Epigenetic changes during B-cell differentiation generate distinct DNA methylation signatures specific for B-cell subsets, including memory B cells (MBCs) and plasma cells (PCs). Waldenström ...macroglobulinemia (WM) is a B-cell malignancy uniquely comprising a mixture of lymphocytic and plasmacytic phenotypes. Here, we integrated genome-wide DNA methylation, transcriptome, mutation, and phenotypic features of tumor cells from 35 MYD88-mutated WM patients in relation to normal plasma and B-cell subsets. Patients naturally segregate into 2 groups according to DNA methylation patterns, related to normal MBC and PC profiles, and reminiscent of other memory and PC-derived malignancies. Concurrent analysis of DNA methylation changes in normal and WM development captured tumor-specific events, highlighting a selective reprogramming of enhancer regions in MBC-like WM and repressed and heterochromatic regions in PC-like WM. MBC-like WM hypomethylation was enriched in motifs belonging to PU.1, TCF3, and OCT2 transcription factors and involved elevated MYD88/TLR pathway activity. PC-like WM displayed marked global hypomethylation and selective overexpression of histone genes. Finally, WM subtypes exhibited differential genetic, phenotypic, and clinical features. MBC-like WM harbored significantly more clonal CXCR4 mutations (P = .015), deletion 13q (P = .006), splenomegaly (P = .02), and thrombocytopenia (P = .004), whereas PC-like WM harbored more deletion 6q (P = .012), gain 6p (P = .033), had increased frequencies of IGHV3 genes (P = .002), CD38 expression (P = 4.1e-5), and plasmacytic differentiation features (P = .008). Together, our findings illustrate a novel approach to subclassify WM patients using DNA methylation and reveal divergent molecular signatures among WM patients.
We previously reported a rare germline variant (c.1-6531) that resulted in allele-specific expression (ASE) of death-associated protein kinase 1 (DAPK1) and predisposition to chronic lymphocytic ...leukemia (CLL). We investigated a cohort of CLL patients lacking this mutation for the presence of ASE of DAPK1. We developed a novel strategy that combines single-nucleotide primer extension (SNuPE) with MALDI-TOF mass spectrometry, and detected germline DAPK1 ASE in 17 out of 120 (14.2%) CLL patients associated with a trend towards younger age at diagnosis. ASE was absent in 63 healthy controls. Germline cells of CLL patients with ASE showed increased levels of DNA methylation in the promoter region, however, neither genetic nor further epigenetic aberrations could be identified in the DAPK1 5' upstream regulatory region, within distinct exons or in the 3'-UTR. We identified B-lymphoid malignancy related cell line models harboring allelic imbalance and found that allele-specific methylation in DAPK1 is associated with ASE. Our data indicate that ASE at the DAPK1 gene locus is a recurrent event, mediated by epigenetic mechanisms and potentially predisposing to CLL.
Abstract
NK cells are known to be developmentally blocked and functionally inhibited in patients with acute myeloid leukemia (AML), resulting in poor clinical outcomes. In this study, we demonstrate ...that whereas NK cells are inhibited, closely related type 1 innate lymphoid cells (ILC1s) are enriched in the bone marrow of leukemic mice and in patients with AML. Because NK cells and ILC1s share a common precursor (ILCP), we asked if AML acts on the ILCP to alter developmental potential. A combination of ex vivo and in vivo studies revealed that AML skewing of the ILCP toward ILC1s and away from NK cells represented a major mechanism of ILC1 generation. This process was driven by AML-mediated activation of the aryl hydrocarbon receptor (AHR), a key transcription factor in ILCs, as inhibition of AHR led to decreased numbers of ILC1s and increased NK cells in the presence of AML. These results demonstrate a mechanism of ILC developmental skewing in AML and support further preclinical study of AHR inhibition in restoring normal NK cell development and function in the setting of AML.
