Pre-prints

Sheehan C, Hu L, Cognet G, Croley G, Nguyen TT, Thomas-Toth A, Agovino D, Jonker PB, Sadullozoda M, Ziolkowski LM, Martin JK, Beutel AK, Dano R, Khan MA, Halbrook CJ, Macleod KF, Weber CR, LaBelle JL, Muir A (2025). Tumor nutrient stress gives rise to a drug tolerant cell state in pancreatic cancer. bioRxiv.

Kent JR, Abbott KL, Nordgren R, Deik A, Das NK, Waite M, Kunchok T, Shevzov-Zebrun A, Christiansen N, Siadek A, Bryan DS, Ferguson MK, Donington JS, Muir A, Shah YM, Clish CB, Vander Heiden MG, Madariaga ML, Hsu PP (2025). Intraoperative arteriovenous patient sampling to assess in situ non-small cell lung cancer metabolism. bioRxiv.

Billingham LK, DeLay SL, Tripathi S, Olson I, Zilinger K, Subbiah J, Wang Z, Sadagopan NS, Chia T-y, Najem H, Cognet G, Katz J, Vázquez-Cervantes GI, Wang S, Wan H, Lipshutz AB, Murphy AR, Duffy J, Balyasnikova IV, Zhang P, Heiland DH, Ahmed AU, Lee-Chang C, Heimberger AB, Perry JSA, Muir A, Chandel NS, Miska J (2025). Microglial Fructose Metabolism Is Essential for Glioblastoma Growth. bioRxiv.

Buj R, Cole AR, Danielson J, Xu J, Hurd D, Kishore A, Kedziora KM, Chen J, Yang B, Barras D, Uboveja A, Amalric A, Apiz Saab JJ, Wickramasinghe J, Tangudu NK, Levasseur E, Wang H, Minasyan A, Dadey RE, Sharrow AC, Vendetti FP, Rivadeneira DB, Bakkenist CJ, Delgoffe GM, Hempel N, Snyder NW, Bao R, Soloff AC, Kirkwood JM, Laniti DD, Kossenkov AV, Muir A, Das J, Davar D, Mesaros C, Aird KM (2025). CDKN2ALow cancer cells outcompete macrophages for microenvironmental zinc to drive immunotherapy resistance. bioRxiv.

Hecht F, Zocchi M, Tuttle ET, Ward NP, Smith B, Kang YP, Cazarin J, Soares ZG, Ozgurses ME, Zhao H, Sheehan C, Alimohammadi F, Munger LD, Trivedi D, Asantewaa G, Blick-Nitko SK, Zoeller JJ, Chen Y, Vasiliou V, Turner BM, Muir A, Coloff JL, Munger J, DeNicola GM, Harris IS (2024). Catabolism of extracellular glutathione supplies amino acids to support tumor growth. bioRxiv.

Whyte D, Vande Voorde J, Sumpton D, Dhayade S, Dornier E, Moore M, Novo D, Peters J, Wiesheu R, Mackey JBG, McFarlane AJ, Fercoq F, Fisher S, Caballero CD, Gilroy K, Redmond KL, Mitchell LE, Anderson E, Thomson G, Dzierozynski LN, Apiz Saab JJ, Lewis CA, Muir A, Halbrook CJ, Strathdee D, Jackstadt R, Nixon C, Dunne P, Steele CW, Carlin LM, Macpherson IR, Roberts EW, Coffelt SB, Blyth K, Sansom OJ, Norman JC, Clarke CJ (2024). Uridine Phosphorylase-1 supports metastasis of mammary cancer by altering immune and extracellular matrix landscapes of the lung. bioRxiv.

Meliton AY, Cetin-Atalay R, Tian Y, Szafran JCH, Shin KWD, Cho T, Sun KA, Woods PS, Shamaa OR, Chen B, Muir A, Mutlu GM, Hamanaka RB (2023). Mitochondrial One-Carbon Metabolism is Required for TGF-β-Induced Glycine Synthesis and Collagen Protein Production. bioRxiv.

