To better understand the molecular basis of resistance to azacitidine (AZA) therapy in myelodysplastic syndromes (MDS) and acute myeloid leukemia with myelodysplasia-related changes (AML-MRC), we performed RNA sequencing on pre-treatment CD34+ hematopoietic stem/progenitor cells (HSPCs) isolated from 25 MDS/AML-MRC patients of the discovery cohort (10 AZA responders (RD), six stable disease, nine progressive disease (PD) during AZA therapy) and from eight controls. Eleven MDS/AML-MRC samples were also available for analysis of selected metabolites, along with 17 additional samples from an independent validation cohort. Except for two patients, the others did not carry isocitrate dehydrogenase (IDH)1/2 mutations. Transcriptional landscapes of the patients' HSPCs were comparable to those published previously, including decreased signatures of active cell cycling and DNA damage response in PD compared to RD and controls. In addition, PD-derived HSPCs revealed repressed markers of the tricarboxylic acid cycle, with IDH2 among the top 50 downregulated genes in PD compared to RD. Decreased citrate plasma levels, downregulated expression of the (ATP)-citrate lyase and other transcriptional/metabolic networks indicate metabolism-driven histone modifications in PD HSPCs. Observed histone deacetylation is consistent with transcription-nonpermissive chromatin configuration and quiescence of PD HSPCs. This study highlights the complexity of the molecular network underlying response/resistance to hypomethylating agents.

1st Department of Medicine 1st Faculty of Medicine Charles University and General University Hospital 128 08 Prague Czech Republic

1st Faculty of Medicine Charles University 121 08 Prague Czech Republic

Department of Biology Faculty of Medicine and Dentistry Palacky University Olomouc 775 15 Olomouc Czech Republic

Department of Clinical and Molecular Pathology Faculty of Medicine and Dentistry Palacky University Olomouc and University Hospital Olomouc 775 15 Olomouc Czech Republic

Institute of Hematology and Blood Transfusion 128 20 Prague Czech Republic

Institute of Pathology 1st Faculty of Medicine Charles University and General University Hospital 128 08 Prague Czech Republic

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Silverman L.R., Demakos E.P., Peterson B.L., Kornblith A.B., Holland J.C., Odchimar-Reissig R., Stone R.M., Nelson D., Powell B.L., DeCastro C.M., et al. Randomized Controlled Trial of Azacitidine in Patients With the Myelodysplastic Syndrome: A Study of the Cancer and Leukemia Group B. J. Clin. Oncol. 2002;20:2429–2440. doi: 10.1200/JCO.2002.04.117. PubMed DOI

Silverman L.R., McKenzie D.R., Peterson B.L., Holland J.F., Backstrom J.T., Beach C.L., Larson R.A. Further Analysis of Trials With Azacitidine in Patients With Myelodysplastic Syndrome: Studies 8421, 8921, and 9221 by the Cancer and Leukemia Group B. J. Clin. Oncol. 2006;24:3895–3903. doi: 10.1200/JCO.2005.05.4346. PubMed DOI

Fenaux P., Mufti G.J., Hellstrom-Lindberg E., Santini V., Finelli C., Giagounidis A., Schoch R., Gattermann N., Sanz G., List A., et al. Efficacy of Azacitidine Compared with That of Conventional Care Regimens in the Treatment of Higher-Risk Myelodysplastic Syndromes: A Randomised, Open-Label, Phase III Study. Lancet Oncol. 2009;10:223–232. doi: 10.1016/S1470-2045(09)70003-8. PubMed DOI PMC

Platzbecker U. Treatment of MDS. Blood. 2019;133:1096–1107. doi: 10.1182/blood-2018-10-844696. PubMed DOI

Santini V., Prebet T., Fenaux P., Gattermann N., Nilsson L., Pfeilstöcker M., Vyas P., List A.F. Minimizing Risk of Hypomethylating Agent Failure in Patients with Higher-Risk MDS and Practical Management Recommendations. Leuk. Res. 2014;38:1381–1391. doi: 10.1016/j.leukres.2014.09.008. PubMed DOI

Sekeres M.A., Cutler C. How We Treat Higher-Risk Myelodysplastic Syndromes. Blood. 2014;123:829–836. doi: 10.1182/blood-2013-08-496935. PubMed DOI

Santini V. How I Treat MDS after Hypomethylating Agent Failure. Blood. 2019;133:521–529. doi: 10.1182/blood-2018-03-785915. PubMed DOI