•Individuals with MBL who have a high-risk epigenetic/immunogenetic signature show significant risk of progression to CLL requiring therapy.•The signature improves prediction of clinical outcomes ...compared with other established prognostic indicators regardless of MBL/CLL designation.
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Monoclonal B-cell lymphocytosis (MBL) progresses to chronic lymphocytic leukemia (CLL) requiring therapy at 1% to 5% per year. Improved prediction of progression would greatly benefit individuals with MBL. Patients with CLL separate into 3 distinct epigenetic subtypes (epitypes) with high prognostic significance, and recently the intermediate epitype has been shown to be enriched for high-risk immunoglobulin lambda variable (IGLV) 3-21 rearrangements, impacting outcomes for these patients. Here, we employed this combined strategy to generate the epigenetic and light chain immunoglobulin (ELCLV3-21) signature to classify 219 individuals with MBL. The ELCLV3-21 high-risk signature distinguished MBL individuals with a high probability of progression (39.9% and 71.1% at 5 and 10 years, respectively). ELCLV3-21 improved the accuracy of predicting time to therapy for individuals with MBL compared with other established prognostic indicators, including the CLL international prognostic index (c-statistic, 0.767 vs 0.668, respectively). Comparing ELCLV3-21 risk groups in MBL vs a cohort of 226 patients with CLL revealed ELCLV3-21 high-risk individuals with MBL had significantly shorter time to therapy (P = .003) and reduced overall survival (P = .03) compared with ELCLV3-21 low-risk individuals with CLL. These results highlight the power of the ELCLV3-21 approach to identify individuals with a higher likelihood of adverse clinical outcome and may provide a more accurate approach to classify individuals with small B-cell clones.
Monoclonal B-cell lymphocytosis (MBL) progresses to chronic lymphocytic leukemia at a low rate (1%-5%/year), and improved prediction of those patients whose disease is prone to progress will have a significant impact on patients with MBL. Abdelbaky and colleagues combined epigenetic and light-chain immunoglobulin signatures of 219 individuals with MBL and defined a high-risk group that has a significantly shorter time to therapy and reduced overall survival. This offers the opportunity to provide better prognostic information to patients and tailor their follow-up.
MicroRNAs (miRNAs) are post‐transcriptional regulators of gene expression and their deregulation is involved in tumor development. Epigenetic gene silencing in cancer by DNA methylation contributes ...to the silencing of tumor‐suppressor genes, including miRNAs. We have recently shown that the promoter of miR‐708 is aberrantly methylated in chronic lymphocytic leukemia (CLL). To characterize the molecular signaling networks that are influenced by miR‐708, we performed a luciferase‐based screen evaluating the effects of ectopic miR‐708 expression on leukemia‐relevant signaling pathways. We found that miR‐708 strongly repressed NF‐κB signaling, a pathway known to be deregulated in CLL. Among the predicted miR‐708 targets was IKKβ (inhibitor of kappa light polypeptide gene enhancer in B cells, kinase‐β/IKBKB), a key kinase facilitating NF‐κB signaling. We validated the interaction of miR‐708 with the 3′‐untranslated region of IKKβ and found that miR‐708 overexpression represses endogenous IKKβ. Phosphorylation of the IKKβ target IκBα and expression of known NF‐κB target genes were impaired by miR‐708. Furthermore, we identified an enhancer region downstream of the miR‐708 promoter that displays a distinct DNA methylation status in CLL. High enhancer methylation is significantly correlated with lower miR‐708 expression and is predominantly found in patients with poor prognosis and shorter time to treatment. These results demonstrate that miR‐708 regulates the NF‐κB pathway by targeting IKKβ, and that methylation of a key enhancer region contributes to its suppression in CLL.
What's new?
