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Metabolomics Integration with Gene expression profiling Elucidates IL4I1 as Modulator of Ibrutinib Resistance in ABC large B cell Lymphoma

ABSTRACT: Drug resistant acute B-cell lymphoma cells were analyzed via LC-MS metabolomics to identify deregulated metabolic pathways that are associated with drug resistance.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Human

SUBMITTER: Jiangjiang Zhu Lalit Sehgal

PROVIDER: MSV000087059 | MassIVE | Tue Mar 16 11:23:00 GMT 2021

REPOSITORIES: MassIVE

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Integration of Metabolomics and Gene Expression Profiling Elucidates IL4I1 as Modulator of Ibrutinib Resistance in ABC-Diffuse Large B Cell Lymphoma.

Choueiry Fouad F Singh Satishkumar S Sircar Anuvrat A Laliotis Georgios G Sun Xiaowei X Chavdoula Evangelia E Zhang Shiqi S Helmig-Mason JoBeth J Hart Amber A Epperla Narendranath N Tsichlis Philip P Baiocchi Robert R Alinari Lapo L Zhu Jiangjiang J Sehgal Lalit L

Cancers 20210429 9

Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma (NHL). B-cell NHLs rely on Bruton's tyrosine kinase (BTK) mediated B-cell receptor signaling for survival and disease progression. However, they are often resistant to BTK inhibitors or soon acquire resistance after drug exposure resulting in the drug-tolerant form. The drug-tolerant clones proliferate faster, have increased metabolic activity, and shift to oxidative phosphorylation; however, how this metabolic program ...[more]

PMID: 33946867

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GNPS - Metabolomics Integration with Gene expression profiling Elucidates IL4I1 as Modulator of Ibrutinib Resistance in ABC large B cell Lymphoma

Project description:Drug resistant acute B-cell lymphoma cells were analyzed via LC-MS metabolomics to identify deregulated metabolic pathways that are associated with drug resistance.

2021-03-16 | MSV000087059 | GNPS

Resistance to PRMT5-targeted therapy in mantle cell lymphoma

Project description:Mantle cell lymphoma (MCL) is an incurable B-cell non-Hodgkin lymphoma, and patients who relapse on targeted therapies have poor prognosis. Protein arginine methyltransferase 5 (PRMT5), an enzyme essential for B-cell transformation, drives multiple oncogenic pathways and is overexpressed in MCL. Despite the antitumor activity of PRMT5 inhibition (PRT-382/PRT-808), drug resistance was observed in a patient-derived xenograft (PDX) MCL model. Decreased survival of mice engrafted with these PRMT5 inhibitor-resistant cells vs treatment-naive cells was observed (P = .005). MCL cell lines showed variable sensitivity to PRMT5 inhibition. Using PRT-382, cell lines were classified as sensitive (n = 4; 50% inhibitory concentration [IC50], 20-140 nM) or primary resistant (n = 4; 340-1650 nM). Prolonged culture of sensitive MCL lines with drug escalation produced PRMT5 inhibitor-resistant cell lines (n = 4; 200-500 nM). This resistant phenotype persisted after prolonged culture in the absence of drug and was observed with PRT-808. In the resistant PDX and cell line models, symmetric dimethylarginine reduction was achieved at the original PRMT5 inhibitor IC50, suggesting activation of alternative resistance pathways. Bulk RNA sequencing of resistant cell lines and PDX relative to sensitive or short-term-treated cells, respectively, highlighted shared upregulation of multiple pathways including mechanistic target of rapamycin kinase [mTOR] signaling (P < 10-5 and z score > 0.3 or < 0.3). Single-cell RNA sequencing analysis demonstrated a strong shift in global gene expression, with upregulation of mTOR signaling in resistant PDX MCL samples. Targeted blockade of mTORC1 with temsirolimus overcame the PRMT5 inhibitor-resistant phenotype, displayed therapeutic synergy in resistant MCL cell lines, and improved survival of a resistant PDX.

2024-04-09 | GSE229517 | GEO

Proteaphagy contributes to bortezomib resistance in mantle cell lymphoma

Project description:TUBE and GST enrichment followed by 1D-gel-LC-MS analysis on cell exract from bortezomib (BTZ)-resistant or sensitive mantle cell lymphoma cells.