Itzykson R., Thépot S., Quesnel B., Dreyfus F., Beyne-Rauzy O., Turlure P., Vey N., Recher C., Dartigeas C., Legros L., et al. Prognostic Factors for Response and Overall Survival in 282 Patients with Higher-Risk Myelodysplastic Syndromes Treated with Azacitidine. Blood. 2011;117:403–411. doi: 10.1182/blood-2010-06-289280. PubMed DOI

Döhner H., Dolnik A., Tang L., Seymour J.F., Minden M.D., Stone R.M., del Castillo T.B., Al-Ali H.K., Santini V., Vyas P., et al. Cytogenetics and Gene Mutations Influence Survival in Older Patients with Acute Myeloid Leukemia Treated with Azacitidine or Conventional Care. Leukemia. 2018;32:2546–2557. doi: 10.1038/s41375-018-0257-z. PubMed DOI PMC

Nazha A., Sekeres M.A., Bejar R., Rauh M.J., Othus M., Komrokji R.S., Barnard J., Hilton C.B., Kerr C.M., Steensma D.P., et al. Genomic Biomarkers to Predict Resistance to Hypomethylating Agents in Patients With Myelodysplastic Syndromes Using Artificial Intelligence. JCO Precis. Oncol. 2019;3:1–11. doi: 10.1200/PO.19.00119. PubMed DOI PMC

Bejar R., Lord A., Stevenson K., Bar-Natan M., Pérez-Ladaga A., Zaneveld J., Wang H., Caughey B., Stojanov P., Getz G., et al. TET2 Mutations Predict Response to Hypomethylating Agents in Myelodysplastic Syndrome Patients. Blood. 2014;124:2705–2712. doi: 10.1182/blood-2014-06-582809. PubMed DOI PMC

Traina F., Visconte V., Elson P., Tabarroki A., Jankowska A.M., Hasrouni E., Sugimoto Y., Szpurka H., Makishima H., O’Keefe C.L., et al. Impact of Molecular Mutations on Treatment Response to DNMT Inhibitors in Myelodysplasia and Related Neoplasms. Leukemia. 2014;28:78–87. doi: 10.1038/leu.2013.269. PubMed DOI

Al-Issa K., Mikkael A.S., Nielsen A.D., Jha B., Przychodzen B., Aly M., Carraway H.E., Advani A.S., Patel B., Clemente M.J., et al. TP53 Mutations and Outcome in Patients with Myelodysplastic Syndromes (MDS) Blood. 2016;128:4336. doi: 10.1182/blood.V128.22.4336.4336. DOI

Takahashi K., Patel K., Bueso-Ramos C., Zhang J., Gumbs C., Jabbour E., Kadia T., Andreff M., Konopleva M., DiNardo C., et al. Clinical Implications of TP53 Mutations in Myelodysplastic Syndromes Treated with Hypomethylating Agents. Oncotarget. 2016;7:14172–14187. doi: 10.18632/oncotarget.7290. PubMed DOI PMC

DiNardo C.D., Patel K.P., Garcia-Manero G., Luthra R., Pierce S., Borthakur G., Jabbour E., Kadia T., Pemmaraju N., Konopleva M., et al. Lack of Association of IDH1, IDH2 and DNMT3A Mutations with Outcome in Older Patients with Acute Myeloid Leukemia Treated with Hypomethylating Agents. Leuk. Lymphoma. 2014;55:1925–1929. doi: 10.3109/10428194.2013.855309. PubMed DOI PMC

Voso M.T., Santini V., Fabiani E., Fianchi L., Criscuolo M., Falconi G., Guidi F., Hohaus S., Leone G. Why Methylation Is Not a Marker Predictive of Response to Hypomethylating Agents. Haematologica. 2014;99:613–619. doi: 10.3324/haematol.2013.099549. PubMed DOI PMC

Treppendahl M.B., Kristensen L.S., Grønbæk K. Predicting Response to Epigenetic Therapy. J. Clin. Investig. 2014;124:47–55. doi: 10.1172/JCI69737. PubMed DOI PMC

Wang H., Li Y., Lv N., Li Y., Wang L., Yu L. Predictors of Clinical Responses to Hypomethylating Agents in Acute Myeloid Leukemia or Myelodysplastic Syndromes. Ann. Hematol. 2018;97:2025–2038. doi: 10.1007/s00277-018-3464-9. PubMed DOI

