Long Non-Coding RNAs as Molecular Signatures for Canine B-Cell Lymphoma Characterization

Background: Diffuse large B-cell lymphoma (DLBCL), marginal zone lymphoma (MZL) and follicular lymphoma (FL) are the most common B-cell lymphomas (BCL) in dogs. Recent investigations have demonstrated overlaps of these histotypes with the human counterparts, including clinical presentation, biologic behavior, tumor genetics, and treatment response. The molecular mechanisms that underlie canine BCL are still unknown and new studies to improve diagnosis, therapy, and the utilization of canine species as spontaneous animal tumor models are undeniably needed. Recent work using human DLBCL transcriptomes has suggested that long non-coding RNAs (lncRNAs) play a key role in lymphoma pathogenesis and pinpointed a restricted number of lncRNAs as potential targets for further studies. Results: To expand the knowledge of non-coding molecules involved in canine BCL, we used transcriptomes obtained from a cohort of 62 dogs with newly-diagnosed multicentric DLBCL, MZL and FL that had undergone complete staging work-up and were treated with chemotherapy or chemo-immunotherapy. We developed a customized R pipeline performing a transcriptome assembly by multiple algorithms to uncover novel lncRNAs, and delineate genome-wide expression of unannotated and annotated lncRNAs. Our pipeline also included a new package for high performance system biology analysis, which detects high-scoring network biological neighborhoods to identify functional modules. Moreover, our customized pipeline quantified the expression of novel and annotated lncRNAs, allowing us to subtype DLBCLs into two main groups. The DLBCL subtypes showed statistically different survivals, indicating the potential use of lncRNAs as prognostic biomarkers in future studies. Conclusions: In this manuscript, we describe the methodology used to identify lncRNAs that differentiate B-cell lymphoma subtypes and we interpreted the biological and clinical values of the results. We inferred the potential functions of lncRNAs to obtain a comprehensive and integrative insight that highlights their impact in this neoplasm.

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Circulating long non-coding RNAs HOTAIR, Linc-p21, GAS5 and XIST expression profiles in diffuse large B-cell lymphoma: association with R-CHOP responsiveness

Scientific Reports ◽

10.1038/s41598-021-81715-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mahmoud A. Senousy ◽

Aya M. El-Abd ◽

Raafat R. Abdel-Malek ◽

Sherine M. Rizk

Keyword(s):

B Cell ◽

Cell Lymphoma ◽

Expression Profiles ◽

International Prognostic Index ◽

Prognostic Index ◽

B Cell Lymphoma ◽

Diagnostic Tools ◽

Large B Cell Lymphoma ◽

Non Coding Rnas ◽

Large B Cell

AbstractThe reliable identification of diffuse large B-cell lymphoma (DLBCL)-specific targets owns huge implications for its diagnosis and treatment. Long non-coding RNAs (lncRNAs) are implicated in DLBCL pathogenesis; however, circulating DLBCL-related lncRNAs are barely investigated. We investigated plasma lncRNAs; HOTAIR, Linc-p21, GAS5 and XIST as biomarkers for DLBCL diagnosis and responsiveness to R-CHOP therapy. Eighty-four DLBCL patients and thirty-three healthy controls were included. Only plasma HOTAIR, XIST and GAS5 were differentially expressed in DLBCL patients compared to controls. Pretreatment plasma HOTAIR was higher, whereas GAS5 was lower in non-responders than responders to R-CHOP. Plasma GAS5 demonstrated superior diagnostic accuracy (AUC = 0.97) whereas a panel of HOTAIR + GAS5 superiorly discriminated responders from non-responders by ROC analysis. In multivariate analysis, HOTAIR was an independent predictor of non-response. Among patients, plasma HOTAIR, Linc-p21 and XIST were correlated. Plasma GAS5 negatively correlated with International Prognostic Index, whereas HOTAIR positively correlated with performance status, denoting their prognostic potential. We constructed the lncRNAs-related protein–protein interaction networks linked to drug response via bioinformatics analysis. In conclusion, we introduce plasma HOTAIR, GAS5 and XIST as potential non-invasive diagnostic tools for DLBCL, and pretreatment HOTAIR and GAS5 as candidates for evaluating therapy response, with HOTAIR as a predictor of R-CHOP failure. We provide novel surrogates for future predictive studies in personalized medicine.

