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922 results for “Chronic lymphocytic leukemia”
Detection of early seeding of Richter transformation in chronic lymphocytic leukemia: scRNA-seq data
<p>Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high–B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seed- ing of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT.</p> <p>This repository contains the processed scRNA-seq data (expression matrices, Seurat objects, metadata) related with this publication.</p>
A Study of Zanubrutinib (BGB-3111) Versus Ibrutinib in Participants With Relapsed/Refractory Chronic Lymphocytic Leukemia
ClinicalTrials.gov study NCT03734016. IPD Sharing: YES. Countries: 15. Publications: 10.
Ofatumumab vs Physician's Choice in Subjects With Bulky Fludarabine-Refractory Chronic Lymphocytic Leukemia
ClinicalTrials.gov study NCT01313689. IPD Sharing: UNDECIDED. Countries: 17. Publications: 1.
Ofatumumab Added to Fludarabine-Cyclophosphamide vs Fludarabine-Cyclophosphamide Combination in Relapsed Subjects With Chronic Lymphocytic Leukemia
ClinicalTrials.gov study NCT00824265. IPD Sharing: UNDECIDED. Countries: 18. Publications: 3.
Ofatumumab + Chlorambucil vs Chlorambucil Monotherapy in Previously Untreated Patients With Chronic Lymphocytic Leukemia
ClinicalTrials.gov study NCT00748189. IPD Sharing: YES. Countries: 17. Publications: 3.
Associated code and data for "A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia (doi: 10.1007/978-1-0716-4290-0_18)".
<p>This deposit contains the data, code, and analysis to recreate the results in the manuscript - Tuulikki Suomela, Liang Zhang, Julio Vera, Heiko Bruns, Xin Lai. A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia. Methods Mol. Biol., 2883, 403–426. <a href="https://www.researchgate.net/publication/387267721_A_Practical_Guideline_for_MicroRNA_Sequencing_Data_Analysis_in_Chronic_Lymphocytic_Leukemia">https://doi.org/10.1007/978-1-0716-4290-0_18</a>.</p> <p>The pipeline allows users to perform end-to-end analysis of bulk miRNA sequencing data, including quality control of FastQ files, mapping of read counts to miRNA genes using miRBase or Reference genome, quantification of miRNA read counts, differential gene expression analysis using DEseq2, gene set enrichment analysis using curated cancer hallmark gene sets, and identification of miRNA targets.</p> <p>If you have used the code for your research, please cite the original publication. Thank you very much.</p>
Identifying a novel ferroptosis-related prognostic score for predicting prognosis in chronic lymphocytic leukemia
<p><span><strong>Background</strong>:</span><span> Chronic lymphocytic leukemia (CLL) is the most common leukemia in the western world. Although the treatment landscape for CLL is rapidly evolving, there are still some patients who remain drug resistance or disease refractory. Ferroptosis is a type of lipid peroxidation-induced cell death and has been suggested with a prognostic value in several cancers. Our research aims to build a prognostic model to improve risk stratification in CLL patients and facilitate more accurate assessment for clinical management.</span></p> <p><span><strong>Methods</strong>: </span><span>The differentially expressed ferroptosis-related genes (</span><span>FRGs) in CLL were filtered through univariate Cox regression analysis based on public databases. Least Absolute Shrinkage and Selection Operator (LASSO) Cox algorithms were performed to construct a prognostic risk model. CIBERSORT and single-sample gene set enrichment analysis (ssGSEA) were performed to estimate the immune infiltration score and immune-related pathways. A total of thirty-six CLL patients in our center were enrolled in this study as a validation cohort. Moreover, a nomogram model was established to predict the prognosis.