Activated B-cell-like Subgroup Research Articles

Cell-of-Origin Subtype Prediction of Diffuse Large B-Cell Lymphoma Using Gene Expression and Proteomic Data

IntroductionDiffuse large B-cell lymphoma (DLBCL) subtypes can be identified based on immunohistochemistry, somatic mutation and gene expression profiles. These cell-of-origin (COO) subtypes have distinct biological and pathogenic characteristics. In addition, studies have shown the association of COO with drug response such as with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) as well as targeted therapy. Therefore, proper assessment of COO subgroup is an important step in treatment selection and outcome. In this study, we sought to develop predictive COO models using RNA-Seq based gene expression profiling and plasma proteomic data, focusing on the two defined major DLBCL subtypes - germinal center B cell-like (GCB) and activated B cell-like (ABC).MethodsCOO subgroups of patient samples were assigned by the Hans algorithm. Data from archival formalin-fixed paraffin-embedded (FFPE) tissues were obtained using the Illumina HiSeq platform (RNA-Seq). A subset of samples were used as a training set to select differentially expressed genes (DEGs) in ABC vs. GCB lymphomas to build support vector machine (SVM) classification models. The model with best leave-one-out cross validation (LOOCV) on the training set was applied to the remaining samples to assess its initial predictive power. Gene set enrichment analysis (GSEA, Broad Institute) and key pathway analysis (KPA, Clarivate Analytics) were also utilized to further explore the underlying biology of each COO subtype. Protein expression data using the Olink Proteomics platform was obtained from baseline patient plasma samples. Protein biomarkers to differentiate ABC and GCB subgroups were identified from a set of training samples and evaluated in independent cohorts. Due to notable batch effect, batch information was included and specified as a random factor in the model.ResultsGenes identified by Scott et al. (Blood 2014) for COO assignment were first tested in our RNA-Seq training data of 6 GCB and 8 ABC samples. Thirteen of 15 gene markers showed significant differences between the ABC and GCB subgroups. From these markers, we further selected 6 to build machine learning models based on fold change, false discovery rate and entropy. This 6-gene signature include 3 markers relatively up-regulated in ABC subtype and 3 up-regulated in GCB subtype. A SVM model with these genes achieved 100% LOOCV on the training data and correctly predicted COO of 20/22 samples in the validating cohort with 1 GCB and 1 ABC samples misclassified. These two samples were also misclassified if a larger panel of signature genes from Scott et al. (Blood 2014) was used. KPA on the DEGs from ABC vs. GCB predicted the activation of NFKB1and STAT4/5 transcription factors as key elements upstream of the DEGs, indicating promoted signaling of NFкB and STAT pathways in ABC subgroup. On the other hand, REST was predicted as an inhibited upstream regulator of some DEGs. RCOR1, a corepressor of REST, has significantly lower expression level in the ABC subgroup in our data. These may imply the inhibition of REST/RCOR1 pathway in ABC patients.Plasma protein data from two studies were used to form a training set with 21 GCB and 6 ABC. A set of differentially expressed analytes from ABC vs. GCB were identified which included several targets of the NFкB pathway. In an independent cohort containing 5 GCB and 4 ABC plasma samples, many of these same plasma proteins showed differential expression profiles between ABC and GCB, making them potential blood-based biomarkers for COO determination.ConclusionsIn this study, we built a SVM model with a subset of genes from Scott et al. (Blood 2014) to accurately predict COO of refractory DLBCL from archival FFPE tissue. Further analyses of the RNA-Seq data disclosed alterations in key transcriptional hubs between the different COO subgroups. Olink plasma data from independent cohorts demonstrated potential protein markers for a plasma-based differentiation of the ABC and GCB subtypes. These biomarkers and machine learning models are being further validated using additional datasets. DisclosuresLiu:Incyte Research Institute: Employment, Equity Ownership. Lu:Incyte Research Institute: Employment, Equity Ownership. Dong:Incyte Research Institute: Employment, Equity Ownership. Liu:Incyte Research Institute: Employment, Equity Ownership. Salinas:Incyte Research Institute: Employment, Equity Ownership. Owens:Incyte Research Institute: Employment, Equity Ownership. Pratta:Incyte Research Institute: Employment, Equity Ownership. Smith:Incyte Research Institute: Employment, Equity Ownership. Tada:Incyte Research Institute: Employment, Equity Ownership. Newton:Incyte Research Institute: Employment, Equity Ownership. Burn:Incyte Research Institute: Employment, Equity Ownership.

