Leveraging autophagy and pyrimidine metabolism to target pancreatic cancer
Posted on: 24 July 2025
Preprint posted on 5 June 2025
Two is better than one: Pancreatic ductal adenocarcinoma cells can become resistant to treatment with autophagy inhibitors, but combination with pyrimidine analogues shows promise.
Selected by Hannah Pletcher
Categories: biochemistry, cancer biology, cell biology, molecular biology
Background:
Pancreatic ductal adenocarcinoma (PDA) is a highly lethal cancer, with a five-year survival rate of only 13.3% (Cancer of the Pancreas – Cancer Stat Facts, n.d.). Recently, studies have focused on the role of autophagy in PDA. Autophagy can be thought of as recycling: the process of breaking down and reusing organelles and proteins through the lysosome (Yamamoto et al., 2023), which is especially important during nutrient deprivation and hypoxia. In PDA, autophagy is increased (Yang et al., 2011), where it recycles metabolites to support carbon metabolism and nucleotide homeostasis.
The reliance of PDA cells on autophagy makes it an appealing therapeutic target (Towers & Thorburn, 2016), but autophagy and lysosome inhibitors like chloroquine have shown limited clinical success (Karasic et al., 2019) due to low specificity, low bioavailability, and the development of resistance. To work towards better therapeutic strategies for PDA, the Towers lab sought to understand if PDA cells can become resistant to autophagy inhibitors, and if so, how PDA cells adapt and alter their metabolism to survive (Dufresne et al., 2025). By understanding how PDA cells respond to prolonged autophagy inhibitor treatment, they identified potential metabolic liabilities to treat in combination with autophagy inhibitors.
Key Findings:
PDA cells resistant to autophagy inhibitors cannot induce autophagy but still survive and grow: The team developed PDA cells resistant to an autophagy inhibitor (hydroxychloroquine) or an inhibitor to upstream kinases UlK1/2 (MRT68921), hereby referred to as resistant PDA cells. Resistant PDA cells are viable and actively proliferate, albeit slightly slower than control PDA cells. Using a tandem fluorescent autophagy reporter, they show that resistant PDA cells do not induce autophagy under amino acid starvation, while control PDA cells do. Therefore, resistant PDA cells must have adapted to circumvent autophagy to survive and grow.
Resistant PDA cells have altered TCA cycle flux: RNA-seq showed metabolic differences in resistant PDA cells compared to the control PDA cells. In canonical tricarboxylic acid (TCA) cycle flux, pyruvate is decarboxylated to acetyl-CoA to enter the TCA cycle. Using tracing and metabolomics, the team identified signatures for decreased pyruvate decarboxylation in resistant PDA cells.
Resistant PDA cells use pyruvate carboxylation to replenish the TCA cycle: Resistant PDA cells actively proliferate and have functional mitochondria in basal conditions, so they must be adapting to decreased pyruvate decarboxylation. The researchers showed that pyruvate is instead carboxylated by pyruvate carboxylase to replenish the TCA cycle in resistant PDA cells.
Resistant PDA cells have increased pyrimidine salvage: Pyrimidine metabolism regulates pyruvate decarboxylation, so defects in pyrimidine metabolism could be the cause of the altered TCA cycle flux exhibited by resistant PDA cells. RNA-seq showed defects in pyrimidine metabolism, and resistant PDA cells have decreased free pyrimidine pools compared to control PDA cells. Pyrimidines can be made de novo or salvaged, and analysis of these pathways revealed decreases in de novo pyrimidine synthesis but increases in pyrimidine salvage. Therefore, the authors suggest that resistant PDA cells increase pyrimidine salvage to support nucleotide homeostasis for proliferation.
Resistant PDA cells are hypersensitive to pyrimidine analogues: Given that resistant PDA cells rely on pyrimidine salvage to support their growth, the team tested whether these cells would be more sensitive to compounds that have similar structures as pyrimidines, known as pyrimidine analogues, as a potential therapeutic strategy. When compared to standard of care treatments and clinical targets, resistant PDA cells only showed decreased viability when treated with pyrimidine analogues that are metabolized through the pyrimidine salvage pathway. Resistant PDA cells take up more pyrimidines, so they are hypersensitive to pyrimidine analogues.
Dual treatment of autophagy inhibitors and pyrimidine analogues is a potential therapeutic strategy for PDA: Combining autophagy inhibitors with pyrimidine analogues caused cell death in PDA cells. They validated this phenotype in vivo with a more bioavailable autophagy inhibitor and saw a decrease in tumor size in mice.
What I liked/why this new work is important:
The authors propose a model in which PDA cells rewire the TCA cycle and rely on pyrimidine salvage to support their proliferation when resistant to autophagy. Therefore, these resistant cells are hypersensitive to pyrimidine analogues as a potential therapeutic strategy. I really enjoyed the characterization of the metabolic rewiring that resistant PDA cells undergo and how the team used this information to inform a potential treatment strategy. Further, I appreciated that the authors used a variety of model systems to test their hypotheses – they developed resistant cell lines derived from both male and female mice and a human PDA cell line, they translated their work to mouse models, and they utilized patient-derived organoids.