</span></p> <p><span><strong>Results</strong>: </span><span>A total of differentially expressed 15 FRGs with prognostic significance were screened out. After minimizing the potential risk of overfitting, we constructed a novel ferroptosis-related prognostic score (FPS) model with nine FRGs (AKR1C3, BECN1, CAV1, CDKN2A, CXCL2, JDP2, SIRT1, SLC1A5 and SP1), and stratified patients into low-risk and high-risk groups. Kaplan–Meier analysis showed that patients with high FPS had worse overall survival (OS) (P<0.0001) and treatment-free survival (TFS) (P<0.0001). ROC curves evaluated the prognostic prediction ability of the FPS model. Additionally, the immune cell types and immune-related pathways were correlated with the risk scores in CLL patients. In the validation cohort, the results confirmed </span><span>that the </span><span>high</span><span>-</span><span>risk group was related to worse OS (P<0.0001), progress-free survival (PFS) (P=0.0140) and TFS (P=0.0072). </span><span>In</span><span> the multivariate analysis, only FPS (P=0.011) and CLL-IPI (P=0.010) were independent risk indicators for OS. Furthermore, we established a nomogram including FPS and CLL-IPI which could strongly and reliably predict individual prognosis.</span></p> <p><span><strong>Conclusion</strong>: </span><span>A novel FPS model could be used in CLL for prognostic prediction. The model index may also facilitate the development of new clinical ferroptosis-targeted therapies in patients with CLL.</span></p>
CancerEpiSys – Integrative analysis of epigenetic networks that determine the chronic lymphocytic leukemia disease state
<p>A public repository of data processed for Mallm, Iskar, Ishaque et. al. 2018 Linking aberrant chromatin features in chronic lymphocytic leukemia to deregulated transcription factor networks</p> <p><strong>Website:</strong> http://www.cancerepisys.org/cancerepisys/index.html</p> <p><strong>Github:</strong> https://github.com/CancerEpiSys/Mallm-et-al-processing-scripts</p> <p><strong>Research mission</strong></p> <p><em>CancerEpiSys</em> is a BMBF funded research project with the <a href="http://www.bmbf.de/foerderungen/15063.php">CancerSys program</a> that dissects the epigenetic networks associated with chronic lymphocytic leukemia (CLL) to develop novel diagnostic and therapeutic approaches for the disease. It has been initiated based on the emerging view that signals encoded in the DNA sequence, epigenetic modifications (e.g. DNA methylation, post-translational histone modifications), non-coding RNAs and nucleosome positioning are not independently regulated properties. Rather, these chromatin features are governed by an interconnected network of molecular processes that determine the cellular gene expression program. Any errors that occur in the interplay of these factors can lead to aberrant gene regulation associated with cancer. To rationalize the mode of action of novel ‘epigenetic’ drugs in cancer therapy that change properties of this network, we will dissect experimentally and mathematically the interdependence of these processes, focusing on CLL.</p> <p>The main objectives of <em>CancerEpiSys</em> are: (i) deciphering the relation of DNA sequence, epigenetic modifications, nucleosome positioning and aberrant gene expression in CLL, (ii) the identification of epigenetic network morphologies that describe the response to the epigenetic drugs panobinostat and 3-deazaneplanocin (DZNep) that inhibit histone deacetylases and methyltransferases, (iii) the characterization of epigenetic markers and chromatin features of CLL patient subgroups, and (iv) the integration of results into an analysis scheme for the epigenetic aberrations most relevant for prognostication, prediction of treatment relapse and stratification of patients with respect to therapeutic options. Moreover, our results will inform novel therapeutic approaches that target gene-expression programs at the epigenetic level to sensitize cancer cells towards apoptosis and anti-growth signals.</p>
CHROMATIN ACTIVATION PROFILING OF STEREOTYPED CHRONIC LYMPHOCYTIC LEUKEMIAS
