PBX3 and MEIS1 Cooperate in Hematopoietic Cells to Drive Acute Myeloid Leukemias Characterized by a Core Transcriptome of the MLL-Rearranged Disease

Overexpression of HOXA/MEIS1/PBX3 homeobox genes is the hallmark of mixed lineage leukemia (MLL)-rearranged acute myeloid leukemia (AML). HOXA9 and MEIS1 are considered to be the most critical targets of MLL fusions and their co-expression rapidly induces AML. MEIS1 and PBX3 are not individually able to transform cells and were therefore hypothesized to function as cofactors of HOXA9. However, in this study we demonstrate that co-expression of PBX3 and MEIS1 (PBX3/MEIS1), without ectopic expression of a HOX gene, is sufficient for transformation of normal mouse hematopoietic stem/progenitor cells in vitro. Moreover, PBX3/MEIS1 overexpression also caused AML in vivo, with a leukemic latency similar to that caused by forced expression of MLL-AF9, the most common form of MLL fusions. Furthermore, gene expression profiling of hematopoietic cells demonstrated that PBX3/MEIS1 overexpression, but not HOXA9/MEIS1, HOXA9/PBX3 or HOXA9 overexpression, recapitulated the MLL-fusion-mediated core transcriptome, particularly upregulation of the endogenous Hoxa genes. Disruption of the binding between MEIS1 and PBX3 diminished PBX3/MEIS1-mediated cell transformation and HOX gene upregulation. Collectively, our studies strongly implicate the PBX3/MEIS1 interaction as a driver of cell transformation and leukemogenesis, and suggest that this axis may play a critical role in the regulation of the core transcriptional programs activated in MLL-rearranged and HOX-overexpressing AML. Therefore, targeting the MEIS1/PBX3 interaction may represent a promising therapeutic strategy to treat these AML subtypes

miR-22 has a potent anti-tumour role with therapeutic potential in acute myeloid leukaemia

MicroRNAs are subject to precise regulation and have key roles in tumorigenesis. In contrast to the oncogenic role of miR-22 reported in myelodysplastic syndrome (MDS) and breast cancer, here we show that miR-22 is an essential anti-tumour gatekeeper in de novo acute myeloid leukaemia (AML) where it is significantly downregulated. Forced expression of miR-22 significantly suppresses leukaemic cell viability and growth in vitro, and substantially inhibits leukaemia development and maintenance in vivo. Mechanistically, miR-22 targets multiple oncogenes, including CRTC1, FLT3 and MYCBP, and thus represses the CREB and MYC pathways. The downregulation of miR-22 in AML is caused by TET1/GFI1/EZH2/SIN3A-mediated epigenetic repression and/or DNA copy-number loss. Furthermore, nanoparticles carrying miR-22 oligos significantly inhibit leukaemia progression in vivo. Together, our study uncovers a TET1/GFI1/EZH2/SIN3A/miR-22/CREB-MYC signalling circuit and thereby provides insights into epigenetic/genetic mechanisms underlying the pathogenesis of AML, and also highlights the clinical potential of miR-22-based AML therapy

Cell‐free DNA 5‐hydroxymethylcytosine as a marker for common cancer detection

Abstract Background Early cancer detection can dramatically improve clinical outcomes and greatly reduce economic burden of patients. Plasma cell–free DNA (cfDNA) 5‐hydroxymethylcytosine (5hmC) is an emerging epigenetic marker for cancer diagnosis. However, the utility of such marker has not been investigated in many common cancers yet. The purpose of this study was to evaluate 5hmC in plasma cfDNA for an early detection of common cancers. Methods We used a highly sensitive nano‐5hmC‐Seal method and profiled the genome‐wide distribution of 5hmC in plasma cfDNA from 384 patients with bladder, breast, colorectal, kidney, lung or prostate cancer and 221 controls. Genes and signalling pathways with differential hydroxymethylation were analysed. We used machine learning to develop 5hmC signatures for cancer detection and cancer‐origin determination in the training sets and validated the signatures in the validation sets. Results We identified genes and signalling pathways with aberrant DNA hydroxymethylation in six cancers. We discovered a pan‐cancer signature that detected all six cancers with a sensitivity of 68.6% and a specificity of 96.6% and cancer–specific signatures with a sensitivity of 80.0% for breast cancer, 88.9% for kidney cancer, 94.1% for lung cancer and 96.4% for prostate cancer, and a specificity of 100% for all except lung (96.2%). The sensitivity of cancer–specific signatures was 89.3%–100.0% for early‐stage cancers. The lung cancer–specific signature achieved a sensitivity of 98.0% and a specificity of 82.3% in an independent patient cohort with different ethnic backgrounds. Additionally, we discovered a 5hmC signature that could accurately determine cancer origin. Conclusions We demonstrated that plasma cfDNA 5hmC is a highly sensitive biomarker for common cancer detection. Our genome‐wide analysis of 5hmC in six cancers reveals new target genes and signalling pathways with therapeutic potential for common cancers

Classification of Acute Myeloid Leukemia by Cell-Free DNA 5-Hydroxymethylcytosine