Oellerich T., Schneider C., Thomas D., Knecht K.M., Buzovetsky O., Kaderali L., Schliemann C., Bohnenberger H., Angenendt L., Hartmann W., et al. Selective Inactivation of Hypomethylating Agents by SAMHD1 Provides a Rationale for Therapeutic Stratification in AML. Nat. Commun. 2019;10:3475. doi: 10.1038/s41467-019-11413-4. PubMed DOI PMC

Gu X., Tohme R., Tomlinson B., Sakre N., Hasipek M., Durkin L., Schuerger C., Grabowski D., Zidan A.M., Radivoyevitch T., et al. Decitabine- and 5-Azacytidine Resistance Emerges from Adaptive Responses of the Pyrimidine Metabolism Network. Leukemia. 2020;35:1023–1036. doi: 10.1038/s41375-020-1003-x. PubMed DOI PMC

Diesch J., Zwick A., Garz A.-K., Palau A., Buschbeck M., Götze K.S. A Clinical-Molecular Update on Azanucleoside-Based Therapy for the Treatment of Hematologic Cancers. Clin. Epigenetics. 2016;8:71. doi: 10.1186/s13148-016-0237-y. PubMed DOI PMC

Daver N., Boddu P., Garcia-Manero G., Yadav S.S., Sharma P., Allison J., Kantarjian H. Hypomethylating Agents in Combination with Immune Checkpoint Inhibitors in Acute Myeloid Leukemia and Myelodysplastic Syndromes. Leukemia. 2018;32:1094–1105. doi: 10.1038/s41375-018-0070-8. PubMed DOI PMC

DiNardo C.D., Pratz K., Pullarkat V., Jonas B.A., Arellano M., Becker P.S., Frankfurt O., Konopleva M., Wei A.H., Kantarjian H.M., et al. Venetoclax Combined with Decitabine or Azacitidine in Treatment-Naive, Elderly Patients with Acute Myeloid Leukemia. Blood. 2019;133:7–17. doi: 10.1182/blood-2018-08-868752. PubMed DOI PMC

Garcia-Manero G., Kazmierczak M., Fong C.Y., Montesinos P., Venditti A., Mappa S., Spezia R., Adès L. A Phase 3 Randomized Study (PRIMULA) of the Epigenetic Combination of Pracinostat, a Pan-Histone Deacetylase (HDAC) Inhibitor, with Azacitidine (AZA) in Patients with Newly Diagnosed Acute Myeloid Leukemia (AML) Unfit for Standard Intensive Chemotherapy (IC) Blood. 2019;134:2652.

Pericole F.V., Lazarini M., de Paiva L.B., da Silva Santos Duarte A., Vieira Ferro K.P., Niemann F.S., Roversi F.M., Olalla Saad S.T. BRD4 Inhibition Enhances Azacitidine Efficacy in Acute Myeloid Leukemia and Myelodysplastic Syndromes. Front. Oncol. 2019;9:16. doi: 10.3389/fonc.2019.00016. PubMed DOI PMC

Yalniz F.F., Berdeja J.G., Maris M.B., Lyons R.M., Reeves J.A., Essell J.H., Patel P., Sekeres M., Hughes A., Mappa S., et al. A Phase II Study of Addition of Pracinostat to a Hypomethylating Agent in Patients with Myelodysplastic Syndromes Who Have Not Responded to Previous Hypomethylating Agent Therapy. Br. J. Haematol. 2020;188:404–412. doi: 10.1111/bjh.16173. PubMed DOI

Cheng Y., He C., Wang M., Ma X., Mo F., Yang S., Han J., Wei X. Targeting Epigenetic Regulators for Cancer Therapy: Mechanisms and Advances in Clinical Trials. Signal. Transduct. Target. Ther. 2019;4:62. doi: 10.1038/s41392-019-0095-0. PubMed DOI PMC

Pan D., Rampal R., Mascarenhas J. Clinical Developments in Epigenetic-Directed Therapies in Acute Myeloid Leukemia. Blood Adv. 2020;4:970–982. doi: 10.1182/bloodadvances.2019001245. PubMed DOI PMC

