DeBerardinis Lab at UT Southwestern Medical Center

❤️

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...

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/...

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

I do believe the part about embracing the mothers

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

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...

🍹 @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

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...

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

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.

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...

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

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.

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.

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.

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.

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.

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).

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.

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.

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...

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...

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

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

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.

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.

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.

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...

And I mean that with the greatest respect for Ozzy.

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

I ❤️ SCD1. Congrats!

It's a pleasure Walter - keep up the great work!

Apologies for the massive photo of my face.

An unexpected career in cancer metabolism Nature Cancer - Ralph DeBerardinis obtained an MD and PhD from the University of Pennsylvania, then trained in Pediatrics and Medical Genetics at Children’s Hospital of Philadelphia. He moved...

Thanks Nature Cancer for the chance to reflect on some factors that led me to study cancer metabolism. For the trainees and other young scientists: the critical events that shape your career might not be obvious while they are happening. Keep an open mind and trust your instincts.

rdcu.be/evi4I

Just in case the grad school or postdoc office see this post ... I would like to clarify that none of the *trainees* are still here after 10 years.