team for this study.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 29

3/If metabolic pathways are not conserved between patient and PDX, we shouldn't use PDXs to test metabolic therapies. We hope the paper will improve the efficiency of cancer metabolism studies in PDXs by showing which pathways withstand transplantation.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 29

2/The metabolic features we analyzed include isotope tracing with 13C-glucose (performed in patients and mice) and metabolomic profiling, evaluated over 6 passages in mice to assess both the fidelity and durability of PDX metabolic heterogeneity.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 29

1/Patient-derived xenografts (PDXs) are used in preclinical testing of cancer therapies, including metabolic therapies. We determined which metabolic properties are retained, and which are lost, when melanomas from patients are implanted and passaged as PDXs in mice.
www.nature.com/articles/s42...

Conservation and divergence of metabolic phenotypes between patient tumours and matched xenografts - Nature Metabolism

Rao and Cai et al. perform a detailed metabolic comparison between primary tumours from patients and their matching xenografts, which identify conserved as well as divergent metabolic patterns.

www.nature.com

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 22

And I mean that with the greatest respect for Ozzy.

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DeBerardinis Lab at UT Southwestern Medical Center @rjdlab.bsky.social · Jul 22

If Ozzy Osbourne could write Crazy Train, I can write one more paragraph of a research summary.

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