Belickova M., Merkerova Dostálová M.D., Votavova H., Valka J., Vesela J., Pejsova B., Hajkova H., Klema J., Cermak J., Jonasova A. Up-Regulation of Ribosomal Genes Is Associated with a Poor Response to Azacitidine in Myelodysplasia and Related Neoplasms. Int. J. Hematol. 2016;104:566–573. doi: 10.1007/s12185-016-2058-3. PubMed DOI

Lübbert M., Ihorst G., Sander P.N., Bogatyreva L., Becker H., Wijermans P.W., Suciu S., Bissé E., Claus R. Elevated Fetal Haemoglobin Is a Predictor of Better Outcome in MDS/AML Patients Receiving 5-Aza-2′-Deoxycytidine (Decitabine) Br. J. Haematol. 2017;176:609–617. doi: 10.1111/bjh.14463. PubMed DOI

Unnikrishnan A., Papaemmanuil E., Beck D., Deshpande N.P., Verma A., Kumari A., Woll P.S., Richards L.A., Knezevic K., Chandrakanthan V., et al. Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes. Cell Rep. 2017;20:572–585. doi: 10.1016/j.celrep.2017.06.067. PubMed DOI

Gruber E., Franich R.L., Shortt J., Johnstone R.W., Kats L.M. Distinct and Overlapping Mechanisms of Resistance to Azacytidine and Guadecitabine in Acute Myeloid Leukemia. Leukemia. 2020;34:3388–3392. doi: 10.1038/s41375-020-0973-z. PubMed DOI

Herwig R., Hardt C., Lienhard M., Kamburov A. Analyzing and Interpreting Genome Data at the Network Level with ConsensusPathDB. Nat. Protoc. 2016;11:1889–1907. doi: 10.1038/nprot.2016.117. PubMed DOI

Ali A., Penneroux J., Dal Bello R., Massé A., Quentin S., Unnikrishnan A., Hernandez L., Raffoux E., Ben Abdelali R., Renneville A., et al. Granulomonocytic Progenitors Are Key Target Cells of Azacytidine in Higher Risk Myelodysplastic Syndromes and Acute Myeloid Leukemia. Leukemia. 2018;32:1856–1860. doi: 10.1038/s41375-018-0076-2. PubMed DOI

Beerman I., Seita J., Inlay M.A., Weissman I.L., Rossi D.J. Quiescent Hematopoietic Stem Cells Accumulate DNA Damage during Aging That Is Repaired upon Entry into Cell Cycle. Cell Stem Cell. 2014;15:37–50. doi: 10.1016/j.stem.2014.04.016. PubMed DOI PMC

Pearl L.H., Schierz A.C., Ward S.E., Al-Lazikani B., Pearl F.M.G. Therapeutic Opportunities within the DNA Damage Response. Nat. Rev. Cancer. 2015;15:166–180. doi: 10.1038/nrc3891. PubMed DOI

Nabatiyan A., Szüts D., Krude T. Induction of CAF-1 Expression in Response to DNA Strand Breaks in Quiescent Human Cells. Mol. Cell. Biol. 2006;26:1839–1849. doi: 10.1128/MCB.26.5.1839-1849.2006. PubMed DOI PMC

Vitale I., Manic G., De Maria R., Kroemer G., Galluzzi L. DNA Damage in Stem Cells. Mol. Cell. 2017;66:306–319. doi: 10.1016/j.molcel.2017.04.006. PubMed DOI

Shin J.J., Schröder M.S., Caiado F., Wyman S.K., Bray N.L., Bordi M., Dewitt M.A., Vu J.T., Kim W.-T., Hockemeyer D., et al. Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells. Cell Rep. 2020;32:108093. doi: 10.1016/j.celrep.2020.108093. PubMed DOI PMC

Stevens B.M., Khan N., D’Alessandro A., Nemkov T., Winters A., Jones C.L., Zhang W., Pollyea D.A., Jordan C.T. Characterization and Targeting of Malignant Stem Cells in Patients with Advanced Myelodysplastic Syndromes. Nat. Commun. 2018;9:3694. doi: 10.1038/s41467-018-05984-x. PubMed DOI PMC

Guo B., Zhai D., Cabezas E., Welsh K., Nouraini S., Satterthwait A.C., Reed J.C. Humanin Peptide Suppresses Apoptosis by Interfering with Bax Activation. Nature. 2003;423:456–461. doi: 10.1038/nature01627. PubMed DOI