Mechanisms by which microRNAs (miRNAs) become deregulated in chronic lymphocytic leukemia (CLL) are largely unknown, but for miR‐708, a potential tumor suppressor, aberrant promoter methylation may be at fault. Here, miR‐708 overexpression was associated with IKKβ repression and impaired expression of genes targeted by NF‐κB. Regulation of miR‐708 in CLL occurred at a distal enhancer element, where elevated enhancer methylation was correlated with reduced miR‐708 expression. Increased miR‐708 methylation was found primarily in CLL patients with poor prognosis. The findings shed light on a possible functional connection between an epigenetic mark and regulation of a highly disease‐relevant pathway.
Patient-reported outcome measures (PROMs) are recommended for capturing meaningful outcomes in clinical trials. The use of PROMs for children with acute lower respiratory infections (ALRIs) has not ...been systematically reported. We aimed to identify and characterise patient-reported outcomes and PROMs used in paediatric ALRI studies and summarise their measurement properties.
Medline, Embase and Cochrane were searched (until April 2022). Studies that reported on patient-reported outcome (or measure) use or development and included subjects aged <18 years with ALRIs were included. Study, population and patient-reported outcome (or measure) characteristics were extracted.
Of 2793 articles identified, 18 met inclusion criteria, including 12 PROMs. Two disease-specific PROMs were used in settings in which they had been validated. The Canadian Acute Respiratory Illness and Flu Scale was the most frequently used disease-specific PROM (five studies). The EuroQol-Five Dimensions-Youth system was the most frequently used generic PROM (two studies). There was considerable heterogeneity in validation methods. The outcome measures identified in this review lack validation for young children and none involve sufficient content validity for use with First Nations children.
There is an urgent need for PROM development that considers the populations in which the burden of ALRI predominates.
In cancer, normal epigenetic patterns are disturbed and contribute to gene expression changes, disease onset, and progression. The cancer epigenome is composed of the epigenetic patterns present in ...the tumor-initiating cell at the time of transformation, and the tumor-specific epigenetic alterations that are acquired during tumor initiation and progression. The precise dissection of these two components of the tumor epigenome will facilitate a better understanding of the biological mechanisms underlying malignant transformation. Chronic lymphocytic leukemia (CLL) originates from differentiating B cells, which undergo extensive epigenetic programming. This poses the challenge to precisely determine the epigenomic ground state of the cell-of-origin in order to identify CLL-specific epigenetic aberrations.
We developed a linear regression model, methylome-based cell-of-origin modeling (Methyl-COOM), to map the cell-of-origin for individual CLL patients based on the continuum of epigenomic changes during normal B cell differentiation.
Methyl-COOM accurately maps the cell-of-origin of CLL and identifies CLL-specific aberrant DNA methylation events that are not confounded by physiologic epigenetic B cell programming. Furthermore, Methyl-COOM unmasks abnormal action of transcription factors, altered super-enhancer activities, and aberrant transcript expression in CLL. Among the aberrantly regulated transcripts were many genes that have previously been implicated in T cell biology. Flow cytometry analysis of these markers confirmed their aberrant expression on malignant B cells at the protein level.
Methyl-COOM analysis of CLL identified disease-specific aberrant gene regulation. The aberrantly expressed genes identified in this study might play a role in immune-evasion in CLL and might serve as novel targets for immunotherapy approaches. In summary, we propose a novel framework for in silico modeling of reference DNA methylomes and for the identification of cancer-specific epigenetic changes, a concept that can be broadly applied to other human malignancies.
