The distinct expression features between chronic phase and B-lymphoblastic crisis samples from patients with CML
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE337046 | GEO | 2026/06/30
REPOSITORIES: GEO
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Project description:Background: Chronic myeloid leukemia (CML) is a biphasic clonal hematopoietic stem cell disorder driven by the Philadelphia chromosome (Ph)-encoded BCR::ABL1 oncogene. The blast phase (BP) in CML progressed from indolent chronic phase (CP), usually has a dismal outcome. Single-cell RNA sequencing (scRNA-seq) have identified the pretreatment features linked to therapy resistance and disease progression. However, data on CML in B-cell lymphoblastic crisis (BLBC) remain limited. Methods: We performed the scRNA-seq on bone marrow cells derived from paired CML-CP and CML-BLBC samples to evaluate their underlying cellular heterogeneity. and. Additionally, we also unveil the distinct gene expression signatures of BLBC samples by comparing with CP samples and de novo Ph-positive (Ph+) B-cell acute lymphoblastic leukemia (B-ALL) samples. Results: By constructing a single-cell atlas, we delineated that the hematopoietic lineage of different patients skewed towards to erythroid or myeloid progenitors at their CP diagnosis respectively, which was consistent with the enrichment of gene sets related to canonical erythroid regulator GATA1 and myeloid regulator EVI1. Patient-specific B-cell progenitor types including PreB, ProB, and ImmatureB cells further illustrated the clear inter-tumor heterogeneity within CML-BLBC samples. Comparative analysis revealed that CP cells presented strong proliferation and oxidative phosphorylation characteristics, and BLBC cell populations had a series of unique expression features encompassing elevated stemness and relative quiescence, enhanced inflammatory (interferon gamma [IFN-γ], IFN-α, IL12, and IL6) and apoptotic signaling pathways, as well as ed previously unreported augmentation in ERBB2 and epithelial to mesenchymal transition (EMT) pathways. In single-cell data of CML-BLBC, we also confirmed a remarkably increased expression of DNTT which has been shown to predict BLBC transformation at diagnosis. Importantly, CD24 displayed a striking upregulation in CML-BLBC samples when compared with both the CML-CP and Ph+ B-ALL samples, suggesting the potential as a target in the future therapy of patients with CML-BLBC. Conclusion: In summary, our study presents a single-cell atlas which portrays the cellular heterogeneity and distinct cell state of CML-CP and CML-BLBC samples, as well as abnormal high expression of CD24 in patients with CML-BLBC. These findings may imply unique functional behaviors and therapeutic vulnerabilities of CML-BLBC, and thereby facilitating the development of detection methods, further enabling the identification of high-risk CP patients at diagnosis, and preventing the progression to BP through further early intervention.
2026-06-02 | GSE333588 | GEO
Project description:Chronic myeloid leukemia (CML) may transform from a chronic phase (CP) into blast crisis (BC), which is often incurable. Herein, we report that miR-142 deficit acquired by T lymphocytes contributes to BC transformation by promoting immune escape. We observe that T cells of BC patients lack miR-142 and are fewer and exhausted compared with CP patients. Similarly, BC miR-142−/−/BCR/ABL+/+ mouse presents with T lymphopenia compared with the CP miR-142+/+/BCR/ABL+/+ mouse. In the BC mouse, miR-142 deficit impairs thymic differentiation of lymphoid-primed multipotent progenitors (LMPP) into mature T cells and redirects them toward myeloid lineage. The fewer mature T cells in the BC mouse are enriched with exhausted T effectors. MiR-142 deficit, driven by leukemic blasts-secreted inflammatory cytokines (i.e., IL-6), induces T cell hypofunction by preventing the metabolic reprogramming that allows activated T cells to thrive and expand. This ultimately results in an increase in T cell spontaneous apoptosis and BC immune escape. In fact, NSG mice transplanted with BC CML LSKs and miR-142 KO T cells had shorter survival than mice transplanted with BC CML LSKs and miR-142 wild-typewt T cells. Conversely, BC patient-derived xenograft (PDX) mice receiving autologous T cells and synthetic miR-142 lived longer than those receiving autologous T cells and scramble RNA. Combination of tyrosine kinase inhibitors (TKI) plus synthetic miR-142 and/or PD-1 antibody induced a prolonged survival compared to TKI alone, suggesting that harnessing the host immune system with synthetic miR-142 and immunocheckpoint inhibitors along with BCR/ABL inhibition may provide novel therapeutic opportunities.