Sun D., Luo M., Jeong M., Rodriguez B., Xia Z., Hannah R., Wang H., Le T., Faull K.F., Chen R., et al. Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging That Reinforce Self-Renewal. Cell Stem Cell. 2014;14:673–688. doi: 10.1016/j.stem.2014.03.002. PubMed DOI PMC

Cabezas-Wallscheid N., Klimmeck D., Hansson J., Lipka D.B., Reyes A., Wang Q., Weichenhan D., Lier A., von Paleske L., Renders S., et al. Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis. Cell Stem Cell. 2014;15:507–522. doi: 10.1016/j.stem.2014.07.005. PubMed DOI

Poloni A., Goteri G., Zizzi A., Serrani F., Trappolini S., Costantini B., Mariani M., Olivieri A., Catarini M., Centurioni R., et al. Prognostic Role of Immunohistochemical Analysis of 5 Mc in Myelodysplastic Syndromes. Eur. J. Haematol. 2013;91:219–227. doi: 10.1111/ejh.12145. PubMed DOI

Gawlitza A.L., Speith J., Rinke J., Sajzew R., Müller E.K., Schäfer V., Hochhaus A., Ernst T. 5-Azacytidine Modulates CpG Methylation Levels of EZH2 and NOTCH1 in Myelodysplastic Syndromes. J. Cancer Res. Clin. Oncol. 2019;145:2835–2843. doi: 10.1007/s00432-019-03016-9. PubMed DOI

Grövdal M., Karimi M., Tobiasson M., Reinius L., Jansson M., Ekwall K., Ungerstedt J., Kere J., Greco D., Hellström-Lindberg E. Azacitidine Induces Profound Genome-Wide Hypomethylation in Primary Myelodysplastic Bone Marrow Cultures but May Also Reduce Histone Acetylation. Leukemia. 2014;28:411–413. doi: 10.1038/leu.2013.265. PubMed DOI

Tobiasson M., Abdulkadir H., Lennartsson A., Katayama S., Marabita F., Paepe A.D., Karimi M., Krjutskov K., Einarsdottir E., Grövdal M., et al. Comprehensive Mapping of the Effects of Azacitidine on DNA Methylation, Repressive/Permissive Histone Marks and Gene Expression in Primary Cells from Patients with MDS and MDS-Related Disease. Oncotarget. 2017;8:28812–28825. doi: 10.18632/oncotarget.15807. PubMed DOI PMC

Kuendgen A., Müller-Thomas C., Lauseker M., Haferlach T., Urbaniak P., Schroeder T., Brings C., Wulfert M., Meggendorfer M., Hildebrandt B., et al. Efficacy of Azacitidine Is Independent of Molecular and Clinical Characteristics—An Analysis of 128 Patients with Myelodysplastic Syndromes or Acute Myeloid Leukemia and a Review of the Literature. Oncotarget. 2018;9:27882–27894. doi: 10.18632/oncotarget.25328. PubMed DOI PMC

Yu J., Li Y., Li T., Li Y., Xing H., Sun H., Sun L., Wan D., Liu Y., Xie X., et al. Gene Mutational Analysis by NGS and Its Clinical Significance in Patients with Myelodysplastic Syndrome and Acute Myeloid Leukemia. Exp. Hematol. Oncol. 2020;9:2. doi: 10.1186/s40164-019-0158-5. PubMed DOI PMC

Reid M.A., Dai Z., Locasale J.W. The Impact of Cellular Metabolism on Chromatin Dynamics and Epigenetics. Nat. Cell Biol. 2017;19:1298–1306. doi: 10.1038/ncb3629. PubMed DOI PMC

Pollyea D.A., Stevens B.M., Jones C.L., Winters A., Pei S., Minhajuddin M., D’Alessandro A., Culp-Hill R., Riemondy K.A., Gillen A.E., et al. Venetoclax with Azacitidine Disrupts Energy Metabolism and Targets Leukemia Stem Cells in Patients with Acute Myeloid Leukemia. Nat. Med. 2018;24:1859–1866. doi: 10.1038/s41591-018-0233-1. PubMed DOI PMC

Coller H.A. The Paradox of Metabolism in Quiescent Stem Cells. FEBS Lett. 2019;593:2817–2839. doi: 10.1002/1873-3468.13608. PubMed DOI PMC

Nakamura-Ishizu A., Ito K., Suda T. Hematopoietic Stem Cell Metabolism during Development and Aging. Dev. Cell. 2020;54:239–255. doi: 10.1016/j.devcel.2020.06.029. PubMed DOI PMC