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Genome-wide profiling identifies a DNA methylation signature that associates with TET2 mutations in diffuse large B-cell lymphoma

Haematologica ◽

10.3324/haematol.2013.088740 ◽

2013 ◽

Vol 98 (12) ◽

pp. 1912-1920 ◽

Cited By ~ 85

Author(s):

F. Asmar ◽

V. Punj ◽

J. Christensen ◽

M. T. Pedersen ◽

A. Pedersen ◽

...

Keyword(s):

Dna Methylation ◽

B Cell ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Large B Cell Lymphoma ◽

Genome Wide ◽

Large B Cell

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Genome-wide DNA methylation and RNA-seq analyses identify genes and pathways associated with doxorubicin resistance in a canine diffuse large B-cell lymphoma cell line

PLoS ONE ◽

10.1371/journal.pone.0250013 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0250013

Author(s):

Chia-Hsin Hsu ◽

Hirotaka Tomiyasu ◽

Chi-Hsun Liao ◽

Chen-Si Lin

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

B Cell ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Rna Seq ◽

Doxorubicin Resistance ◽

Large B Cell Lymphoma ◽

Genome Wide ◽

Large B Cell

Doxorubicin resistance is a major challenge in the successful treatment of canine diffuse large B-cell lymphoma (cDLBCL). In the present study, MethylCap-seq and RNA-seq were performed to characterize the genome-wide DNA methylation and differential gene expression patterns respectively in CLBL-1 8.0, a doxorubicin-resistant cDLBCL cell line, and in CLBL-1 as control, to investigate the underlying mechanisms of doxorubicin resistance in cDLBCL. A total of 20289 hypermethylated differentially methylated regions (DMRs) were detected. Among these, 1339 hypermethylated DMRs were in promoter regions, of which 24 genes showed an inverse correlation between methylation and gene expression. These 24 genes were involved in cell migration, according to gene ontology (GO) analysis. Also, 12855 hypermethylated DMRs were in gene-body regions. Among these, 353 genes showed a positive correlation between methylation and gene expression. Functional analysis of these 353 genes highlighted that TGF-β and lysosome-mediated signal pathways are significantly associated with the drug resistance of CLBL-1. The tumorigenic role of TGF-β signaling pathway in CLBL-1 8.0 was further validated by treating the cells with a TGF-β inhibitor(s) to show the increased chemo-sensitivity and intracellular doxorubicin accumulation, as well as decreased p-glycoprotein expression. In summary, the present study performed an integrative analysis of DNA methylation and gene expression in CLBL-1 8.0 and CLBL-1. The candidate genes and pathways identified in this study hold potential promise for overcoming doxorubicin resistance in cDLBCL.

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‘Piperazining’ the catalytic gatekeepers: unraveling the pan-inhibition of SRC kinases; LYN, FYN and BLK by masitinib

Future Medicinal Chemistry ◽

10.4155/fmc-2018-0354 ◽

2019 ◽

Vol 11 (18) ◽

pp. 2365-2380

Author(s):

Aimen K Aljoundi ◽

Clement Agoni ◽

Fisayo A Olotu ◽

Mahmoud ES Soliman

Keyword(s):

Molecular Dynamics ◽

B Cell ◽

Molecular Dynamics Simulations ◽

Molecular Mechanisms ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Dynamics Simulation ◽

Large B Cell Lymphoma ◽

Dynamics Simulations ◽

Large B Cell

Aim: Blocking oncogenic signaling of B-cell receptor (BCR) has been explored as a viable strategy in the treatment of diffuse large B-cell lymphoma. Masitinib is shown to multitarget LYN, FYN and BLK kinases that propagate BCR signals to downstream effectors. However, the molecular mechanisms of its selectivity and pan-inhibition remain elusive. Materials & methods: This study therefore employed molecular dynamics simulations coupled with advanced post-molecular dynamics simulation techniques to unravel the structural mechanisms that inform the reported multitargeting ability of masitinib. Results: Molecular dynamics simulations revealed initial selective targeting of catalytic residues (Asp334/Glu335 – LYN; Asp130/Asp148/Glu54 – FYN; Asp89 – BLK) by masitinib, with high-affinity interactions via its piperazine ring at the entrance of the ATP-binding pockets, before systematic access into the hydrophobic deep pocket grooves. Conclusion: Identification of these ‘gatekeeper’ residues could open up a novel paradigm of structure-based design of highly selective pan-inhibitors of BCR signaling in the treatment of diffuse large B-cell lymphoma.