Clinical significance and detection of microRNA‐21 in serum of patients with diffuse large B‐cell lymphoma in Chinese population

Expression patterns of microRNAs in serum are involved in potentially non-invasive biomarkers for various diseases. The purpose of this study is to examine the expression of miR-21 in serum of patients with diffuse large B-cell lymphoma (DLBCL) and to validate the significance of miR-21 in early diagnosis, genotyping, treatment options as well as its prognosis estimates of Chinese DLBCL. miR-21 expression was detected by fluorescent quantity polymerase chain reaction (qPCR) in 9 DLBCL cell lines (OCI-Ly1, OCI-Ly3, OCI-Ly4, OCI-Ly7, OCI-Ly8, OCI-Ly10, OCI-Ly18, OCI-Ly19, and HBL), as well as in tumor tissue and serum samples from patients with DLBCL (germinal center B-cell-like (GCB) DLBCL 32; activated B-cell-like (ABC) DLBCL 30) and 50 healthy subjects. Expression of miR-21 was increased in DLBCL cell lines. Compared with the miR-21 expression of GCB subgroup (OCI-Ly1, OCI-Ly4, OCI-Ly7, OCI-Ly8, OCI-Ly18, OCI-Ly19), ABC subgroup (OCI-Ly3, OCI-Ly10, and HBL) has higher expression (t = 11.18, P < 0.01). Circulating miR-21 level in sera from patients with DLBCLwas associated with matched tumor tissue (r(2) = 0.931, P < 0.0001). Consistent with the in vitro, miR-21 expression levels in serum of patients with DLBCL [21.38(10.26-45.21)] were higher than those in serum of control cases [1.87(1.05-3.97); U = 168, P = 0.000]. Moreover, miR-21 expression levels in serum of patients with subgroup ABC [28.68(14.92~98.44)] were higher than that of patients with subgroup GCB [18.3(7.32~33.46); U = 336, P = 0.043]. miR-21 expression in serum of DLBCL with stage I and II were higher than those in stage III and IV (U = 62, P = 0.013 in GCB type; U = 53, P = 0.014 in ABC type). Compared with relapse-free survival in patients with DLBCL, high expression of miR-21 was associated with well prognosis (U = 259, P = 0.035). miR-21 expressed in the serum of patients with DLBCL from Chinese was associated with clinical stage, molecular subgroup, and prognosis estimates. miR-21 may be served as a biomarker in early diagnosis, genotyping, treatment options, and prognosis estimating of Chinese DLBCL.

Central nervous system lymphoma in immunocompetent patients: The North Shore-Long Island Jewish Health System experience

Of the 74 immunocompetent patients diagnosed between July 2004 and June 2011 at the North Shore University Hospital and Long Island Jewish Medical Center with primary central nervous system lymphoma, 71 (95.9%) had diffuse large B-cell lymphomas (DLBCL). The median patient age was 68years (range: 19–87years) with a slight male preponderance (1.1:1). The overall median survival time was 21months. For patients older than 70years, the median survival time was 8months while for those 70years or younger, the median survival time was 27months (p<0.01). Female patients had a worse prognosis than male patients (p<0.05, median survival time, 17months compared to 23months). We had enough data from 52 of these 71 patients to define the lymphomas as either germinal center B-cell-like (GCB) or activated B-cell-like (ABC) DLBCL. Of these 52 patients, 42 (80.8%) had ABC DLBCL while only 10 (19.2%) had GCB DLBCL. The patients in the GCB subgroup seemed to survive longer than the patients in the ABC subgroup, although the difference did not reach statistical significance. No statistically significant difference in overall survival was seen between patients with BCL-6 positive or negative DLBCL; or between patients with BCL-2 positive or negative DLBCL.