Raffel S., Falcone M., Kneisel N., Hansson J., Wang W., Lutz C., Bullinger L., Poschet G., Nonnenmacher Y., Barnert A., et al. BCAT1 Restricts AKG Levels in AML Stem Cells Leading to IDHmut-like DNA Hypermethylation. Nature. 2017;551:384–388. doi: 10.1038/nature24294. PubMed DOI

Rashkovan M., Ferrando A. Metabolic Dependencies and Vulnerabilities in Leukemia. Genes Dev. 2019;33:1460–1474. doi: 10.1101/gad.326470.119. PubMed DOI PMC

Kinnaird A., Zhao S., Wellen K.E., Michelakis E.D. Metabolic Control of Epigenetics in Cancer. Nat. Rev. Cancer. 2016;16:694–707. doi: 10.1038/nrc.2016.82. PubMed DOI

Etchegaray J.-P., Mostoslavsky R. Interplay between Metabolism and Epigenetics: A Nuclear Adaptation to Environmental Changes. Mol. Cell. 2016;62:695–711. doi: 10.1016/j.molcel.2016.05.029. PubMed DOI PMC

Wellen K.E., Hatzivassiliou G., Sachdeva U.M., Bui T.V., Cross J.R., Thompson C.B. ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation. Science. 2009;324:1076–1080. doi: 10.1126/science.1164097. PubMed DOI PMC

Ghoshal K., Datta J., Majumder S., Bai S., Kutay H., Motiwala T., Jacob S.T. 5-Aza-Deoxycytidine Induces Selective Degradation of DNA Methyltransferase 1 by a Proteasomal Pathway That Requires the KEN Box, Bromo-Adjacent Homology Domain, and Nuclear Localization Signal. Mol. Cell. Biol. 2005;25:4727–4741. doi: 10.1128/MCB.25.11.4727-4741.2005. PubMed DOI PMC

Issa J.-P.J., Kantarjian H.M. Targeting DNA Methylation. Clin. Cancer Res. 2009;15:3938–3946. doi: 10.1158/1078-0432.CCR-08-2783. PubMed DOI PMC

Solly F., Koering C., Mohamed A.M., Maucort-Boulch D., Robert G., Auberger P., Flandrin-Gresta P., Adès L., Fenaux P., Kosmider O., et al. An MiRNA–DNMT1 Axis Is Involved in Azacitidine Resistance and Predicts Survival in Higher-Risk Myelodysplastic Syndrome and Low Blast Count Acute Myeloid Leukemia. Clin. Cancer Res. 2017;23:3025–3034. doi: 10.1158/1078-0432.CCR-16-2304. PubMed DOI

Vispé S., Deroide A., Davoine E., Desjobert C., Lestienne F., Fournier L., Novosad N., Bréand S., Besse J., Busato F., et al. Consequences of Combining SiRNA-Mediated DNA Methyltransferase 1 Depletion with 5-Aza-2′-Deoxycytidine in Human Leukemic KG1 Cells. Oncotarget. 2015;6:15265–15282. doi: 10.18632/oncotarget.3317. PubMed DOI PMC

Kimura H. Transcription of Mouse DNA Methyltransferase 1 (Dnmt1) Is Regulated by Both E2F-Rb-HDAC-Dependent and -Independent Pathways. Nucleic Acids Res. 2003;31:3101–3113. doi: 10.1093/nar/gkg406. PubMed DOI PMC

Singh V., Sharma P., Capalash N. DNA Methyltransferase-1 Inhibitors as Epigenetic Therapy for Cancer. Curr. Cancer Drug Targets. 2013;13:379–399. doi: 10.2174/15680096113139990077. PubMed DOI

Wong K.K., Lawrie C.H., Green T.M. Oncogenic Roles and Inhibitors of DNMT1, DNMT3A, and DNMT3B in Acute Myeloid Leukaemia. Biomark Insights. 2019;14:117727191984645. doi: 10.1177/1177271919846454. PubMed DOI PMC

Daugas E., Nochy D., Ravagnan L., Loeffler M., Susin S.A., Zamzami N., Kroemer G. Apoptosis-Inducing Factor (AIF): A Ubiquitous Mitochondrial Oxidoreductase Involved in Apoptosis. FEBS Lett. 2000;476:118–123. doi: 10.1016/S0014-5793(00)01731-2. PubMed DOI

