@article{scheidemantle_duan_lodge_cummings_hilovsky_pham_wang_kennedy_liu_2024, title={Data-dependent and -independent acquisition lipidomics analysis reveals the tissue-dependent effect of metformin on lipid metabolism}, volume={20}, ISSN={["1573-3890"]}, DOI={10.1007/s11306-024-02113-2}, number={3}, journal={METABOLOMICS}, author={Scheidemantle, Grace and Duan, Likun and Lodge, Mareca and Cummings, Magdalina J. and Hilovsky, Dalton and Pham, Eva and Wang, Xiaoqiu and Kennedy, Arion and Liu, Xiaojing}, year={2024}, month={May} }
 @article{patel_cooper_kadakia_allen_duan_luo_williams_liu_locasale_kirsch_2024, title={Targeting glutamine metabolism improves sarcoma response to radiation therapy in vivo}, volume={7}, ISSN={["2399-3642"]}, DOI={10.1038/s42003-024-06262-x}, abstractNote={Diverse tumor metabolic phenotypes are influenced by the environment and genetic lesions. Whether these phenotypes extend to rhabdomyosarcoma (RMS) and how they might be leveraged to design new therapeutic approaches remains an open question. Thus, we utilized a Pax7}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Patel, Rutulkumar and Cooper, Daniel E. and Kadakia, Kushal T. and Allen, Annamarie and Duan, Likun and Luo, Lixia and Williams, Nerissa T. and Liu, Xiaojing and Locasale, Jason W. and Kirsch, David G.}, year={2024}, month={May} }
 @article{tsai_chuang_li_yu_tzeng_teoh_lindblad_di matteo_cheng_hsueh_et al._2023, title={Immunoediting instructs tumor metabolic reprogramming to support immune evasion}, volume={35}, ISSN={["1932-7420"]}, DOI={10.1016/j.cmet.2022.12.003}, abstractNote={Immunoediting sculpts immunogenicity and thwarts host anti-tumor responses in tumor cells during tumorigenesis; however, it remains unknown whether metabolic programming of tumor cells can be guided by immunosurveillance. Here, we report that T cell-mediated immunosurveillance in early-stage tumorigenesis instructs c-Myc upregulation and metabolic reprogramming in tumor cells. This previously unexplored tumor-immune interaction is controlled by non-canonical interferon gamma (IFNγ)-STAT3 signaling and supports tumor immune evasion. Our findings uncover that immunoediting instructs deregulated bioenergetic programs in tumor cells to empower them to disarm the T cell-mediated immunosurveillance by imposing metabolic tug-of-war between tumor and infiltrating T cells and forming the suppressive tumor microenvironment.}, number={1}, journal={CELL METABOLISM}, author={Tsai, Chin-Hsien and Chuang, Yu-Ming and Li, Xiaoyun and Yu, Yi-Ru and Tzeng, Sheue-Fen and Teoh, Shao Thing and Lindblad, Katherine E. and Di Matteo, Mario and Cheng, Wan-Chen and Hsueh, Pei-Chun and et al.}, year={2023}, month={Jan}, pages={118-+} }
 @article{liu_duan_liu_wang_2023, title={Metabolomic Analysis of Uterine Luminal Fluid During the Peri-Implantation Period of Pregnancy in Pigs}, volume={101}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skad068.046}, abstractNote={Abstract}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Liu, Bangmin and Duan, Likun and Liu, Xiaojing and Wang, Xiaoqiu}, year={2023}, month={May} }
 @article{duan_cooper_scheidemantle_locasale_kirsch_liu_2022, title={C-13 tracer analysis suggests extensive recycling of endogenous CO2 in vivo}, volume={10}, ISSN={["2049-3002"]}, DOI={10.1186/s40170-022-00287-8}, abstractNote={Abstract}, number={1}, journal={CANCER & METABOLISM}, author={Duan, Likun and Cooper, Daniel E. and Scheidemantle, Grace and Locasale, Jason W. and Kirsch, David G. and Liu, Xiaojing}, year={2022}, month={Jul} }
 @article{duan_scheidemantle_lodge_cummings_pham_wang_kennedy_liu_2022, title={Prioritize biologically relevant ions for data-independent acquisition (BRI-DIA) in LC-MS/MS-based lipidomics analysis}, volume={18}, ISSN={["1573-3890"]}, DOI={10.1007/s11306-022-01913-8}, abstractNote={Data-dependent acquisition (DDA) is the most commonly used MS/MS scan method for lipidomics analysis on orbitrap-based instrument. However, MS instrument associated software decide the top N precursors for fragmentation, resulting in stochasticity of precursor selection and compromised consistency and reproducibility. We introduce a novel workflow using biologically relevant lipids to construct inclusion list for data-independent acquisition (DIA), named as BRI-DIA workflow.To ensure consistent coverage of biologically relevant lipids in LC-MS/MS-based lipidomics analysis.Biologically relevant ion list was constructed based on LIPID MAPS and lipidome atlas in MS-DIAL 4. Lipids were extracted from mouse tissues and used to assess different MS/MS scan workflow (DDA, BRI-DIA, and hybrid mode) on LC-Orbitrap Exploris 480 mass spectrometer.DDA resulted in more MS/MS events, but the total number of unique lipids identified by three methods (DDA, BRI-DIA, and hybrid MS/MS scan mode) is comparable (580 unique lipids across 44 lipid subclasses in mouse liver). Major cardiolipin molecular species were identified by data generated using BRI-DIA and hybrid methods and allowed calculation of cardiolipin compositions, while identification of the most abundant cardiolipin CL72:8 was missing in data generated using DDA method, leading to wrong calculation of cardiolipin composition.The method of using inclusion list comprised of biologically relevant lipids in DIA MS/MS scan is as efficient as traditional DDA method in profiling lipids, but offers better consistency of lipid identification, compared to DDA method. This study was performed using Orbitrap Exploris 480, and we will further evaluate this workflow on other platforms, and if verified by future work, this biologically relevant ion fragmentation workflow could be routinely used in many studies to improve MS/MS identification capacities.}, number={8}, journal={METABOLOMICS}, author={Duan, Likun and Scheidemantle, Grace and Lodge, Mareca and Cummings, Magdalina J. and Pham, Eva and Wang, Xiaoqiu and Kennedy, Arion and Liu, Xiaojing}, year={2022}, month={Jul} }
 @article{karampelias_rezanejad_rosko_duan_lu_pazzagli_bertolino_cesta_liu_korbutt_et al._2021, title={Reinforcing one-carbon metabolism via folic acid/Folr1 promotes beta-cell differentiation}, volume={12}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-021-23673-0}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Karampelias, Christos and Rezanejad, Habib and Rosko, Mandy and Duan, Likun and Lu, Jing and Pazzagli, Laura and Bertolino, Philippe and Cesta, Carolyn E. and Liu, Xiaojing and Korbutt, Gregory S. and et al.}, year={2021}, month={Jun} }