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Genome‐wide DNA methylation analysis using MethylCap‐seq in canine high‐grade B‐cell lymphoma

Journal of Leukocyte Biology ◽

10.1002/jlb.2a0820-673r ◽

2020 ◽

Author(s):

Chia‐Hsin Hsu ◽

Hirotaka Tomiyasu ◽

Jih‐Jong Lee ◽

Chun‐Wei Tung ◽

Chi‐Hsun Liao ◽

...

Keyword(s):

Dna Methylation ◽

B Cell ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

High Grade ◽

Methylation Analysis ◽

Genome Wide ◽

Dna Methylation Analysis

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Aberrant Somatic Hypermutation in Extranodal Marginal Zone B-Cell Lymphoma of MALT Type.

Blood ◽

10.1182/blood.v106.11.417.417 ◽

2005 ◽

Vol 106 (11) ◽

pp. 417-417 ◽

Cited By ~ 3

Author(s):

Alexander Deutsch ◽

Ariane Aigelsreiter ◽

Christine Beham-Schmid ◽

Alfred Beham ◽

Werner Linkesch ◽

...

Keyword(s):

B Cell ◽

Malt Lymphoma ◽

Marginal Zone ◽

De Novo ◽

Cell Lymphoma ◽

Somatic Hypermutation ◽

B Cell Lymphoma ◽

Chromosomal Translocations ◽

Genome Wide ◽

Balanced Translocations

Abstract Extranodal marginal zone B-cell lymphoma of mucosa associated lymphoid tissue (MALT lymphoma) accounts for approximately 7% to 8% of all non-Hodgkin lymphomas (NHLs) being the third most frequent histological subtype. The gastrointestinal tract - particularly the stomach - is the most common site of MALT lymphoma comprising 50% of all cases, but virtually every organ may be affected by this type of lymphoma. Transformation (or de novo emergence at extranodal sites) in diffuse large B-cell lymphoma (DLBCL) occurs but - according to the WHO criteria - is considered as separate entity. The understanding of the molecular biology of MALT lymphoma has significantly improved following the recent cloning of recurrent balanced translocations such as t(11;18) or t(14;18), but a mechanism for genome-wide instability during MALT lymphomagenesis has not been described. We have reported that the somatic hypermutation process (SHM) physiologically aimed at mutating the immunoglobulin variable gene (IgV) aberrantly targets multiple proto-oncogenes in >50% of DLCBL (Pasqualucci et al., Nature412:341, 2001). Consequently, multiple mutations are introduced in the 5′ region of genes including known proto-oncogenes such as PIM-1, PAX-5, Rho/TTF and c-MYC. To further investigate whether aberrant somatic hypermutation (ASHM) also occurs in MALT lymphoma, we studied the mutation profile of these genes in 17 MALT lymphomas (6 of gastric- and 11 of nongastric origin) and 18 extranodal DLBCL (10 gastric, 8 nongastric). Mutations in one or more genes were detected in 15 of 17 (88.2%) cases of MALT lymphoma and in all of 18 (100%) cases of extranodal DLBCL. 7 of 17 (41.2%) and 15 of 18 (83.3%) carried mutations in two or more genes in the MALT- and DLBC-lymphoma group, respectively. Overall, mutations in PIM-1 occurred in 5 of 17 (29.4%) cases with MALT lymphoma and in 10 of 18 (55.5%) in extranodal DLBCL cases. For PAX-5, the distribution of mutated cases between MALT- and DLBC-lymphoma was 6 of 17 (35.3%) and 10 of 18 (55.5%), for Rho/TTF 3 of 17 (17.6%) and 8 of 18 (44.4%) and for c-MYC 9 of 17 (52.9%) and 12 of 18 (66.6%), respectively. A total of 99 sequence variants were found in 35 cases, 29 in the MALT lymphomas and 70 in extranodal DLBCL. Although the mutations were almost exclusively single base pair substitutions (n=98 ), an insertion was also present (n=1). Mutations were of somatic origins, occur independent of chromosomal translocations to the Ig loci and share features of the IgV SHM process including bias for transition over transversion, preferential hotspot (RGYW/WRCY) targeting and restriction to the first 1–2Kb from the promoter. The mean mutation frequency in mutated MALT lymphomas was with 0.045 x10−2/bp 1.7 fold lower compared to 0.08 x10−2/bp in mutated extranodal DLBCL. Further in PIM-1, PAX-5 and c-MYC some of the mutations were found to affect coding exons, leading to amino acid exchanges, thus potentially altering gene function. These data indicate that aberrant SHM is associated with extranodal DLBCL and MALT lymphoma, likewise. By mutating regulatory and coding sequences of the targeted genes and by possibly favouring chromosomal translocations ASHM may represent a major contributor to their pathogenesis. ASHM may further support a model of MALT lymphomagenesis leading from an antigen driven lesion to transformed MALT lymphoma finally evolving to overt DLBCL.