Abstract
Recently, a novel knowledge bank (KB) approach to predict outcomes of individual patients with acute myeloid leukemia (AML) was developed using unbiased machine learning. To validate its ...prognostic value, we analyzed 1612 adults with de novo AML treated on Cancer and Leukemia Group B front-line trials who had pretreatment clinical, cytogenetics, and mutation data on 81 leukemia/cancer-associated genes available. We used receiver operating characteristic (ROC) curves and the area under the curve (AUC) to evaluate the predictive values of the KB algorithm and other risk classifications. The KB algorithm predicted 3-year overall survival (OS) probability in the entire patient cohort (AUC
KB
= 0.799), and both younger (< 60 years) (AUC
KB
= 0.747) and older patients (AUC
KB
= 0.770). The KB algorithm predicted non-remission death (AUC
KB
= 0.860) well but was less accurate in predicting relapse death (AUC
KB
= 0.695) and death in first complete remission (AUC
KB
= 0.603). The KB algorithm’s 3-year OS predictive value was higher than that of the 2017 European LeukemiaNet (ELN) classification (AUC
2017ELN
= 0.707,
p
< 0.001) and 2010 ELN classification (AUC
2010ELN
= 0.721,
p
< 0.001) but did not differ significantly from that of the 17-gene stemness score (AUC
17-gene
= 0.732,
p
= 0.10). Analysis of additional cytogenetic and molecular markers not included in the KB algorithm revealed that taking into account atypical complex karyotype, infrequent recurrent balanced chromosome rearrangements and mutational status of the
SAMHD1
,
AXL
and
NOTCH1
genes may improve the KB algorithm. We conclude that the KB algorithm has a high predictive value that is higher than those of the 2017 and 2010 ELN classifications. Inclusion of additional genetic features might refine the KB algorithm.
IntroductionAcute respiratory infections (ARI) are the most common cause of paediatric hospitalisation. There is an urgent need to address ongoing critical knowledge gaps in ARI management. The ...Pragmatic Adaptive Trial for Respiratory Infections in Children (PATRIC) Clinical Registry will evaluate current treatments and outcomes for ARI in a variety of paediatric patient groups. The registry will provide a platform and data to inform a number of PATRIC clinical trials, testing various interventions in ARI treatment and management to optimise paediatric ARI care.Methods and analysisThe PATRIC Clinical Registry is a single-centre, prospective observational registry recruiting from a tertiary paediatric Emergency Department in Western Australia. Through characterising demographic, clinical, treatment and outcome data, the PATRIC Clinical Registry will improve our understanding of antibiotic utilisation and ARI outcomes in children.Ethics and disseminationThe PATRIC Clinical Registry is conducted in accordance with the Declaration of Helsinki, and the International Council for Harmonisation (ICH) Guidelines for Good Clinical Practice (CPMP/ICH/13595) July 1996. Approval is provided by the Child and Adolescent Health Service Human Research Ethics Committee (HREC). Study results will be communicated by presentation and publication (HREC: RGS0000003078.)Trial registration numberAustralian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12619000903189. UTN: U1111-1231-3365.
The surface receptor FcγRIIIA (CD16a) is encoded by the
gene and is acquired by human NK cells during maturation. NK cells bind the Fc portion of IgG via CD16a and execute Ab-dependent cell-mediated ...cytotoxicity, which is critical for the effectiveness of several antitumor mAb therapies. The role of epigenetic regulatory mechanisms controlling transcriptional and posttranscriptional CD16 expression in NK cells is unknown. In this study, we compared specific patterns of DNA methylation and expression of
with
, which differ in cell type-specific expression despite displaying nearly identical genomic sequences. We identified a sequence within the
promoter that selectively exhibits reduced methylation in CD16a
NK cells versus CD16a
NK cells and neutrophils. This region contained the transcriptional start site of the most highly expressed CD16a isoform in NK cells. Luciferase assays revealed remarkable cell-type specificity and methylation-dependent activity of
versus
-derived sequences. Genomic differences between
and
are enriched at CpG dinucleotides, and mutation of variant CpGs reversed cell-type specificity. We further identified miR-218 as a posttranscriptional negative regulator of CD16a in NK cells. Forced overexpression of miR-218 in NK cells knocked down CD16a mRNA and protein expression. Moreover, miR-218 was highly expressed in CD16a
NK cells compared with CD16a
NK cells. Taken together, we propose a system of
regulation in human NK cells in which CpG dinucleotide sequences and concurrent DNA methylation confer developmental and cell type-specific transcriptional regulation, whereas miR-218 provides an additional layer of posttranscriptional regulation during the maturation process.
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