Quantitative Proteomics Reveals that miR-155 Regulates the PI3K-AKT Pathway in Diffuse Large B-Cell Lymphoma

The aberrant expression of microRNA-155 (miR-155), which has emerged as having a significant impact on the biological characteristics of lymphocytes, plays important roles in B-cell malignancies, such as diffuse large B-cell lymphoma (DLBCL). DLBCL is the most common non-Hodgkin's lymphoma in the adult population, accounting for approximately 40% of newly diagnosed non-Hodgkin's lymphoma cases globally. To determine the specific function of miR-155, a quantitative proteomics approach was applied to examine the inhibitory effects of miR-155 on protein synthesis in DLBCL cells. PIK3R1 (p85α), a negative regulator of the phosphatidylinositol 3-kinase (PI3K)-AKT pathway, was identified as a direct target of miR-155. A luciferase reporter was repressed through the direct interaction of miR-155 and the p85α 3'-untranslated region, and overexpression of miR-155 down-regulated both the transcription and translation of p85α. The PI3K-AKT signaling pathway was highly activated by the sustained overexpression of miR-155 in DHL16 cells, whereas knockdown of miR-155 in OCI-Ly3 cells diminished AKT activity. Taken together, our results reveal a novel target involved in miR-155 biological characteristics and provide a molecular link between the overexpression of miR-155 and the activation of PI3K-AKT in DLBCL.

Abstract 5568: Constitutively activation of STAT3 is a prognostic factor in activated B-cell subtype of diffuse large B-cell lymphoma

Abstract We have previously reported aberrant activation of the signal transducer and activator of transcription 3 (STAT3) pathway promotes cell proliferation and survival in the activated B-cell-like (ABC) subtype, but not in the germinal center B-cell-like (GCB) subtype of diffuse large B-cell lymphoma (DLBCL). Herein, we investigated the effects of small molecular inhibitors of STAT3 in sensitizing DLBCL cell to chemotherapy drugs. ABC-DLBCL lines Ly3 and Pfeiffer were more resistant to vincristine-induced cell death than GCB-DLBCL cells Ly1 and Ly7 were. In ABC-DLBCL cells, constitutive activation of STAT3 provided survival signal and inhibited vincristine-induced apoptosis, while inhibition of STAT3 signaling abrogated IL-6 secretion and promoted cell apoptosis. STAT3 inhibitor and chemotherapy drugs synergistically induced cell apoptosis, with increased caspases 3/7 activity and PARP cleavage, in ABC-DLBCL cells but not in the GCB-DLBCL cells. The effect was correlated with reduced expression of MCL1 in these cells. To investigate the prognostic significance of STAT3 activation in DLBCL patients, we evaluated the levels of phospho-Tyr705-STAT3 (PY-STAT3) expression by immunohistochemistry in a cohort of 309 DLBCL patients treated with R-CHOP regimen. The ABC-DLBCL subgroup had significantly higher number of PY-STAT3 positive cases compared to the GCB subgroup (59.4% vs 36.2%; P = 0.003). Constitutive activation of STAT3 pathway has a significant impact on the overall-survival (OS) and event-free-survival (EFS) in the entire DLBCL cohort (OS, P = 0.010; EFS, P = 0.006) and in the ABC subgroup (OS, P = 0.062; EFS, P=0.016). Moreover, we constructed a subgroup of genes representing STAT3 activation from the gene expression profiling data of STAT3-siRNA treated ABC cell lines and primary DLBCL samples. Attributions of these genes include repression with the STAT3 knockdown in DLBCL cell lines, overexpression in the PY-STAT3-positive DLBCL tumors, and containing one or more STAT3 binding motif within their promoter regions. Eleven genes were obtained when trained this gene subgroup with patient survival through a semi-supervised algorithm. Averaged expression of the eleven genes predicted the OS (P &amp;lt; 0.001) and EFS (P &amp;lt; 0.001) in the entire DLBCL cohort, as well as in the ABC-DLBCL subgroup (OS, P = 0.029; EFS, P = 0.025). In conclusion, our study demonstrated that STAT3 activation is a significant prognostic factor in DLBCL and suggested that STAT3 may be a new therapeutic target in this aggressive malignancy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5568. doi:1538-7445.AM2012-5568