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Targeting Positive Cofactor 4 induces autophagic cell death in MYC-expressing diffuse large B cell lymphoma

10.21203/rs.3.rs-421070/v1 ◽

2021 ◽

Author(s):

Le Ma ◽

Qiang Gong ◽

Zelin Chen ◽

Yu Wang ◽

Xu Tan ◽

...

Keyword(s):

Cell Death ◽

B Cell ◽

Molecular Mechanisms ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Autophagic Cell Death ◽

Large B Cell Lymphoma ◽

Large B Cell

Abstract Background: The MYC-expressing diffuse large B-cell lymphoma (DLBCL) is one of the refractory lymphomas. The pathogenesis of MYC-expressing DLBCL is still unclear, and there is a lack of effective therapy. In this study, we have explored the clinical significance and the molecular mechanisms of transcription co-activator 4 (PC4) in MYC-expressing DLBCL.Methods: We investigated PC4 expression in 54 cases of DLBCL patients’ tissues and matched normal specimens, and studied the molecular mechanisms of PC4 in MYC-expressing DLBCL both in vitro and in vivo.Results: We reported for the first time that targeting c-Myc could induce autophagic cell death in MYC-expressing DLBCL cell lines. We next characterized that PC4 was an upstream regulator of c-Myc, and PC4 was overexpressed in DLBCL and was closely related to clinical staging, prognosis and c-Myc expression. Further, our in vivo and in vitro studies revealed that PC4 knockdown could induce autophagic cell death of MYC-expressing DLBCL. And inhibition of c-Myc mediated aerobic glycolysis and activation of AMPK / mTOR signaling pathway were responsible for the autophagic cell death induced by PC4 knockdown in MYC-expressing DLBCL. Through the CHIP, DLRTM and EMSA assay, we also found that PC4 exerted its oncogenic functions by directly binding to c-Myc promoters.Conclusions: PC4 exerts its oncogenic functions by directly binding to c-Myc promoters. Inhibition of PC4 can induce autophagic cell death of MYC-expressing DLBCL. Our study provides novel insights into the functions and mechanisms of PC4 in MYC-expressing DLBCL, and suggests that PC4 might be a promising therapeutic target for MYC-expressing DLBCL.

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Distinct Molecular Subtypes of Diffuse Large B Cell Lymphoma Patients Treated with Rituximab-CHOP Are Associated with Different Clinical Outcomes and Molecular Mechanisms

BioMed Research International ◽

10.1155/2021/5514726 ◽

2021 ◽

Vol 2021 ◽

pp. 1-13

Author(s):

Haifeng Yu ◽

Shuailing Peng ◽

Shuiyun Han ◽

Xi Chen ◽

Qinghua Lyu ◽

...