2022-02-28 | PXD011867 | Pride

Diffuse Large B Cell Lymphoma cell line with Acquired Resistance to PI3Kδ Inhibitor Idelalisib

Project description:RNAseq profile of TMD8 cell lines resistant to Idelalisib treatment. Idelalisib resistant TMD8 cells were generated by continuous passage in the presence of 1 μM idelalisib for 8 weeks until stable resistance to idelalisib was established. Parallel cultures were grown in the presence of 0.1% DMSO as passage-matched, drug-sensitive control lines. Sensitive and resistant TMD8 cells were clonally isolated through two rounds of single cell limiting dilution

2017-02-17 | GSE93156 | GEO

Integrative Gene Expression Profiling Reveals G6PD-Mediated Resistance to RNA-Directed Nucleoside Analogues in B-Cell Neoplasms

Project description:8-amino-adenosine (8-NH2-Ado) inhibits RNA synthesis and specifically inhibits synthesis of mRNAs with short half-lives. We hypothesize that the mRNAs affected code for proteins important in apoptosis and glucose metabolism. Gene Expression Arrays will help us understand which gene families may be affected by this drug and give us a better understanding of mechanism of action of this drug 1. MM.1S cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs. (myeloma cells sensitive to the drug) 2. U266 cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs. (myeloma cells resistant to the drug). 3. Jeko cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs. (Mantle cell lymphoma cells sensitive to drug) 4. Granta cells treated with 8-amino-adenosine for 0, 5 hrs and 17 hrs. (Mantle cell lymphoma cells resistant to drug).

2012-05-31 | E-GEOD-38145 | biostudies-arrayexpress

Long noncoding RNA expression in rituximab-sensitive and -resistant diffuse large B-cell lymphoma cell lines

Project description:Diffuse large B-cell lymphoma is an aggressive tumor, killing approximately 200,000 people each year. Rituximab, a recombinant monoclonal CD20 antibody, added to the treatment scheme in 1997 improved both progression-free survival and general survival rate. Despite the existing treatment and relatively high cure rate, 30-40% of the patients develop a relapse or are originally resistant. Long noncoding RNAs (lncRNAs) have been implicated as regulators of numerous important cancer-related processes, including establishment and maintenance of anti-cancer drug resistance. However, their role in DLBCL resistance to the treatment is poorly understood. In this study, we analyzed gene expression in DLBCL cell lines, either sensitive or resistant to rituximab.

2021-01-03 | GSE159852 | GEO

Comparing gene expression in ABT-199 (venetoclax) sensitive and resistant diffuse large B cell lymphoma cell (DLBCL) lines

Project description:RNA-sequencing was performed to evaluate gene expression changes between ABT-199 (venetoclax) sensitive and resistant matched diffuse large B cell lymphoma cell lines

2024-06-20 | GSE252306 | GEO

Hypomethylating agents sensitize diffuse large B-cell lymphoma to venetoclax

Project description:We established acquired venetoclax resistant OCI-LY1R cell line by treating venetoclax sensitive parental OCI-Ly1 cell line with increasing doses of venetoclax up till 1µM. Parental OCI-Ly1 and venetoiclax-resistant OCI-Ly1R cells were treated with vehicle control or decitabine at 1uM for 3 days. We found that decitabine differantially regulated gene expression in venetoclax sensitive and resistant cells. With gene set enrichment analysis, we identified two pathways that were deregulated by decitabine in both cell lines.

2023-07-25 | GSE223598 | GEO

Diffuse large B-cell lymphoma gene expression profiling array VFN-D2.

Project description:The dataset contains data from 12 samples hybridized on Illumina HumanHT-12 array. -patient's primary lymphoma cells obtained from malignant ascites (P2-A1, P2-A2) -patient's non-malignant B-cells (CTRL1, CTRL2) -lymphoma cell line named UPF4D established from the patient's primary lymphoma cells after 15 and 75 days of in vitro cultivation (UPF4D-D15A, UPF4D-D15B, UPF4D-D75) -cells established by xenotransplantation of UPF4D cell line isolated ex vivo from infiltrated murine kidney (UPF4D-K) -cells established by xenotransplantation of UPF4D cell line isolated ex vivo from subcutaneously growing lymphoma (UPF4D-SC) -patient-derived xenograft (PDX) cells named VFN-D2 established by xenotransplantation of primary lymphoma cells into immunodeficient mice isolated ex vivo from the infiltrated murine kidneys (VFN-D2-K1, VFN-D2-K2) -patient-derived xenograft (PDX) cells named VFN-D2 established by xenotransplantation of primary lymphoma cells into immunodeficient mice isolated ex vivo from subcutaneously growing lymphoma (VFN-D2-SC). Samples were sorted using CD19-microbeads (Miltenyi). For xenotransplantation, NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice (referred to as NSG mice) were used.

2017-02-24 | GSE95290 | GEO

Expression data at drug-sensitive and drug-resistant phases of canine B-cell lymphoma

Project description:Multidrug resistance (MDR) is one of the major obstacles during the chemotherapy in lymphoma patients. Although there have been various molecules associated with acquisition of MDR phenotype in human tumor cells, MDR of tumor cells have not been successfully overcome. Canine lymphoma is thought to be a spontaneous animal model of human lymphoma because it shares many similarities with human non-Hodgkin’s lymphoma. We conducted a comprehensive analysis of changes in gene expression profiles of canine lymphoma cells by microarray analysis using tumor cell samples at drug-sensitive and drug-resistant phases in 6 dogs. It was revealed that expression of the molecules related to chemotaxis and inflammation were down regulated in MDR phases.

2017-04-01 | GSE83274 | GEO

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