Gimple, R. C., Yang, K., Halbert, M. E., Agnihotri, S. & Rich, J. N. Brain cancer stem cells: resilience through adaptive plasticity and hierarchical heterogeneity. Nat. Rev. Cancer 22, 497–514 (2022).
Wang, W. & Zou, W. Amino acids and their transporters in T cell immunity and cancer therapy. Mol. Cell 80, 384–395 (2020).
Lieu, E. L., Nguyen, T., Rhyne, S. & Kim, J. Amino acids in cancer. Exp. Mol. Med. 52, 15–30 (2020).
Olin-Sandoval, V. et al. Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism. Nature 572, 249–253 (2019).
Wu, Z. et al. TPO-induced metabolic reprogramming drives liver metastasis of colorectal cancer CD110+ tumor-initiating cells. Cell Stem Cell 17, 47–59 (2015).
Jackson, C. M., Choi, J. & Lim, M. Mechanisms of immunotherapy resistance: lessons from glioblastoma. Nat. Immunol. 20, 1100–1109 (2019).
Singh, S. K. et al. Identification of human brain tumour initiating cells. Nature 432, 396–401 (2004).
Bao, S. et al. Glioma stem cells promote radioresistance by preferential activation of the DNA damage response. Nature 444, 756–760 (2006).
Maddocks, O. D. K. et al. Modulating the therapeutic response of tumours to dietary serine and glycine starvation. Nature 544, 372–376 (2017).
Gao, X. et al. Dietary methionine influences therapy in mouse cancer models and alters human metabolism. Nature 572, 397–401 (2019).
Fang, Y. et al. Histone crotonylation promotes mesoendodermal commitment of human embryonic stem cells. Cell Stem Cell 28, 748–763 (2021).
Dai, S. K. et al. Histone crotonylation regulates neural stem cell fate decisions by activating bivalent promoters. EMBO Rep. 22, e52023 (2021).
Minet, P. et al. Clinical and biochemical outcome of a patient with pyridoxine-dependent epilepsy treated by triple therapy (pyridoxine supplementation, lysine-restricted diet, and arginine supplementation). Acta Neurol. Belg. 121, 1669–1675 (2021).
Kava, M. P. et al. Beneficial outcome of early dietary lysine restriction as an adjunct to pyridoxine therapy in a child with pyridoxine dependant epilepsy due to Antiquitin deficiency. JIMD Rep. 54, 9–15 (2020).
Zinnanti, W. J. et al. A diet-induced mouse model for glutaric aciduria type I. Brain 129, 899–910 (2006).
Biagosch, C. et al. Elevated glutaric acid levels in Dhtkd1-/Gcdh- double knockout mice challenge our current understanding of lysine metabolism. Biochim. Biophys. Acta Mol. Basis Dis. 1863, 2220–2228 (2017).
Suva, M. L. et al. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell 157, 580–594 (2014).
Su, A. et al. The folate cycle enzyme MTHFR is a critical regulator of cell response to MYC-targeting therapies. Cancer Discov. 10, 1894–1911 (2020).
Okada, M. et al. Targeting folate metabolism is selectively cytotoxic to glioma stem cells and effectively cooperates with differentiation therapy to eliminate tumor-initiating cells in glioma xenografts. Int. J. Mol. Sci. 22, 11633 (2021).
Wang, X. et al. Targeting pyrimidine synthesis accentuates molecular therapy response in glioblastoma stem cells. Sci. Transl. Med. 11, eaau4972 (2019).
Wang, X. et al. Purine synthesis promotes maintenance of brain tumor initiating cells in glioma. Nat. Neurosci. 20, 661–673 (2017).
Hajji, N. et al. Arginine deprivation alters microglial polarity and synergizes with radiation to eradicate non-arginine-auxotrophic glioblastoma tumors. J. Clin. Invest. 132, e142137 (2022).
Mack, S. C. et al. Chromatin landscapes reveal developmentally encoded transcriptional states that define human glioblastoma. J. Exp. Med. 216, 1071–1090 (2019).
The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008).