Future Directions and Questions for the Authors:
- While the overall trends are the same, I found it interesting that the hydroxychloroquine resistant PDA cells have stronger phenotypes in general than the MRT68921 resistant PDA cells (for example, Fig. 2C-D, Fig. 3H, Fig. 4A). Do you think this is because MRT68921 is targeting the autophagy pathway more upstream of hydroxychloroquine, or do you think there is another reason?
- I really appreciated that you developed and tested both male- and female-derived resistant PDA cells. Overall, did you find that the cell lines behaved similarly, or did you notice any striking differences between the sexes?
- When looking at the fates of pyruvate, did you see any differences in lactate production or excretion? I think it would be interesting to see if pyruvate is mainly being fluxed into the TCA cycle or if pyruvate is also excreted as lactate due to build up in the resistant PDA cells.
References:
Cancer of the Pancreas—Cancer Stat Facts. (n.d.). SEER. Retrieved June 24, 2025, from https://seer.cancer.gov/statfacts/html/pancreas.html
Dufresne, S., Kuna, R. S., Wong, K., Komarla, A., Rock, A., Rosada-Encarnación, J., Shen, C., Mondal, P., Parham, L. R., Izidro Layng, F., Peck, K. L., Fowler, A., Lowy, A. M., Engle, D., Tiriac, H., Shaw, R., Cosford, N., Metallo, C., & Towers, C. (2025). Leveraging autophagy and pyrimidine metabolism to target pancreatic cancer. BioRxiv: The Preprint Server for Biology, 2025.06.05.656904. https://doi.org/10.1101/2025.05.29.656904
Karasic, T. B., O’Hara, M. H., Loaiza-Bonilla, A., Reiss, K. A., Teitelbaum, U. R., Borazanci, E., De Jesus-Acosta, A., Redlinger, C., Burrell, J. A., Laheru, D. A., Von Hoff, D. D., Amaravadi, R. K., Drebin, J. A., & O’Dwyer, P. J. (2019). Effect of Gemcitabine and nab-Paclitaxel With or Without Hydroxychloroquine on Patients With Advanced Pancreatic Cancer: A Phase 2 Randomized Clinical Trial. JAMA Oncology, 5(7), 993–998. https://doi.org/10.1001/jamaoncol.2019.0684
Towers, C. G., & Thorburn, A. (2016). Therapeutic Targeting of Autophagy. EBioMedicine, 14, 15–23. https://doi.org/10.1016/j.ebiom.2016.10.034
Yamamoto, H., Zhang, S., & Mizushima, N. (2023). Autophagy genes in biology and disease. Nature Reviews Genetics, 24(6), 382–400. https://doi.org/10.1038/s41576-022-00562-w
Yang, S., Wang, X., Contino, G., Liesa, M., Sahin, E., Ying, H., Bause, A., Li, Y., Stommel, J. M., Dell’Antonio, G., Mautner, J., Tonon, G., Haigis, M., Shirihai, O. S., Doglioni, C., Bardeesy, N., & Kimmelman, A. C. (2011). Pancreatic cancers require autophagy for tumor growth. Genes & Development, 25(7), 717–729. https://doi.org/10.1101/gad.2016111
doi: https://doi.org/10.1242/prelights.41105
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| List by | Nadja Hümpfer et al. |
Fibroblasts
The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!
| List by | Osvaldo Contreras |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
| List by | Alex Eve |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
| List by | Ana Dorrego-Rivas |
Planar Cell Polarity – PCP
This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.
| List by | Ana Dorrego-Rivas |
BioMalPar XVI: Biology and Pathology of the Malaria Parasite
[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria
| List by | Dey Lab, Samantha Seah |
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Cell Polarity
Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.
| List by | Yamini Ravichandran |
TAGC 2020
Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20
| List by | Maiko Kitaoka et al. |
3D Gastruloids
A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.
| List by | Paul Gerald L. Sanchez and Stefano Vianello |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
| List by | Hiral Shah |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
| List by | Madhuja Samaddar et al. |
EMBL Seeing is Believing – Imaging the Molecular Processes of Life
Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019
| List by | Dey Lab |
Autophagy
Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.
| List by | Sandra Malmgren Hill |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
| List by | Rob Hynds |
Cellular metabolism
A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.
| List by | Pablo Ranea Robles |
BSCB/BSDB Annual Meeting 2019
Preprints presented at the BSCB/BSDB Annual Meeting 2019
| List by | Dey Lab |
MitoList
This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.
| List by | Sandra Franco Iborra |
ASCB/EMBO Annual Meeting 2018
This list relates to preprints that were discussed at the recent ASCB conference.