Published papers

Whyte D, Fisher SL, McKenzie CG, Sumpton D, Dhayade S, Dornier E, Moore M, Novo D, Peters J, Wiesheu R, Gounis MD, Watt DM, Mackey JB, McFarlane AJ, Fercoq F, Dehesa Caballero C, Redmond KL, Mitchell LE, Anderson E, Thomson G, Hedley A, Clark W, Leroi S, Dzierozynski LN, Apiz Saab JJ, Lewis CA, Muir A, Halbrook CJ, Strathdee D, Jackstadt R, Nixon C, Dunne P, Carlin LM, Macpherson IR, Roberts EW, Coffelt SB, Blyth K, Sansom OJ, Norman JC, Vande Voorde J, Clarke CJ (2025). Uridine phosphorylase-1 supports metastasis by altering immune and extracellular matrix landscapes. Pubmed.

Wang Y, Wilfahrt D, Jonker PB, Lontos K, Chufan C, Cameron B, Xie B, Peralta RM, Schoedel ER, Gunn WG, AminiTabrizi R, Shah H, Rivadeneira DB, Muir A*, Delgoffe GM* (2025). Tumour interstitial fluid-enriched phosphoethanolamine suppresses T cell function. Link. News and Views. News Coverage.

Jonker PB, Sadullozoda M, Cognet G, Apiz Saab JJ, Sokol KH, Wu VX, Kumari D, Sheehan C, Ozgurses ME, Agovino D, Croley G, Patel SA, Bock-Hughes A, Macleod KF, Shah H, Lien EC, Muir A (2025). Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis. Pubmed.

Yu A, Yesilkanal AE, Thakur A, Wang F, Yang Y, Phillips W, Wu X, Muir A, He X, Spitz F, Yang L (2024). HYENA detects non-coding genes activated by distal enhancers in cancer. Pubmed.

Tharp KM, Kersten K, Maller O, Timblin GA, Stashko C, Canale FP, Menjivar RE, Hayward MK, Berestjuk I, ten Hoeve J, Samad B, Ironside AJ, di Magliano MP, Muir A, Geiger R, Combes AJ, Weaver VM (2024). Tumor-associated macrophages restrict CD8+ T cell function through collagen deposition and metabolic reprogramming of the breast cancer microenvironment. Pubmed.

Wolf MM, Madden MZ, Arner EN, Bader JE, Ye X, Vlach L, Tigue ML, Landis MD, Jonker PB, Hatem Z, Steiner KK, Gaines DK, Reinfeld BI, Hathaway ES, Zin F, Tantawy MN, Haake SM, Jonasch E, Muir A, Weiss VL, Beckerman KE, Rathmell WK, Rathmell JC (2024). VHL loss reprograms the immune landscape to promote an inflammatory myeloid microenvironment in renal tumorigenesis. Pubmed.

Abbott KL, Ali A, Reinfeld BI, Deik AAI, Subudhi S, Landis MS, Hongo RA, Young KL, Kunchok T, Nabel CS, Crowder KD, Kent JR, Madariaga MLL, Jain RK, Beckermann KE, Lewis CA, Clish CB, Muir A, Rathmell WK, Rathmell JC, Vander Heiden MG (2024). Metabolite profiling of human renal cell carcinoma reveals tissue-origin dominance in nutrient availability. Pubmed.

Fan H, Xia S, Xiang J, Li Y, Ross MO, Lim SA, Yang F, Tu J, Xie L, Dougherty U, Zhang FQ, Zheng Z, Zhang R, Wu R, Dong L, Su R, Chen X, Althaus T, Riedell PA, Jonker PB, Muir A, Lesinski GB, Rafiq S, Dhodapkar MV, Stock W, Odenike O, Patel AA, Opferman J, Tsuji T, Matsuzaki J, Shah H, Faubert B, Elf SE, Layden B, Bissonnette BM, He Y-Y, Kline J, Mao H, Odunsi K, Gao X, Chi H, He C, Chen J (2023). Trans-vaccenic acid reprograms CD8+ T cells and anti-tumor immunity. Pubmed.

Hasslluhn MC, Decker-Farrell AR, Vlahos L, Thomas DH, Curiel-Garcia A, Maurer HC, Wasko UN, Tomassoni L, Sastra SA, Palermo CF, Dalton TC, Ma A, Li F, Tolosa EJ, Hibshoosh H, Fernandez-Zapico ME, Muir A, Califano A, Olive KP (2023). Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression. Pubmed.