<p>We used chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) with an antibody for the H3K27ac (a bona fide histone mark for regulatory element activation) in sorted CLL cells from 46 CLL, including 21 cases from stereotyped subsets #1, #2, #4, and #8, and 15 normal B cell subpopulations. To understand their functional impact, we integrated our data with 16 RNA-seq data.</p> <p><strong>Files description:</strong><br> - <a href="https://zenodo.org/api/files/fb018e48-adb4-4750-a3e7-5188ac0a4123/H3K27ac_freq2_FDR_consensus_2022.txt?versionId=887e281e-526d-403d-a59d-4ac3e5773305">H3K27ac_freq2_FDR_consensus_2022.txt</a> count matrix from H3K27ac signals<br> - <a href="https://zenodo.org/api/files/fb018e48-adb4-4750-a3e7-5188ac0a4123/H3K27ac_FDR_consensus_norm.Combat_2022.txt?versionId=4a17abb5-0c95-42cc-b573-d11e0de2f484">H3K27ac_FDR_consensus_norm.Combat_2022.txt</a> count matrix from H3K27ac signals after batch effect correction<br> - <a href="https://zenodo.org/api/files/fb018e48-adb4-4750-a3e7-5188ac0a4123/RNAseq_norm.Combat_results.txt">RNAseq_norm.Combat_results.txt</a> count matrix from RNAseq after batch effect correction<br> - <a href="https://zenodo.org/api/files/fb018e48-adb4-4750-a3e7-5188ac0a4123/signature_RESAMPLING_ss8VSucll_2022.txt?versionId=806b1776-1571-4675-bc1c-3f0c29bf892e">signature_RESAMPLING_ss8VSucll_2022.txt</a> differentially acetylated regions between U-CLL and stereotyped subset #8 applying random sampling 100 times with a range of samples from 5 to n-1 in each category. The regions showing frequency >=20% were considered significant regions.</p>
Extension Study of Idelalisib in Participants With Chronic Lymphocytic Leukemia (CLL) Who Participated in GS-US-312-0116 (NCT01539512)
ClinicalTrials.gov study NCT01539291. IPD Sharing: YES. Countries: 5. Publications: 1.
Evaluate the Efficacy and Safety of TGR-1202 in Participants With Chronic Lymphocytic Leukemia Who Are Intolerant to Prior Therapy
ClinicalTrials.gov study NCT02742090. IPD Sharing: YES. Countries: 1. Publications: 1.
A Phase 2 Open-Label Study of the Efficacy and Safety of ABT-199 (GDC-0199) in Chronic Lymphocytic Leukemia (CLL) Subjects With Relapse or Refractory to B-Cell Receptor Signaling Pathway Inhibitor The
ClinicalTrials.gov study NCT02141282. IPD Sharing: YES. Countries: 1. Publications: 3.
Pembrolizumab Alone or With Idelalisib or Ibrutinib in Treating Patients With Relapsed or Refractory Chronic Lymphocytic Leukemia or Other Low-Grade B-Cell Non-Hodgkin Lymphomas
ClinicalTrials.gov study NCT02332980. IPD Sharing: Not stated. Countries: 1. Publications: 1.
FCR Versus FC Alone in the Treatment of Chronic Lymphocytic Leukemia (CLL) in Relapsed Patients
ClinicalTrials.gov study NCT00090051. IPD Sharing: Not stated. Countries: 17. Publications: 2.
Vorinostat, Cladribine, and Rituximab in Treating Patients With Mantle Cell Lymphoma, Relapsed Chronic Lymphocytic Leukemia, or Relapsed B Cell Non-Hodgkin's Lymphoma
ClinicalTrials.gov study NCT00764517. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Comparison of the Treatments of Obinutuzumab + Venetoclax Versus Obinutuzumab + Chlorambucil in Patients With Chronic Lymphocytic Leukemia
ClinicalTrials.gov study NCT02242942. IPD Sharing: Not stated. Countries: 21. Publications: 9.
Immuno-Augmentation With GM-CSF of Pneumococcal Vaccine in Chronic Lymphocytic Leukemia Patients
ClinicalTrials.gov study NCT00323557. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Acalabrutinib and High Frequency Low Dose Subcutaneous Rituximab in Patients With Previously Untreated Chronic Lymphocytic Leukemia / Small Lymphocytic Lymphoma
ClinicalTrials.gov study NCT03788291. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Ofatumumab, Pentostatin, and Cyclophosphamide in Treating Patients With Untreated Chronic Lymphocytic Leukemia or Small Lymphocytic Lymphoma
ClinicalTrials.gov study NCT01024010. IPD Sharing: Not stated. Countries: 1. Publications: 2.
A Study of MabThera (Rituximab) Plus Chlorambucil in Participants With Chronic Lymphocytic Leukemia.
ClinicalTrials.gov study NCT00532129. IPD Sharing: NO. Countries: 1. Publications: 1.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.