Integrated transcriptomic and genomic analysis improves prediction of complete remission and survival in elderly patients with acute myeloid leukemia

EEPD1 regulates inflammation and endothelial apoptosis in atherosclerosis through KLF4-EEPD1-ERK axis

BACKGROUND

Inflammation and endothelial apoptosis are implicated in the advancement of atherosclerosis. EEPD1 holds a pivotal position in the repair of DNA damage and contributes to the progression of multiple cancers. However, the role of EEPD1 in cardiovascular diseases needs to be explored further, especially in atherosclerosis.

METHODS

We constructed EEPD1 and ApoE (apolipoprotein E)-deficient mice to assess how EEPD1 influences endothelial inflammation and apoptosis within atherosclerotic plaques. High-throughput RNA sequencing of human aortic endothelial cell groups treated with siCon+TNFα and siEEPD1+TNFα identified notable disparities in the MAPK pathway between groups. Chromatin immunoprecipitation and luciferase reporter assay confirmed that KLF4 directly regulates EEPD1.

RESULTS

Further examination of gene expression data revealed elevated EEPD1 concentrations in atherosclerotic plaques of patients, which findings were corroborated in the aortas of ApoE-/- mice. Present study demonstrated that adhesion molecule expression, endothelial apoptosis, aortic root plaques and macrophage accumulation were markedly ameliorated in EEPD1-/-ApoE-/- mice compared to WT ApoE-/- mice. Functional analysis revealed that increase in EEPD1 promotes ERK phosphorylation and significantly increases endothelial apoptosis and inflammation in atherosclerosis, which was abrogated by inhibition of ERK phosphorylation. We found KLF4 to be the transcription repressor of EEPD1 through luciferase assay and chromatin immunoprecipitation, and KLF4 inhibition abrogated the amelioration of endothelial apoptosis and inflammation caused by EEPD1 deletion.

CONCLUSIONS

Collectively, this study revealed that EEPD1 deletion can lead to amelioration of atherosclerosis through the KLF4-EEPD1-ERK axis. Hence, targeting EEPD1 could be a promising therapeutic strategy for patients with atherosclerosis.

Acute myeloid leukemia with peripheral lymph node involvement in dogs: A retrospective study of 23 cases

Acute myeloid leukemia (AML) can infiltrate extramedullary tissues, such as the liver, spleen, and lymph nodes and can be difficult to differentiate from lymphoma in cytologic and histologic specimens. Our goal was to identify cytologic features that would support a diagnosis of AML in peripheral lymph node aspirates, for which we used the term extramedullary AML (eAML). Medical records of 23 dogs with a diagnosis of AML and archived lymph node aspirate smears from 2016 to 2024 were reviewed across 4 institutions. Inclusion criteria included ≥50% myeloid blasts plus differentiating myeloid cells in lymph node smears, confirmation of myeloid lineage by flow cytometric analysis, and complete medical records. Peripheral lymphadenopathy was the reason for presentation (9/23, 39%) or was found incidentally on physical examination (14/23, 61%). Most dogs were bi- or pancytopenic (18/23, 78%), with blasts identified in blood smears of 18 dogs (78%). Initial lymph node aspirate interpretations included hematopoietic neoplasia (8/21, 38%), AML (6/21, 29%), lymphoma (5/21, 24%), lymphoid hyperplasia (1/21, 5%), and granulocytic precursor infiltrates (1/21, 5%). On lymph node smear review, cytologic features supporting an eAML were differentiating granulocytes, blasts with myeloid features or promonocytes, dysplastic changes in myeloid cells, and retention of residual lymphocytes. The median survival was 22 days (range = 1-360 days), and 69% of 16 dogs given chemotherapy or glucocorticoids lived for 30 days or more. Our study highlights the importance of hemogram results and lymph node aspirate smear examination for morphologic features of myeloid differentiation to help diagnose eAML in lymph node smears.