Keyword(s):

Overall Survival ◽

T Cell ◽

B Cell ◽

Molecular Mechanisms ◽

Molecular Subtypes ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Training Set ◽

Large B Cell Lymphoma ◽

Large B Cell

Objective. Our purpose was to characterize distinct molecular subtypes of diffuse large B cell lymphoma (DLBCL) patients treated with rituximab-CHOP (R-CHOP). Methods. Two gene expression datasets of R-CHOP-treated DLBCL patients were downloaded from GSE10846 ( n = 233 , training set) and GSE31312 ( n = 470 , validation set) datasets. Cluster analysis was presented via the ConsensusClusterPlus package in R. Using the limma package, differential expression analysis was utilized to identify feature genes. Kaplan-Meier survival analysis was presented to compare the differences in the prognosis between distinct molecular subtypes. Correlation between molecular subtypes and clinical features was analyzed. Based on the sets of highly expressed genes, biological functions were explored by gene set enrichment analysis (GSEA). Several feature genes were validated in the molecular subtypes via qRT-PCR and western blot. Results. DLBCL samples were clustered into two molecular subtypes. Samples in subtype I displayed poorer overall survival time in the training set ( p < 0.0001 ). Consistently, patients in subtype I had shorter overall survival ( p = 0.0041 ) and progression-free survival time ( p < 0.0001 ) than those in subtype II. Older age, higher stage, and higher international prognostic index (IPI) were found in subtype I. In subtype I, T cell activation, lymphocyte activation, and immune response were distinctly enriched, while cell adhesion, migration, and motility were significantly enriched in subtype II. T cell exhaustion-related genes including TIM3 ( p < 0.001 ), PD-L1 ( p < 0.0001 ), LAG3 ( p < 0.0001 ), CD160 ( p < 0.001 ), and CD244 ( p < 0.001 ) were significantly highly expressed in subtype I than subtype II. Conclusion. Two molecular subtypes were constructed in DLBCL, which were characterized by different clinical outcomes and molecular mechanisms. Our findings may offer a novel insight into risk stratification and prognosis prediction for DLBCL patients.

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Molecular Genetics of Relapsed Diffuse Large B-Cell Lymphoma: Insight into Mechanisms of Therapy Resistance

Cancers ◽

10.3390/cancers12123553 ◽

2020 ◽

Vol 12 (12) ◽

pp. 3553

Author(s):

Madeleine R. Berendsen ◽

Wendy B. C. Stevens ◽

Michiel van den Brand ◽

J. Han van Krieken ◽

Blanca Scheijen

Keyword(s):

B Cell ◽

Molecular Mechanisms ◽

Cell Lymphoma ◽

Treatment Options ◽

B Cell Lymphoma ◽

Therapy Resistance ◽

Genetic Alterations ◽

Comprehensive Overview ◽

Large B Cell Lymphoma ◽

Large B Cell

The majority of patients with diffuse large B-cell lymphoma (DLBCL) can be treated successfully with a combination of chemotherapy and the monoclonal anti-CD20 antibody rituximab. Nonetheless, approximately one-third of the patients with DLBCL still experience relapse or refractory (R/R) disease after first-line immunochemotherapy. Whole-exome sequencing on large cohorts of primary DLBCL has revealed the mutational landscape of DLBCL, which has provided a framework to define novel prognostic subtypes in DLBCL. Several studies have investigated the genetic alterations specifically associated with R/R DLBCL, thereby uncovering molecular pathways linked to therapy resistance. Here, we summarize the current state of knowledge regarding the genetic alterations that are enriched in R/R DLBCL, and the corresponding pathways affected by these gene mutations. Furthermore, we elaborate on their potential role in mediating therapy resistance, also in connection with findings in other B-cell malignancies, and discuss alternative treatment options. Hence, this review provides a comprehensive overview on the gene lesions and molecular mechanisms underlying R/R DLBCL, which are considered valuable parameters to guide treatment.

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Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma

Blood Advances ◽

10.1182/bloodadvances.2019000175 ◽

2019 ◽

Vol 3 (19) ◽

pp. 2790-2799 ◽

Cited By ~ 3

Author(s):

Brian C.-H. Chiu ◽

Zhou Zhang ◽

Qiancheng You ◽

Chang Zeng ◽

Elizabeth Stepniak ◽

...

Keyword(s):

Prognostic Factors ◽

B Cell ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Free Dna ◽

Large B Cell Lymphoma ◽

Genome Wide ◽

Key Points ◽

Prognostic Implications ◽

Large B Cell

Key Points Genome-wide 5hmC loci can be profiled in 1 to 2 ng of cfDNA from blood plasma and correlate with clinical features of DLBCL. 5hmC in cfDNA collected at the time of DLBCL diagnosis is associated with EFS and OS, independent of established prognostic factors.

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