Vaquero A., Scher M., Lee D., Erdjument-Bromage H., Tempst P., Reinberg D. Human SirT1 Interacts with Histone H1 and Promotes Formation of Facultative Heterochromatin. Mol. Cell. 2004;16:93–105. doi: 10.1016/j.molcel.2004.08.031. PubMed DOI

Baur A.S., Meugé-Moraw C., Schmidt P.-M., Parlier V., Jotterand M., Delacrétaz F. CD34/QBEND10 Immunostaining in Bone Marrow Biopsies: An Additional Parameterfor the Diagnosis and Classification of Myelodysplastic Syndromes: CD34 in Myelodysplastic Syndromes. Eur. J. Haematol. 2000;64:71–79. doi: 10.1034/j.1600-0609.2000.90047.x. PubMed DOI

Pollyea D.A., Jordan C.T. Therapeutic Targeting of Acute Myeloid Leukemia Stem Cells. Blood. 2017;129:1627–1635. doi: 10.1182/blood-2016-10-696039. PubMed DOI

Thomas D., Majeti R. Biology and Relevance of Human Acute Myeloid Leukemia Stem Cells. Blood. 2017;129:1577–1585. doi: 10.1182/blood-2016-10-696054. PubMed DOI PMC

Will B., Zhou L., Vogler T.O., Ben-Neriah S., Schinke C., Tamari R., Yu Y., Bhagat T.D., Bhattacharyya S., Barreyro L., et al. Stem and Progenitor Cells in Myelodysplastic Syndromes Show Aberrant Stage-Specific Expansion and Harbor Genetic and Epigenetic Alterations. Blood. 2012;120:2076–2086. doi: 10.1182/blood-2011-12-399683. PubMed DOI PMC

Chen J., Kao Y.-R., Sun D., Todorova T.I., Reynolds D., Narayanagari S.-R., Montagna C., Will B., Verma A., Steidl U. Myelodysplastic Syndrome Progression to Acute Myeloid Leukemia at the Stem Cell Level. Nat. Med. 2019;25:103–110. doi: 10.1038/s41591-018-0267-4. PubMed DOI PMC

Shastri A., Will B., Steidl U., Verma A. Stem and Progenitor Cell Alterations in Myelodysplastic Syndromes. Blood. 2017;129:1586–1594. doi: 10.1182/blood-2016-10-696062. PubMed DOI PMC

Mejia-Ramirez E., Florian M.C. Understanding Intrinsic Hematopoietic Stem Cell Aging. Haematologica. 2020;105:22–37. doi: 10.3324/haematol.2018.211342. PubMed DOI PMC

Huang H., Xu C., Gao J., Li B., Qin T., Xu Z., Ren S., Zhang Y., Jiao M., Qu S., et al. Severe Ineffective Erythropoiesis Discriminates Prognosis in Myelodysplastic Syndromes: Analysis Based on 776 Patients from a Single Centre. Blood Cancer J. 2020;10:83. doi: 10.1038/s41408-020-00349-4. PubMed DOI PMC

Sancho M., Diani E., Beato M., Jordan A. Depletion of Human Histone H1 Variants Uncovers Specific Roles in Gene Expression and Cell Growth. PLoS Genet. 2008;4:e1000227. doi: 10.1371/journal.pgen.1000227. PubMed DOI PMC

Hakimi A.A., Reznik E., Lee C.-H., Creighton C.J., Brannon A.R., Luna A., Aksoy B.A., Liu E.M., Shen R., Lee W., et al. An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell. 2016;29:104–116. doi: 10.1016/j.ccell.2015.12.004. PubMed DOI PMC

Rist M.J., Roth A., Frommherz L., Weinert C.H., Krüger R., Merz B., Bunzel D., Mack C., Egert B., Bub A., et al. Metabolite Patterns Predicting Sex and Age in Participants of the Karlsruhe Metabolomics and Nutrition (KarMeN) Study. PLoS ONE. 2017;12:e0183228. doi: 10.1371/journal.pone.0183228. PubMed DOI PMC

Krumsiek J., Mittelstrass K., Do K.T., Stückler F., Ried J., Adamski J., Peters A., Illig T., Kronenberg F., Friedrich N., et al. Gender-Specific Pathway Differences in the Human Serum Metabolome. Metabolomics. 2015;11:1815–1833. doi: 10.1007/s11306-015-0829-0. PubMed DOI PMC

