{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:03:06Z","timestamp":1760058186496,"version":"build-2065373602"},"reference-count":41,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,3,18]],"date-time":"2025-03-18T00:00:00Z","timestamp":1742256000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Novartis, Italy","award":["Not applicable"],"award-info":[{"award-number":["Not applicable"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>Background: Chronic-Phase Chronic Myeloid Leukemia (C-PCML) is defined by the presence of the BCR-ABL1 fusion gene, which encodes a tyrosine kinase protein that drives the uncontrolled proliferation and survival of leukemic stem cells (LSCs). Nilotinib, a tyrosine kinase inhibitor, targets the activity of BCR-ABL1 by reducing aberrant signaling pathways, which drive the regeneration of LSCs. Despite nilotinib\u2019s action, a population of resilient LSCs persist in the bone marrow (BM) and can indeed drive relapse and progression in CML patients. Methods: Our study investigated the gene expression profiling (GEP) of BM CD34+\/lin\u2212 cells from 79 CP-CML patients at diagnosis, compared to the BM CD34+\/lin\u2212 cells from the same patients after 12 months of nilotinib treatment and to the normal counterpart cells from 10 donors (CTRLs). Results: GEP analyses identified 3012 significantly differentially expressed genes across these comparisons. Among these, we focused on certain key genes associated with eight crucial KEGG pathways: CML, cell cycle, JAK-STAT, PI3K-Akt, MAPK, Ras, NF-kB, and ABC transporters. Within these pathways, we observed the up-regulation of several genes at diagnosis compared to both 12 months of nilotinib treatment and the CTRLs. Conclusions: We observed that certain transcriptome features present at diagnosis persisted after 12 months of nilotinib treatment, compared to CTRLs. This suggests that nilotinib may exert selective pressure, potentially supporting the survival and self-renewal of LSCs. Future insights into these pathways could help identify therapeutic targets to improve outcomes in CML.<\/jats:p>","DOI":"10.3390\/cancers17061022","type":"journal-article","created":{"date-parts":[[2025,3,18]],"date-time":"2025-03-18T10:43:51Z","timestamp":1742294631000},"page":"1022","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Bone Marrow CD34+\/lin\u2212 Cells of Patients with Chronic-Phase Chronic Myeloid Leukemia (CP-CML) After 12 Months of Nilotinib Treatment Exhibit a Different Gene Expression Signature Compared to the Diagnosis and the Corresponding Cells from Healthy Subjects"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7659-2968","authenticated-orcid":false,"given":"Alessandra","family":"Trojani","sequence":"first","affiliation":[{"name":"Department of Hematology and Oncology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ester","family":"Pungolino","sequence":"additional","affiliation":[{"name":"Department of Hematology and Oncology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8415-4688","authenticated-orcid":false,"given":"Barbara","family":"Di Camillo","sequence":"additional","affiliation":[{"name":"Department of Information Engineering, University of Padova, 35131 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6409-8391","authenticated-orcid":false,"given":"Luca Emanuele","family":"Bossi","sequence":"additional","affiliation":[{"name":"Department of Hematology and Oncology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3677-0499","authenticated-orcid":false,"given":"Cassandra","family":"Palumbo","sequence":"additional","affiliation":[{"name":"Department of Hematology and Oncology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-3432-3373","authenticated-orcid":false,"given":"Mariella","family":"D\u2019adda","sequence":"additional","affiliation":[{"name":"Department of Hematology and Oncology, ASST Spedali Civili Brescia, 25123 Brescia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandra","family":"Perego","sequence":"additional","affiliation":[{"name":"Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5299-8456","authenticated-orcid":false,"given":"Mauro","family":"Turrini","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Valduce Hospital, 22100 Como, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chiara","family":"Elena","sequence":"additional","affiliation":[{"name":"Department of Hematology Oncology, Foundation IRCCS Policlinico San Matteo, 27100 Pavia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lorenza Maria","family":"Borin","sequence":"additional","affiliation":[{"name":"Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4401-0812","authenticated-orcid":false,"given":"Alessandra","family":"Iurlo","sequence":"additional","affiliation":[{"name":"Hematology