2024-01-31 | GSE254285 | GEO
Project description:Tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL1 fusion tyrosine kinase have revolutionized the treatment of chronic myeloid leukemia (CML). However, the development of TKI resistance and the subsequent transition from the chronic phase (CP) to blast crisis (BC) threaten CML patients. Accumulating evidence suggests that translational control is crucial for cancer development and progression. Here, we performed high throughput CRISPR/Cas9 screening and identified poly(A) binding protein cytoplasmic 1 (PABPC1) as a driver for CML-BC progression. PABPC1 preferentially improved the translation efficiency of multiple leukemogenic mRNAs with long and highly structured 5' untranslated regions, including BCR-ABL1 and its TKI-resistant mutants, through forming biomolecular condensates. Inhibiting PABPC1 significantly suppressed CML cell proliferation and attenuated disease progression, but did not affect normal hematopoiesis seriously. More importantly, we identified two novel PABPC1 inhibitors, 1,10-Phen and ML324, which inhibited BC progression and overcame TKI resistance in murine and human CML. Overall, our work identified PABPC1 as a selective translation enhancing factor in CML-BC, the genetic or pharmacological inhibition of which overcame TKI resistance and suppressed BC progression in CML.
2024-03-01 | GSE198142 | GEO
Project description:Little is known about the impact of DNA methylation on the evolution/progression of chronic myeloid leukemia (CML). We investigated the methylome of CML patients in chronic phase (CP-CML), accelerated phase (AP-CML) and blast crisis (BC-CML) as well as in controls by reduced representation bisulfite sequencing. While only ~600 differentially methylated CpG sites were identified in samples obtained from CP-CML patients compared to controls, ~6,500 differentially methylated CpG sites were found in cells from BC-CML patients. In the majority of affected CpG sites methylation was increased. In CP-CML patients who progressed to AP-CML/BC-CML, we identified up to 897 genes which were methylated at the time of progression but not at the time of diagnosis. Using RNA-sequencing, we observed downregulated expression of many of these genes in BC-CML compared to CP-CML-derived cells. Several of them are well-known tumor suppressor genes or regulators of cell proliferation. 5-aza-2 -deoxycytidine treatment of CML cells resulted in gene re-expression and in a dose-dependent cell growth reduction. Single nucleotide variants of certain epigenetic modifiers during CML progression were not found. Together, our results demonstrate that methylation changes occur frequently during CML progression and may provide a useful basis for revealing new targets of therapy in advanced CML.
2016-08-01 | E-MTAB-4333 | biostudies-arrayexpress
Project description:Little is known about the impact of DNA methylation on the evolution/progression of chronic myeloid leukemia (CML). We investigated the methylome of CML patients in chronic phase (CP-CML), accelerated phase (AP-CML) and blast crisis (BC-CML) as well as in controls by reduced representation bisulfite sequencing. While only ~600 differentially methylated CpG sites were identified in samples obtained from CP-CML patients compared to controls, ~6,500 differentially methylated CpG sites were found in cells from BC-CML patients. In the majority of affected CpG sites methylation was increased. In CP-CML patients who progressed to AP-CML/BC-CML, we identified up to 897 genes which were methylated at the time of progression but not at the time of diagnosis. Using RNA-sequencing, we observed downregulated expression of many of these genes in BC-CML compared to CP-CML-derived cells. Several of them are well-known tumor suppressor genes or regulators of cell proliferation. 5-aza-2 -deoxycytidine treatment of CML cells resulted in gene re-expression and in a dose-dependent cell growth reduction. Single nucleotide variants of certain epigenetic modifiers during CML progression were not found. Together, our results demonstrate that methylation changes occur frequently during CML progression and may provide a useful basis for revealing new targets of therapy in advanced CML.
2016-08-01 | E-MTAB-4341 | biostudies-arrayexpress
Project description:We observed that T cells from patients with blast crisis (BC) chronic myeloid leukemia (CML) lacked miR-142 and were fewer and exhausted compared with those from patients with chronic phase (CP) CML. Accordingly, the BC Mir142−/−BCR/ABL mouse also presented with T lymphopenia compared with the CP Mir142+/+BCR/ABL mouse. The miR-142 deficit impaired thymic differentiation of lymphoid-primed multipotent progenitors (LMPP) into mature T cells and redirected them toward myeloid lineage. The fewer mature T cells that emerged from LMPP differentiation in the BC mouse were enriched with exhausted T effectors. Leukemic blasts-secreted inflammatory cytokines (i.e., IL-6) mediated the miR-142 deficit, which in turn prevented the metabolic reprogramming that allows activated T cells to thrive and expand and promoted expression of the exhaustion marker PD-1. Thus, loss of miR-142 expression ultimately resulted in BC immune escape and disease growth. In fact, immunodeficient mice transplanted with BC CML LSKs and miR-142 KO T cells had shorter survival than those transplanted with BC CML LSKs and miR-142 wild-type T cells. Conversely, BC patient-derived xenograft (PDX) mice receiving autologous T cells and synthetic miR-142 mimic lived longer than those receiving autologous T cells and scramble RNA. Combination of tyrosine kinase inhibitors (TKI) plus synthetic miR-142 and/or PD-1 antibody induced a prolonged survival compared to TKI alone, suggesting that harnessing the host immune system with synthetic miR-142 may provide a novel therapeutic approach for BC CML.