Acute myeloid leukemia treatment outcomes with isocitrate dehydrogenase mutations: A systematic review and meta-analysis

BACKGROUND

Isocitrate dehydrogenase (IDH) gene alterations and acute myeloid leukemia (AML) treatment results remain controversial. This study reviews the literature on IDH mutations in AML to determine the foundation of individualized therapy and improve effectiveness, survival time, and recurrence rate.

METHODS

Seven English and 2 Chinese databases were searched for literature on IDH mutations and AML outcomes. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated.

RESULTS

Twenty studies were included in this analysis. For the prognostic influence of IDH mutation on AML patients, the pooled HRs of overall survival in AML patients were 0.76 (95% CI, 0.63-0.93); the pooled HRs of event-free survival were 1.34 (95% CI, 1.15-1.57; heterogeneity: I2 = 52.2%, P = .027 < 0.05); the pooled HRs of recurrence free survival were 0.79 (95% CI, 0.61-1.02). The pooled HRs of overall survival in AML patients with mutant IDH1 were 1.62 (95% CI, 1.42-1.86) and of mutant IDH2 were 1.07 (95% CI, 0.89-1.29). The pooled HRs for event-free survival in AML patients with mutant IDH1 were 1.71 (95% CI, 1.40-2.08) and of mutant IDH2 were 0.93 (95% CI, 0.65-1.34). No evidence of publication bias was observed.

CONCLUSIONS

Different subtypes of IDH mutations may lead to different AML prognoses, suggesting the feasibility of personalized treatment for AML patients.

Unlocking reproducible transcriptomic signatures for acute myeloid leukaemia: Integration, classification and drug repurposing

Acute myeloid leukaemia (AML) is a highly heterogeneous disease, which lead to various findings in transcriptomic research. This study addresses these challenges by integrating 34 datasets, including 26 control groups, 6 prognostic datasets and 2 single-cell RNA sequencing (scRNA-seq) datasets to identify 10,000 AML-related genes (ARGs). We focused on genes with low variability and high consistency and successfully discovered 191 AML signatures (ASs). Leveraging machine learning techniques, specifically the XGBoost model and our custom framework, we classified AML subtypes with both scRNA-seq and bulk RNA-seq data, complementing the ELN2022 classification approach. Our research also identified promising treatments for AML through drug repurposing, with solasonine showing potential efficacy for high-risk AML patients, supported by molecular docking and transcriptomic analyses. To enhance reproducibility and customizability, we developed CSAMLdb, a user-friendly database platform. It facilitates the reuse and personalized analysis of nearly all results obtained in this research, including single-gene prognostics, multi-gene scoring, enrichment analysis, machine learning risk assessment, drug repositioning analysis and literature abstract named entity recognition. CSAMLdb is available at http://www.csamldb.com.

EEPD1 attenuates radiation-induced cardiac hypertrophy and apoptosis by degrading FOXO3A in cardiomyocytes

Radiation-induced heart disease (RIHD) is a severe delayed complication of thoracic irradiation (IR). Endonuclease/exonuclease/phosphatase family domain-containing 1 ( EEPD1) plays an important role in DNA damage repair, but its role in RIHD is less known. In this study, EEPD1 global knockout mice, C57BL/6J mice, and C57BL/6J mice overexpressing EEPD1 are treated with radiation at a total dose of 20 Gy or 0 Gy. After 9 weeks, echocardiography is used to assess cardiac hypertrophy and apoptosis. The results show that EEPD1 deletion exacerbates radiation-induced cardiac hypertrophy and apoptosis, while EEPD1 overexpression has the opposite effect. Further mechanistic investigations reveal that EEPD1 interacts with FOXO3A and destabilizes it by catalyzing its deubiquitination. Inhibition of FOXO3A ameliorates cardiac hypertrophy and apoptosis after EEPD1 knockdown. Thus, EEPD1 protects against radiation-induced cardiac hypertrophy and apoptosis via destabilization of FOXO3A, which may offer new insight into therapeutic strategies for RIHD.