Vignoli A., Tenori L., Luchinat C., Saccenti E. Age and Sex Effects on Plasma Metabolite Association Networks in Healthy Subjects. J. Proteome Res. 2018;17:97–107. doi: 10.1021/acs.jproteome.7b00404. PubMed DOI

Schvartzman J.M., Thompson C.B., Finley L.W.S. Metabolic Regulation of Chromatin Modifications and Gene Expression. J. Cell Biol. 2018;217:2247–2259. doi: 10.1083/jcb.201803061. PubMed DOI PMC

Diehl K.L., Muir T.W. Chromatin as a Key Consumer in the Metabolite Economy. Nat. Chem. Biol. 2020;16:620–629. doi: 10.1038/s41589-020-0517-x. PubMed DOI PMC

Beisel C., Paro R. Silencing Chromatin: Comparing Modes and Mechanisms. Nat. Rev. Genet. 2011;12:123–135. doi: 10.1038/nrg2932. PubMed DOI

Toffalorio F., Santarpia M., Radice D., Jaramillo C.A., Spitaleri G., Manzotti M., Catania C., Jordheim L.P., Pelosi G., Peters G.J., et al. 5′-Nucleotidase CN-II Emerges as a New Predictive Biomarker of Response to Gemcitabine/Platinum Combination Chemotherapy in Non-Small Cell Lung Cancer. Oncotarget. 2018;9:16437–16450. doi: 10.18632/oncotarget.24505. PubMed DOI PMC

Quagliano A., Gopalakrishnapillai A., Barwe S.P. Understanding the Mechanisms by Which Epigenetic Modifiers Avert Therapy Resistance in Cancer. Front. Oncol. 2020;10:992. doi: 10.3389/fonc.2020.00992. PubMed DOI PMC

Cameron E.E., Bachman K.E., Myöhänen S., Herman J.G., Baylin S.B. Synergy of Demethylation and Histone Deacetylase Inhibition in the Re-Expression of Genes Silenced in Cancer. Nat. Genet. 1999;21:103–107. doi: 10.1038/5047. PubMed DOI

Zhang B., Strauss A.C., Chu S., Li M., Ho Y., Shiang K.-D., Snyder D.S., Huettner C.S., Shultz L., Holyoake T., et al. Effective Targeting of Quiescent Chronic Myelogenous Leukemia Stem Cells by Histone Deacetylase Inhibitors in Combination with Imatinib Mesylate. Cancer Cell. 2010;17:427–442. doi: 10.1016/j.ccr.2010.03.011. PubMed DOI PMC

Kovaka S., Zimin A.V., Pertea G.M., Razaghi R., Salzberg S.L., Pertea M. Transcriptome Assembly from Long-Read RNA-Seq Alignments with StringTie2. Genome Biol. 2019;20:278. doi: 10.1186/s13059-019-1910-1. PubMed DOI PMC

Babicki S., Arndt D., Marcu A., Liang Y., Grant J.R., Maciejewski A., Wishart D.S. Heatmapper: Web-Enabled Heat Mapping for All. Nucleic Acids Res. 2016;44:W147–W153. doi: 10.1093/nar/gkw419. PubMed DOI PMC

Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., Paulovich A., Pomeroy S.L., Golub T.R., Lander E.S., et al. Gene Set Enrichment Analysis: A Knowledge-Based Approach for Interpreting Genome-Wide Expression Profiles. Proc. Natl. Acad. Sci. USA. 2005;102:15545–15550. doi: 10.1073/pnas.0506580102. PubMed DOI PMC

Arber D.A., Orazi A., Hasserjian R., Thiele J., Borowitz M.J., Le Beau M.M., Bloomfield C.D., Cazzola M., Vardiman J.W. The 2016 Revision to the World Health Organization Classification of Myeloid Neoplasms and Acute Leukemia. Blood. 2016;127:2391–2405. doi: 10.1182/blood-2016-03-643544. PubMed DOI

Cheson B.D. Clinical Application and Proposal for Modification of the International Working Group (IWG) Response Criteria in Myelodysplasia. Blood. 2006;108:419–425. doi: 10.1182/blood-2005-10-4149. PubMed DOI

Noncoding RNAs and Their Response Predictive Value in Azacitidine-treated Patients With Myelodysplastic Syndrome and Acute Myeloid Leukemia With Myelodysplasia-related Changes