| List by | Dey Lab, Amanda Haage |
Also in the molecular biology category:
October in preprints – DevBio & Stem cell biology
Each month, preLighters with expertise across developmental and stem cell biology nominate a few recent developmental and stem cell biology (and related) preprints they’re excited about and explain in a single paragraph why. Short, snappy picks from working scientists — a quick way to spot fresh ideas, bold methods and papers worth reading in full. These preprints can all be found in the October preprint list published on the Node.
| List by | Deevitha Balasubramanian et al. |
October in preprints – Cell biology edition
Different preLighters, with expertise across cell biology, have worked together to create this preprint reading list for researchers with an interest in cell biology. This month, most picks fall under (1) Cell organelles and organisation, followed by (2) Mechanosignaling and mechanotransduction, (3) Cell cycle and division and (4) Cell migration
| List by | Matthew Davies et al. |
September in preprints – Cell biology edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading list. This month, categories include: (1) Cell organelles and organisation, (2) Cell signalling and mechanosensing, (3) Cell metabolism, (4) Cell cycle and division, (5) Cell migration
| List by | Sristilekha Nath et al. |
June in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: (1) Cell organelles and organisation (2) Cell signaling and mechanosensation (3) Genetics/gene expression (4) Biochemistry (5) Cytoskeleton
| List by | Barbora Knotkova et al. |
May in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) Biochemistry/metabolism 2) Cancer cell Biology 3) Cell adhesion, migration and cytoskeleton 4) Cell organelles and organisation 5) Cell signalling and 6) Genetics
| List by | Barbora Knotkova et al. |
Keystone Symposium – Metabolic and Nutritional Control of Development and Cell Fate
This preList contains preprints discussed during the Metabolic and Nutritional Control of Development and Cell Fate Keystone Symposia. This conference was organized by Lydia Finley and Ralph J. DeBerardinis and held in the Wylie Center and Tupper Manor at Endicott College, Beverly, MA, United States from May 7th to 9th 2025. This meeting marked the first in-person gathering of leading researchers exploring how metabolism influences development, including processes like cell fate, tissue patterning, and organ function, through nutrient availability and metabolic regulation. By integrating modern metabolic tools with genetic and epidemiological insights across model organisms, this event highlighted key mechanisms and identified open questions to advance the emerging field of developmental metabolism.
| List by | Virginia Savy, Martin Estermann |
April in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell cycle and division 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) (epi)genetics
| List by | Vibha SINGH et al. |
Biologists @ 100 conference preList
This preList aims to capture all preprints being discussed at the Biologists @100 conference in Liverpool, UK, either as part of the poster sessions or the (flash/short/full-length) talks.
| List by | Reinier Prosee, Jonathan Townson |
February in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry and cell metabolism 2) cell organelles and organisation 3) cell signalling, migration and mechanosensing
| List by | Barbora Knotkova et al. |
Community-driven preList – Immunology
In this community-driven preList, a group of preLighters, with expertise in different areas of immunology have worked together to create this preprint reading list.
| List by | Felipe Del Valle Batalla et al. |
January in preprints – the CellBio edition
A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics/gene expression
| List by | Barbora Knotkova et al. |
2024 Hypothalamus GRC
This 2024 Hypothalamus GRC (Gordon Research Conference) preList offers an overview of cutting-edge research focused on the hypothalamus, a critical brain region involved in regulating homeostasis, behavior, and neuroendocrine functions. The studies included cover a range of topics, including neural circuits, molecular mechanisms, and the role of the hypothalamus in health and disease. This collection highlights some of the latest advances in understanding hypothalamic function, with potential implications for treating disorders such as obesity, stress, and metabolic diseases.
| List by | Nathalie Krauth |
BSCB-Biochemical Society 2024 Cell Migration meeting
This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.
| List by | Reinier Prosee |
‘In preprints’ from Development 2022-2023
A list of the preprints featured in Development's 'In preprints' articles between 2022-2023
| List by | Alex Eve, Katherine Brown |
CSHL 87th Symposium: Stem Cells
Preprints mentioned by speakers at the #CSHLsymp23
| List by | Alex Eve |
9th International Symposium on the Biology of Vertebrate Sex Determination
This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.
| List by | Martin Estermann |
Alumni picks – preLights 5th Birthday
This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.
| List by | Sergio Menchero et al. |
CellBio 2022 – An ASCB/EMBO Meeting
This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.
| List by | Nadja Hümpfer et al. |
EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)
A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.
| List by | Alex Eve |
FENS 2020
A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020
| List by | Ana Dorrego-Rivas |
ECFG15 – Fungal biology
Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome
| List by | Hiral Shah |
ASCB EMBO Annual Meeting 2019
A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)
| List by | Madhuja Samaddar et al. |
Lung Disease and Regeneration
This preprint list compiles highlights from the field of lung biology.
| List by | Rob Hynds |
MitoList
This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.
| List by | Sandra Franco Iborra |