Maintaining High-Touch in High-Tech Digital Health Monitoring and Multi-Omics Prognostication: Ethical, Equity, and Societal Considerations in Precision Health for Palliative Care

Advances in digital health, systems biology, environmental monitoring, and artificial intelligence (AI) continue to revolutionize health care, ushering a precision health future. More than disease treatment and prevention, precision health aims at maintaining good health throughout the lifespan. However, how can precision health impact care for people with a terminal or life-limiting condition? We examine here the ethical, equity, and societal/relational implications of two precision health modalities, (1) integrated systems biology/multi-omics analysis for disease prognostication and (2) digital health technologies for health status monitoring and communication. We focus on three main ethical and societal considerations: benefits and risks associated with integration of these modalities into the palliative care system; inclusion of underrepresented and marginalized groups in technology development and deployment; and the impact of high-tech modalities on palliative care's highly personalized and "high-touch" practice. We conclude with 10 recommendations for ensuring that precision health technologies, such as multi-omics prognostication and digital health monitoring, for palliative care are developed, tested, and implemented ethically, inclusively, and equitably.

The Prognostic Value of TP53 Mutations in Adult Acute Myeloid Leukemia: A Meta-Analysis

OBJECTIVE

Mutations of the tumor protein p53 (TP53) gene were considered to be associated with an unfavorable prognosis in acute myeloid leukemia (AML). This meta-analysis aimed to systematically elucidate the prognostic value of TP53 mutation in adult patients with AML.

METHOD

A comprehensive literature search was conducted for eligible studies published before August 2021. The primary endpoint was overall survival (OS). Pooled hazard ratios (HRs) and their 95% confidence intervals (CIs) were calculated for prognostic parameters. Subgroup analyses based on intensive treatment were performed.

RESULTS

Thirty-two studies with 7,062 patients were included. As compared to wild-type carriers, AML patients with TP53 mutations had significantly shorter OS (HR: 2.40, 95% CI: 2.16-2.67, I2: 46.6%). Similar results were found in DFS (HR: 2.87, 95% CI: 1.88-4.38), EFS (HR: 2.56, 95% CI: 1.97-3.31), and RFS (HR: 2.40, 95% CI: 1.79-3.22). Mutant TP53 predicted inferior OS (HR: 2.77, 95% CI: 2.41-3.18) in the intensively treated AML subgroup, compared with the non-intensively treated group (HR: 1.89, 95% CI: 1.58-2.26). Among intensively-treated AML patients, the age of 65 did not affect the prognostic value of TP53 mutations. Besides, TP53 mutation was also strongly associated with an elevated risk of adverse cytogenetics, which conferred a dismal OS in AML patients (HR: 2.03, 95% CI: 1.74-2.37).

CONCLUSION

TP53 mutation exhibits a promising potential for discriminating AML patients with a worse prognosis, thus being capable of serving as a novel tool for prognostication and therapeutic decision-making in the management of AML.

Evaluation of the clinical significance of global mRNA alternative splicing in patients with acute myeloid leukemia

Aberrant alternative splicing (AS) is involved in leukemogenesis. This study explored the clinical impact of alterations in global AS patterns in 341 patients with acute myeloid leukemia (AML) newly diagnosed at the National Taiwan University Hospital and validated it using The Cancer Genome Atlas (TCGA) cohort. While studying normal cord blood CD34⁺ /CD38^- cells, we found that AML cells exhibited significantly different global splicing patterns. AML with mutated TP53 had a particularly high degree of genome-wide aberrations in the splicing patterns. Aberrance in the global splicing pattern was an independent unfavorable prognostic factor affecting the overall survival of patients with AML receiving standard intensive chemotherapy. The integration of global splicing patterns into the 2022 European LeukemiaNet risk classification could stratify AML patients into four groups with distinct prognoses in both our experimental and TCGA cohorts. We further identified four genes with AS alterations that harbored prognostic significance in both of these cohorts. Moreover, these survival-associated AS events are involved in several important cellular processes that might be associated with poor response to intensive chemotherapy. In summary, our study demonstrated the clinical and biological implications of differential global splicing patterns in AML patients. Further studies with larger prospective cohorts are required to confirm these findings.