Division, Fondazione IRCCS Ca\u2019 Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simona","family":"Malato","sequence":"additional","affiliation":[{"name":"Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Unit, 20123 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Spina","sequence":"additional","affiliation":[{"name":"Department of Hematology and Oncology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Luisa","family":"Latargia","sequence":"additional","affiliation":[{"name":"ASST Valle Olona Ospedale di Circolo, 21052 Busto Arstizio, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierangelo","family":"Spedini","sequence":"additional","affiliation":[{"name":"ASST Cremona, 26100 Cremona, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Salvatore","family":"Artale","sequence":"additional","affiliation":[{"name":"ASST Brianza, 20871 Vimercate, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michela","family":"Anghilieri","sequence":"additional","affiliation":[{"name":"ASST Lecco, 23900 Lecco, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Cristina","family":"Carraro","sequence":"additional","affiliation":[{"name":"ASST Fatebenefratelli Sacco, 20157 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristina","family":"Bucelli","sequence":"additional","affiliation":[{"name":"Hematology Division, Fondazione IRCCS Ca\u2019 Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8234-3474","authenticated-orcid":false,"given":"Alessandro","family":"Beghini","sequence":"additional","affiliation":[{"name":"Department of Health Sciences, University of Milano, 20146 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6372-2623","authenticated-orcid":false,"given":"Roberto","family":"Cairoli","sequence":"additional","affiliation":[{"name":"Department of Hematology and Oncology, ASST Grande Ospedale Metropolitano Niguarda, 20162 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,3,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Zhai, X., and Jiang, X. (2022). Properties of Leukemic Stem Cells in Regulating Drug Resistance in Acute and Chronic Myeloid Leukemias. Biomedicines, 10.","DOI":"10.3390\/biomedicines10081841"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/s41408-023-00823-9","article-title":"Management of chronic myeloid leukemia in 2023-common ground and common sense","volume":"13","author":"Senapati","year":"2023","journal-title":"Blood Cancer J."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"175","DOI":"10.7150\/ijbs.86305","article-title":"Mechanisms underlying therapeutic resistance of tyrosine kinase inhibitors in chronic myeloid leukemia","volume":"20","author":"Sun","year":"2024","journal-title":"Int. J. Biol. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2142","DOI":"10.1038\/s41375-021-01306-1","article-title":"Long-term outcomes with frontline nilotinib versus imatinib in newly diagnosed chronic myeloid leukemia in chronic phase: ENESTnd 10-year analysis","volume":"35","author":"Kantarjian","year":"2021","journal-title":"Leukemia"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1186\/s13287-021-02659-1","article-title":"Chronic myeloid leukemia stem cells: Targeting therapeutic implications","volume":"12","author":"Mojtahedi","year":"2021","journal-title":"Stem Cell Res. Ther."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Alves, R., Gon\u00e7alves, A.C., Rutella, S., Almeida, A.M., De Las Rivas, J., Trougakos, I.P., and Sarmento Ribeiro, A.B. (2021). Resistance to Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia-From Molecular Mechanisms to Clinical Relevance. Cancers, 13.","DOI":"10.3390\/cancers13194820"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Muselli, F., Peyron, J.F., and Mary, D. (2019). Druggable Biochemical Pathways and Potential Therapeutic Alternatives to Target Leukemic Stem Cells and Eliminate the Residual Disease in Chronic Myeloid Leukemia. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20225616"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Ito, K., and Ito, K. (2021). Leukemia Stem Cells as a Potential Target to Achieve Therapy-Free Remission in Chronic Myeloid Leukemia. Cancers, 13.","DOI":"10.3390\/cancers13225822"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"E162","DOI":"10.1002\/ajh.25106","article-title":"Nilotinib induced bone marrow CD34+\/lin\u2212Ph+ cells early clearance in newly diagnosed CP-chronic myeloid leukemia","volume":"93","author":"Pungolino","year":"2018","journal-title":"Am. J. Hematol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1111\/ejh.13680","article-title":"Nilotinib-induced bone marrow CD34+\/lin\u2212Ph+ cells early clearance in newly diagnosed CP-Chronic Myeloid Leukemia: Final report of the PhilosoPhi34 study","volume":"107","author":"Pungolino","year":"2021","journal-title":"Eur. J. Haematol."