Epigenetic abnormality is a hallmark of acute myeloid leukemia (AML), and aberrant 5-hydroxymethylcytosine (5hmC) levels are commonly observed in AML patients. As epigenetic subgroups of AML correlate with different clinical outcomes, we investigated whether plasma cell-free DNA (cfDNA) 5hmC could categorize AML patients into subtypes. We profiled the genome-wide landscape of 5hmC in plasma cfDNA from 54 AML patients. Using an unbiased clustering approach, we found that 5hmC levels in genomic regions with a histone mark H3K4me3 classified AML samples into three distinct clusters that were significantly associated with leukemia burden and survival. Cluster 3 showed the highest leukemia burden, the shortest overall survival of patients, and the lowest 5hmC levels in the TET2 promoter. 5hmC levels in the TET2 promoter could represent TET2 activity resulting from mutations in DNA demethylation genes and other factors. The novel genes and key signaling pathways associated with aberrant 5hmC patterns could add to our understanding of DNA hydroxymethylation and highlight the potential therapeutic targets in AML. Our results identify a novel 5hmC-based AML classification system and further underscore cfDNA 5hmC as a highly sensitive marker for AML

Cell-free DNA 5-hydroxymethylcytosine is highly sensitive for MRD assessment in acute myeloid leukemia

Abstract Measurable residual disease (MRD) is an important biomarker in acute myeloid leukemia (AML). However, MRD cannot be detected in many patients using current methods. We developed a highly sensitive 5-hydroxymethylcytosine (5hmC) signature in cell-free DNA by analyzing 115 AML patients and 86 controls. The 5hmC method detected MRD in 20 of 29 patients with negative MRD by multiparameter flow cytometry and 11 of 14 patients with negative MRD by molecular methods. MRD detection by the 5hmC method was significantly associated with relapse-free survival. This novel method can be used in most AML patients and may significantly impact AML patient management

Clinical Predictive Factors of Lower Extremity Deep Vein Thrombosis in Relative High-Risk Patients after Neurosurgery: A Retrospective Study

Introduction. It is acknowledged that patients undergoing neurosurgery with neurological illness are at higher risk of lower extremity deep vein thrombosis (DVT). As an underlying life-threatening complication, the incidence and risk factors for high-risk patients with lower extremity deep vein thrombosis are still controversial in relative high-risk patients after neurosurgery. Materials and Methods. A total of 204 patients who underwent neurosurgery and were considered as a high-risk group of DVT according to times of stay in bed more than 3 days were enrolled in this study. We evaluated the lower extremity DVT by using Color Doppler Ultrasound System (CDUS). Clinical parameters of patients at the time of admission and postoperation were recorded and prepared for further analysis. Early predictive factors for postoperative lower extremity DVT were established. Diagnostic performance of predictive factors was evaluated by using receiver operating characteristic (ROC) curve analysis. Results. The overall incidence rate of DVT in 204 enrolled patients was 30.9%. Multivariate logistic regression indicated that hypertension (OR 3.159, 95% CI 1.465-6.816; P=0.003), higher postoperative D-dimer (OR 1.225, 95% CI 1.016-1.477; P=0.034), female (OR 0.174, 95% CI 0.054-0.568; P=0.004), and lower GCS score (OR 0.809, 95% CI 0.679-0.965; P=0.013) were independently associated with incidence of DVT in patients after neurosurgery. The logistic regression function (LR model) of these four independent risk factors had a better performance on diagnostic value of DVT in patients after neurosurgery. Conclusion. The combined factor was constructed by hypertension, postoperative D-dimer, gender, and GCS score, and it might be a more handy and reliable marker to stratify patients at risk of DVT after neurosurgery

Cell-Free DNA 5-Hydroxymethylcytosine Signatures for Lung Cancer Prognosis

Accurate prognostic markers are essential for guiding effective lung cancer treatment strategies. The level of 5-hydroxymethylcytosine (5hmC) in tissue is independently associated with overall survival (OS) in lung cancer patients. We explored the prognostic value of cell-free DNA (cfDNA) 5hmC through genome-wide analysis of 5hmC in plasma samples from 97 lung cancer patients. In both training and validation sets, we discovered a cfDNA 5hmC signature significantly associated with OS in lung cancer patients. We built a 5hmC prognostic model and calculated the weighted predictive scores (wp-score) for each sample. Low wp-scores were significantly associated with longer OS compared to high wp-scores in the training [median 22.9 versus 8.2 months; p = 1.30 × 10−10; hazard ratio (HR) 0.04; 95% confidence interval (CI), 0.00–0.16] and validation (median 18.8 versus 5.2 months; p = 0.00059; HR 0.22; 95% CI: 0.09–0.57) sets. The 5hmC signature independently predicted prognosis and outperformed age, sex, smoking, and TNM stage for predicting lung cancer outcomes. Our findings reveal critical genes and signaling pathways with aberrant 5hmC levels, enhancing our understanding of lung cancer pathophysiology. The study underscores the potential of cfDNA 5hmC as a superior prognostic tool for guiding more personalized therapeutic strategies for lung cancer patients