Genetic identification of patients with AML older than 60 years achieving long-term survival with intensive chemotherapy

To design a simple and reproducible classifier predicting the overall survival (OS) of patients with acute myeloid leukemia (AML) ≥60 years of age treated with 7 + 3, we sequenced 37 genes in 471 patients from the ALFA1200 (Acute Leukemia French Association) study (median age, 68 years). Mutation patterns and OS differed between the 84 patients with poor-risk cytogenetics and the 387 patients with good (n = 13), intermediate (n = 339), or unmeasured (n = 35) cytogenetic risk. TP53 (hazards ratio [HR], 2.49; P = .0003) and KRAS (HR, 3.60; P = .001) mutations independently worsened the OS of patients with poor-risk cytogenetics. In those without poor-risk cytogenetics, NPM1 (HR, 0.57; P = .0004), FLT3 internal tandem duplications with low (HR, 1.85; P = .0005) or high (HR, 3.51; P < 10-4) allelic ratio, DNMT3A (HR, 1.86; P < 10-4), NRAS (HR, 1.54; P = .019), and ASXL1 (HR, 1.89; P = .0003) mutations independently predicted OS. Combining cytogenetic risk and mutations in these 7 genes, 39.1% of patients could be assigned to a "go-go" tier with a 2-year OS of 66.1%, 7.6% to the "no-go" group (2-year OS 2.8%), and 3.3% of to the "slow-go" group (2-year OS of 39.1%; P < 10-5). Across 3 independent validation cohorts, 31.2% to 37.7% and 11.2% to 13.5% of patients were assigned to the go-go and the no-go tiers, respectively, with significant differences in OS between tiers in all 3 trial cohorts (HDF [Hauts-de-France], n = 141, P = .003; and SAL [Study Alliance Leukemia], n = 46; AMLSG [AML Study Group], n = 223, both P < 10-5). The ALFA decision tool is a simple, robust, and discriminant prognostic model for AML patients ≥60 years of age treated with intensive chemotherapy. This model can instruct the design of trials comparing the 7 + 3 standard of care with less intensive regimens.

Acute myeloid leukaemia in patients we judge as being older and/or unfit

The definition of older age in AML is arbitrary. In the context of the clinical studies, it starts with age ≥60 or ≥65 years and in recent years ≥70 or 75, depending on the selection of the studied population. In clinical practice, with older age, we often mean that the patient is unfit for intensive chemotherapy. Higher age overlaps with categories such as worse performance status, unfitness, comorbidities, poor-risk cytogenetics, adverse mutation patterns, age-related clonal haematopoiesis and specific disease ontogeny. Intensive induction therapy can result in prolonged overall survival, at least in a subset of elderly patients aged up to 75 years despite the reluctance of some physicians and patients to use treatment regimens perceived as toxic. Venetoclax and azacitidine combination is the new standard of comparison for persons unfit for intensive therapy. New oral hypomethylating agent CC-486 as maintenance therapy led to a prolonged overall survival in a randomized trial of patients ≥55 years of age who were in first complete remission, but not eligible for allogeneic stem cell transplantation. Any therapy is better than no therapy, but a substantial proportion of older patients still receive only palliative care. Making a decision for AML diagnosed in older age should be individualized and shared through the dialog with the patient and relatives or cohabitants, considering medical issues and social factors including personal goals. Although we are witnesses of the advances in basic research and therapy, we are still a very long way from curing older patients with AML.