Richards, L. M. et al. Gradient of developmental and injury response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity. Nat. Cancer 2, 157–173 (2021).
Sabari, B. R. et al. Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation. Mol. Cell 58, 203–215 (2015).
Liu, X. et al. MOF as an evolutionarily conserved histone crotonyltransferase and transcriptional activation by histone acetyltransferase-deficient and crotonyltransferase-competent CBP/p300. Cell Discov. 3, 17016 (2017).
Tang, X. et al. Short-chain enoyl-CoA hydratase mediates histone crotonylation and contributes to cardiac homeostasis. Circulation 143, 1066–1069 (2021).
Tan, M. et al. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146, 1016–1028 (2011).
Vanpouille-Box, C., Demaria, S., Formenti, S. C. & Galluzzi, L. Cytosolic DNA sensing in organismal tumor control. Cancer Cell 34, 361–378 (2018).
Chen, Y. G. & Hur, S. Cellular origins of dsRNA, their recognition and consequences. Nat. Rev. Mol. Cell Biol. 23, 286–301 (2022).
Miller, K. N. et al. Cytoplasmic DNA: sources, sensing, and role in aging and disease. Cell 184, 5506–5526 (2021).
Keyser, B. et al. Disease-causing missense mutations affect enzymatic activity, stability and oligomerization of glutaryl-CoA dehydrogenase (GCDH). Hum. Mol. Genet. 17, 3854–3863 (2008).
Qin, Q. et al. Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Genome Biol. 21, 32 (2020).
Roberts, T. C. et al. Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR. Nat. Protoc. 10, 1198–1211 (2015).
Han, H. et al. Small-molecule MYC inhibitors suppress tumor growth and enhance immunotherapy. Cancer Cell 36, 483–497 (2019).
Mehdipour, P. et al. Epigenetic therapy induces transcription of inverted SINEs and ADAR1 dependency. Nature 588, 169–173 (2020).
Zhang, S. M. et al. KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements. Nature 598, 682–687 (2021).
Charoentong, P. et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 18, 248–262 (2017).
Gravendeel, L. A. et al. Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. Cancer Res. 69, 9065–9072 (2009).
Chiappinelli, K. B. et al. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses. Cell 162, 974–986 (2015).
Sheng, W. et al. LSD1 ablation stimulates anti-tumor immunity and enables checkpoint blockade. Cell 174, 549–563 (2018).
Griffin, G. K. et al. Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature 595, 309–314 (2021).
Llorens-Bobadilla, E. et al. Single-cell transcriptomics reveals a population of dormant neural stem cells that become activated upon brain injury. Cell Stem Cell 17, 329–340 (2015).
Snyder, N. W. et al. Production of stable isotope-labeled acyl-coenzyme A thioesters by yeast stable isotope labeling by essential nutrients in cell culture. Anal. Biochem. 474, 59–65 (2015).
Frey, A. J. et al. LC-quadrupole/Orbitrap high-resolution mass spectrometry enables stable isotope-resolved simultaneous quantification and 13C-isotopic labeling of acyl-coenzyme A thioesters. Anal. Bioanal. Chem. 408, 3651–3658 (2016).
Trefely, S., Ashwell, P. & Snyder, N. W. FluxFix: automatic isotopologue normalization for metabolic tracer analysis. BMC Bioinform. 17, 485 (2016).
Zhang, D. et al. Metabolic regulation of gene expression by histone lactylation. Nature 574, 575–580 (2019).
Chen, Y., Kwon, S. W., Kim, S. C. & Zhao, Y. Integrated approach for manual evaluation of peptides identified by searching protein sequence databases with tandem mass spectra. J. Proteome Res. 4, 998–1005 (2005).
Criscione, S. W., Zhang, Y., Thompson, W., Sedivy, J. M. & Neretti, N. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genom. 15, 583 (2014).
Zheng, R. et al. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Res. 47, D729–D735 (2019).
Li, T. et al. TIMER2.0 for analysis of tumor-infiltrating immune cells. Nucleic Acids Res. 48, W509–W514 (2020).
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