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Trojani, A., Pungolino, E., Dal Molin, A., Lodola, M., Rossi, G., D\u2019Adda, M., Perego, A., Elena, C., Turrini, M., and Borin, L. (2019). Nilotinib interferes with cell cycle, ABC transporters and JAK-STAT signaling pathway in CD34+\/lin\u2212 cells of patients with chronic phase chronic myeloid leukemia after 12 months of treatment. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0218444"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"41","DOI":"10.3233\/CBM-170209","article-title":"Wide-transcriptome analysis and cellularity of gene CD34+\/lin\u2212 cells of patients with chronic-phase chronic myeloid leukemia at diagnosis vs. 12 months of first-line nilotinib treatment","volume":"21","author":"Trojani","year":"2017","journal-title":"Cancer Biomark"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e15","DOI":"10.1093\/nar\/gng015","article-title":"Summaries of Affymetrix GeneChip probe level data","volume":"31","author":"Irizarry","year":"2003","journal-title":"Nucleic. Acids Res."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1093\/bioinformatics\/btq431","article-title":"A framework for oligonucleotide microarray preprocessing","volume":"26","author":"Carvalho","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1093\/biostatistics\/kxj037","article-title":"Adjusting batch effects in microarray expression data using empirical Bayes methods","volume":"8","author":"Johnson","year":"2007","journal-title":"Biostatistics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5116","DOI":"10.1073\/pnas.091062498","article-title":"Significance analysis of microarrays applied to the ionizing radiation response","volume":"98","author":"Tusher","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1111\/1467-9868.00346","article-title":"A direct approach to false Discovery Rate","volume":"64","author":"Storey","year":"2002","journal-title":"J. R. Stat. Soc. Ser. B Stat. Methodol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Sherman","year":"2009","journal-title":"Nat. Protoc."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Sherman","year":"2009","journal-title":"Nucleic. Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3356","DOI":"10.3390\/molecules19033356","article-title":"Nilotinib enhances the efficacy of conventional chemotherapeutic drugs in CD34\u207aCD38\u207b stem cells and ABC transporter overexpressing leukemia cells","volume":"19","author":"Wang","year":"2014","journal-title":"Molecules"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Amarante-Mendes, G.P., Rana, A., Datoguia, T.S., Hamerschlak, N., and Brumatti, G. (2022). BCR-ABL1 Tyrosine Kinase Complex Signaling Transduction: Challenges to Overcome Resistance in Chronic Myeloid Leukemia. Pharmaceutics, 14.","DOI":"10.3390\/pharmaceutics14010215"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1039\/C9RA07971H","article-title":"CAY10683 and imatinib have synergistic effects in overcoming imatinib resistance via HDAC2 inhibition in chronic myeloid leukemia","volume":"10","author":"Zhang","year":"2020","journal-title":"RSC Adv."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Duncker, B.P., Chesnokov, I.N., and McConkey, B.J. (2009). The origin recognition complex protein family. Genome Biol., 10.","DOI":"10.1186\/gb-2009-10-3-214"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1016\/j.ccr.2010.03.011","article-title":"Effective Targeting of Quiescent Chronic Myelogenous Leukemia Stem Cells by Histone Deacetylase Inhibitors in Combination with Imatinib Mesylate","volume":"17","author":"Zhang","year":"2010","journal-title":"Cancer Cell"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2348","DOI":"10.1158\/1078-0432.CCR-14-1290","article-title":"Selective Inhibition of HDAC1 and HDAC2 as a Potential Therapeutic Option for B-ALL","volume":"21","author":"Stubbs","year":"2015","journal-title":"Clin. Cancer Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.ebiom.2019.11.004","article-title":"CDK4\/CDK6 inhibition as a novel strategy to suppress the growth and survival of BCR-ABL1T315I+ clones in TKI-resistant CML","volume":"50","author":"Byrgazov","year":"2019","journal-title":"EBioMedicine"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/s41419-025-07434-1","article-title":"CDK6 kinase inhibition unmasks metabolic dependencies in BCR::ABL1+ leukemia","volume":"16","author":"Scheiblecker","year":"2025","journal-title":"Cell Death Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1038\/s41419-018-0905-2","article-title":"Chronic myeloid leukaemia cells require the bone morphogenic protein pathway for cell cycle progression and self-renewal","volume":"9","author":"Toofan","year":"2018","journal-title":"Cell Death Dis."