Decker-Farrell AR, Ma A, Li F, Muir A, Olive KP (2023). Generation and ex vivo culture of murine and human pancreatic ductal adenocarcinoma tissue slice explants. Pubmed.

Abbot KL, Ali A, Casalena D, Do BT, Ferreria R, Cheah JH, Soule CK, Deik A, Kunchok T, Schmidt DR, Renner S, Honeder SE, Wu M, Chan SH, Tseyang T, Stolzfus AT, Michel SLJ, Greaves D, Hsu PP, Ng CW, Zhang CJ, Farsidjani A, Kent JR, Madariaga MLL, Gramatikov IMT, Matheson NJ, Lewis CA, Clish CB, Rees MG, Roth JA, Griner LM, Muir A, Auld DS, Vander Heiden MG (2023). Screening in serum-derived medium reveals differential response to compounds targeting metabolism. Pubmed.

Apiz Saab JJ, Dzierozynski LD, Jonker PB, AminiTabrizi R, Shah H, Menjivar RE, Scott AJ, Nwosu ZC, Zhu Z, Chen RN, Oh M, Sheehan C, Wahl DR, di Magliano MP, Lyssiotis CA, Macleod KF, Weber CR, Muir A (2023). Pancreatic tumors exhibit myeloid-driven amino acid stress and upregulate arginine biosynthesis. Pubmed. News and Views.

Nwosu ZC, Ward MH, Sajjakulnukit P, Poudel P, Ragulan C, Kasperek S, Radyk M, Sutton D, Menjivar RE, Andren A, Apiz-Saab JJ, Tolstyka Z, Brown K, Lee H-J, Dzierozynski LD, He X, PS H, Ugras J, Nyamundanda G, Zhang L, Halbrook CJ, Carpenter CJ, Shi J, Shriver LP, Patti GJ, Muir A, di Magliano MP, Sadanandam A, Lyssiotis CA (2023). Uridine-derived ribose fuels glucose-restricted pancreatic cancer. Pubmed.

Sullivan MR, McGowen K, Liu Q, Akusobi C, Young DC, Mayfield JA, Raman S, Wolf ID, Moody DB, Aldrich CC, Muir A, Rubin EJ (2023). Biotin-dependent cell envelope remodelling is required for Mycobacterium abscessus survival in lung infection. Pubmed.

Sela Y, Li J, Maheswaran S, Norgard RJ, Yuan S, Hubbi ME, Doepner M, Xu JP, Ho ES, Mesaros C, Sheehan C, Croley G, Muir A, Blair IA, Ophir S, Dang CV, Stanger BZ (2022). Bcl-xL enforces a slow-cycling state necessary for survival in the nutrient-deprived microenvironment of pancreatic cancer. Pubmed.

Reinfeld BI, Madden MZ, Wolf MM, Chytil A, Bader JE, Patterson AR, Sugiera A, Cohen AS, Ali A, Do BT, Lewis CA, Muir A, Hongo RA, Young KL, Brown RE, Todd VM, Huffstater T, Abraham A, O’Neil RT, Wilson MT, Xin F, Tantawy MN, Merryman WD, Johnson RW, Williams CS, Mason EF, Mason FM, Beckermann KE, Vander Heiden MG, Manning HC, Rathmell JC, Rathmell WK (2021). Cell-programmed nutrient partitioning in the tumor microenvironment. Pubmed.

Badeaux M, Rolig A, Agnello G, Enzler D, Kasiewicz M, Priddy L, Wiggins J, Muir A, Sullivan M, Van Cleef J, Daige C, Vander Heiden M, Rajamanickam V, Wooldridge J, Redmond W, Rowlinson S (2020). Arginase therapy combines effectively with checkpoint blockade or agonist anti-OX40 immunotherapy to control tumor growth. Pubmed.