2024-03-25 | GSE261798 | GEO
Project description:Tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL1 fusion tyrosine kinase have revolutionized the treatment of chronic myeloid leukemia (CML). However, the development of TKI resistance and the subsequent transition from the chronic phase (CP) to blast crisis (BC) threaten CML patients. Accumulating evidence suggests that translational control is crucial for cancer development and progression. Here, we performed high throughput CRISPR/Cas9 screening and identified poly(A) binding protein cytoplasmic 1 (PABPC1) as a driver for CML-BC progression. PABPC1 preferentially improved the translation efficiency of multiple leukemogenic mRNAs with long and highly structured 5' untranslated regions, including BCR-ABL1 and its TKI-resistant mutants, through forming biomolecular condensates. Inhibiting PABPC1 significantly suppressed CML cell proliferation and attenuated disease progression, but did not affect normal hematopoiesis seriously. More importantly, we identified two novel PABPC1 inhibitors, 1,10-Phen and ML324, which inhibited BC progression and overcame TKI resistance in murine and human CML. Overall, our work identified PABPC1 as a selective translation enhancing factor in CML-BC, the genetic or pharmacological inhibition of which overcame TKI resistance and suppressed BC progression in CML.
2024-12-20 | GSE280878 | GEO
Project description:Tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL1 fusion tyrosine kinase have revolutionized the treatment of chronic myeloid leukemia (CML). However, the development of TKI resistance and the subsequent transition from the chronic phase (CP) to blast crisis (BC) threaten CML patients. Accumulating evidence suggests that translational control is crucial for cancer development and progression. Here, we performed high throughput CRISPR/Cas9 screening and identified poly(A) binding protein cytoplasmic 1 (PABPC1) as a driver for CML-BC progression. PABPC1 preferentially improved the translation efficiency of multiple leukemogenic mRNAs with long and highly structured 5' untranslated regions, including BCR-ABL1 and its TKI-resistant mutants, through forming biomolecular condensates. Inhibiting PABPC1 significantly suppressed CML cell proliferation and attenuated disease progression, but did not affect normal hematopoiesis seriously. More importantly, we identified two novel PABPC1 inhibitors, 1,10-Phen and ML324, which inhibited BC progression and overcame TKI resistance in murine and human CML. Overall, our work identified PABPC1 as a selective translation enhancing factor in CML-BC, the genetic or pharmacological inhibition of which overcame TKI resistance and suppressed BC progression in CML.
2024-12-20 | GSE280879 | GEO
Project description:Tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL1 fusion tyrosine kinase have revolutionized the treatment of chronic myeloid leukemia (CML). However, the development of TKI resistance and the subsequent transition from the chronic phase (CP) to blast crisis (BC) threaten CML patients. Accumulating evidence suggests that translational control is crucial for cancer development and progression. Here, we performed high throughput CRISPR/Cas9 screening and identified poly(A) binding protein cytoplasmic 1 (PABPC1) as a driver for CML-BC progression. PABPC1 preferentially improved the translation efficiency of multiple leukemogenic mRNAs with long and highly structured 5' untranslated regions, including BCR-ABL1 and its TKI-resistant mutants, through forming biomolecular condensates. Inhibiting PABPC1 significantly suppressed CML cell proliferation and attenuated disease progression, but did not affect normal hematopoiesis seriously. More importantly, we identified two novel PABPC1 inhibitors, 1,10-Phen and ML324, which inhibited BC progression and overcame TKI resistance in murine and human CML. Overall, our work identified PABPC1 as a selective translation enhancing factor in CML-BC, the genetic or pharmacological inhibition of which overcame TKI resistance and suppressed BC progression in CML.
2024-12-20 | GSE280877 | GEO
Project description:Title: Gene expression analysis of indolent and aggressive forms of Chronic Myeloid Leukaemia (CML). Description: Chronic Myeloid Leukaemia presents in chronic phase (CP) and terminates in 'blast crisis'. Despite a common abnormality, the duration of CP is variable. The aim is to compare the gene expression profiles of the indolent and aggressive forms of CML. All samples were taken within 3 months of first diagnosis. Indolent patients were defined by chronic phase CML, duration minimum 7 years. Aggressive patients were defined by chronic phase, duration maximum 3 years.
2013-01-30 | E-MIMR-17 | biostudies-arrayexpress