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1007\/s12032-021-01462-5","article-title":"Combating TKI resistance in CML by inhibiting the PI3K\/Akt\/mTOR pathway in combination with TKIs: A review","volume":"38","author":"Singh","year":"2021","journal-title":"Med. Oncol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1016\/j.ygyno.2019.08.028","article-title":"Anti-tumor activity of dual inhibition of phosphatidylinositol 3-kinase and MDM2 against clear cell ovarian carcinoma","volume":"155","author":"Makii","year":"2019","journal-title":"Gynecol. Oncol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/s41467-024-44771-9","article-title":"Activating p53 abolishes self-renewal of quiescent leukaemic stem cells in residual CML disease","volume":"15","author":"Scott","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e827","DOI":"10.1038\/cddis.2013.309","article-title":"PI3K\/mTOR pathway inhibitors sensitize chronic myeloid leukemia stem cells to nilotinib and restore the response of progenitors to nilotinib in the presence of stem cell factor","volume":"4","author":"Airiau","year":"2013","journal-title":"Cell Death Dis."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Li, B., Wan, Q., Li, Z., and Chng, W.J. (2021). Janus Kinase Signaling: Oncogenic Criminal of Lymphoid Cancers. Cancers, 13.","DOI":"10.3390\/cancers13205147"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1016\/j.leukres.2011.12.002","article-title":"Potentiation of Nilotinib-mediated cell death in the context of the bone marrow microenvironment requires a promiscuous JAK inhibitor in CML","volume":"36","author":"Nair","year":"2012","journal-title":"Leuk. Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1976","DOI":"10.1038\/s41375-020-01088-y","article-title":"A novel model of alternative NF-\u03baB pathway activation in anaplastic large cell lymphoma","volume":"35","author":"Wang","year":"2021","journal-title":"Leukemia"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"66287","DOI":"10.18632\/oncotarget.11507","article-title":"The BCR-ABL\/NF-\u03baB signal transduction network: A long lasting relationship in Philadelphia positive Leukemias","volume":"7","author":"Torti","year":"2016","journal-title":"Oncotarget"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Berger, M.G., Lebecque, B., Tassin, T., Dannus, L.T., Berger, J., Soucal, M., Guerci, A., Cony-Makhoul, P., Johnson, H., and Etienne, G. (2021). Efficiency of nilotinib to target chronic phase-chronic myeloid leukaemia primary mature CD34\u2212 and immature CD34+\u2009cells. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-85734-0"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1182\/blood.V99.1.319","article-title":"Primitive, quiescent, Philadelphia-positive stem cells from patients with chronic myeloid leukemia are insensitive to STI571 in vitro","volume":"99","author":"Graham","year":"2002","journal-title":"Blood"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"4016","DOI":"10.1182\/blood-2006-11-057521","article-title":"Nilotinib exerts equipotent antiproliferative effects to imatinib and does not induce apoptosis in CD34+ CML cells","volume":"109","author":"Allan","year":"2007","journal-title":"Blood"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/s41392-022-01168-8","article-title":"Protein tyrosine kinase inhibitor resistance in malignant tumors: Molecular mechanisms and future perspective","volume":"7","author":"Yang","year":"2022","journal-title":"Signal Transduct Target. Ther."},{"key":"ref_41","first-page":"1289","article-title":"MicroRNA-145 promotes the apoptosis of leukemic stem cells and enhances drug-resistant K562\/ADM cell sensitivity to adriamycin via the regulation of ABCE1","volume":"46","author":"Wuxiao","year":"2020","journal-title":"Int. J. Mol. Med."}],"container-title":["Cancers"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2072-6694\/17\/6\/1022\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:56:02Z","timestamp":1760028962000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2072-6694\/17\/6\/1022"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3,18]]},"references-count":41,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,3]]}},"alternative-id":["cancers17061022"],"URL":"https:\/\/doi.org\/10.3390\/cancers17061022","relation":{},"ISSN":["2072-6694"],"issn-type":[{"type":"electronic","value":"2072-6694"}],"subject":[],"published":{"date-parts":[[2025,3,18]]}}}