Francescone R, Vendramini-Costa DB, Franco-Barraza J, Wagner J, Muir A, Gabitova L, Pazina T, Luong T, Shah N, Rollins D, Gupta S, Roshan T, Restifo D, Lau A, Zhou Y, Cai KQ, Hensley H, Nicolas E, Kruger W, Devarajan K, Balachandran S, El-Deiry WS, Vander Heiden MG, Campbell KS, Astsaturov I, Cukierman E (2020). Netrin G1 promotes pancreatic tumorigenesis through cancer associated fibroblast driven nutritional support and immunosuppression. Pubmed.

Romero R, Sanchez-Rivera FJ, Peter MK, Mercer KL, Bhutkar A, Muir A, Gonzalez Robles TJ, Rodriguez SL, Liao LZ, Ng SR, Li L, Colon CI, Naranjo S, Beytagh MC, Lewis CA, Hsu PP, Bronson RT, Vander Heiden MG, Jacks T (2020). Keap1 mutation renders lung adenocarcinomas dependent on Slc33a1. Pubmed.

Sullivan MR, Lewis CA, Muir A (2019). Isolation and Quantification of Metabolite Levels in Murine Tumor Interstitial Fluid by LC/MS. Pubmed.

Sullivan MR, Danai LV, Lewis CA, Chan SH, Gui DY, Kunchok T, Dennstedt EA, Vander Heiden MG, Muir A (2019). Quantification of microenvironmental metabolites in murine cancers reveals determinants of tumor nutrient availability. Pubmed.

Sullivan MR, Mattaini KR, Dennestedt EA , Nguyen AA, Sivanand S, Reilly MF, Meeth K, Muir A, Darnell AM, Bosenberg MW, Lewis CA, Vander Heiden MG (2019). Increased Serine Synthesis Provides an Advantage for Tumors Arising in Tissues Where Serine Levels Are Limiting. Pubmed.

Danai LV, Babic A, Rosenthal MH, Dennestedt E, Muir A, Lien EC, Mayers JR, Tai K, Lau AN, Jones-Sali P, Prado CM, Petersen GM, Takahashi N, Sugimoto M, Yeh JJ, Lopez N, Bardessy N, Castillo CF, Liss AS, Koong AC, Bui J, Yuan C, Welch MW, Brais LK, Kulke MH, Dennis C, Clish CB, Wolpin BM, Vander Heiden MG (2018). Altered exocrine function can drive adipose wasting in early pancreatic cancer. Pubmed.

Sayin VI, LeBoeuf SE, Singh SX, Davidson SM, Biancur D, Guzelhan BS, Alvarez SW, Wu WL, Karakousi TR, Zavitsanou A-M, Ubriaco J, Muir A, Karagiannis D, Morris PJ, Thomas CJ, Possemato R, Vander Heiden MG, Papagiannakopoulos T (2017). Activation of the NRF2 antioxidant program generates an imbalance in central carbon metabolism in cancer. Pubmed.

Muir A, Danai LV, Gui DY, Waingarten CY, Lewis CA, Vander Heiden MG (2017). Environmental cystine drives glutamine anaplerosis and sensitizes cancer cells to glutaminase inhibition. Pubmed.

Mayers, JR, Torrence ME, Danai LV, Papagiannakopoulos T, Davidson SM, Bauer MR, Lau AN, Ji BW, Dixit PD, Hosios AM, Muir A, Chin CR, Freinkman E, Jacks T, Wolpin BM, Vitkup D, Vander Heiden MG (2016). Tissue-of-origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. Pubmed.

Reviews

Sheehan C, Muir A (2025). What’s on the menu?: metabolic constraints in the pancreatic tumor microenvironment. Pubmed.

Cognet G, Muir A (2024). Identifying metabolic limitations in the tumor microenvironment. Link.

Jonker PB, Muir A (2024). Metabolic ripple effects – deciphering how lipid metabolism in cancer interfaces with the tumor microenvironment. Pubmed.

Apiz Saab JJ, Muir A (2023). Tumor interstitial fluid analysis enables the study of microenvironment-cell interactions in cancers. Pubmed

Muir A, Danai LV, Vander Heiden MG (2018). Microenvironmental regulation of cancer cell metabolism: implications for experimental design and translational studies. Pubmed.

Muir A, Vander Heiden MG (2018). The nutrient environment affects therapy. Pubmed.