Primary diffuse large B-cell lymphoma of central nervous system belongs to activated B-cell-like subgroup: a study of 47 cases

To investigate the histogenetic origin of primary central nervous system diffuse large B-cell lymphoma (DLBCL) with respect to the stage of B-cell differentiation, and identification of the relevant prognostic markers. Immunohistochemical staining (EnVision method) for CD10, bcl-6, MUM-1, CD138 and FOXP1 antigens was performed on 47 paraffin-embedded sections. CD10, bcl-6, MUM-1 and FOXP1 expression in the tumor cells were 6.4%, 53.2%, 91.5% and 93.6% respectively. There was no expression of CD138 in all the cases. Among the 47 patients, 43 cases (91.5%) showed an activated B-cell-like (ABC) phenotype: 21 (44.7%) were bcl-6+ and MUM-1+, suggesting an "activated germinal center (GC) B-cell-like" in origin; 22 (46.8%) were exclusively MUM-1+, suggesting an "activated non-GCB" in origin. No significant correlation of the classification and FOXP1 expression found on the outcome (P=0.279 and P=0.154). Most primary central nervous system DLBCL are shown belonging to the ABC subgroup, suggesting that primary central nervous system DLBCL is quite similar to a DLBCL subset, which is derived from late GC to early post-GC B cell. The classification and FOXP1 expression do not show prognostic value in primary central nervous system DLBCL.

Distinctive patterns of BCL6 molecular alterations and their functional consequences in different subgroups of diffuse large B-cell lymphoma

Gene expression profiling of diffuse large B-cell lymphoma (DLBCL) has revealed biologically and prognostically distinct subgroups: germinal center B-cell-like (GCB), activated B-cell-like (ABC) and primary mediastinal (PM) DLBCL. The BCL6 gene is often translocated and/or mutated in DLBCL. Therefore, we examined the BCL6 molecular alterations in these DLBCL subgroups, and their impact on BCL6 expression and BCL6 target gene repression. BCL6 translocations at the major breakpoint region (MBR) were detected in 25 (18.8%) of 133 DLBCL cases, with a higher frequency in the PM (33%) and ABC (24%) subgroups than in the GCB (10%) subgroup. Translocations at the alternative breakpoint region (ABR) were detected in five (6.4%) of 78 DLBCL cases, with three cases in ABC and one case each in the GCB and the unclassifiable subgroups. The translocated cases involved IgH and non-IgH partners in about equal frequency and were not associated with different levels of BCL6 mRNA and protein expression. BCL6 mutations were detected in 61% of DLBCL cases, with a significantly higher frequency in the GCB and PM subgroups (>70%) than in the ABC subgroup (44%). Exon-1 mutations were mostly observed in the GCB subgroup. The repression of known BCL6 target genes correlated with the level of BCL6 mRNA and protein expression in GCB and ABC subgroups but not with BCL6 translocation and intronic mutations. No clear inverse correlation between BCL6 expression and p53 expression was observed. Patients with higher BCL6 mRNA or protein expression had a significantly better overall survival. The biological role of BCL6 in translocated cases where repression of known target genes is not demonstrated is intriguing and warrants further investigation.

Germinal Center B Cell-Like (GCB) and Activated B Cell-Like (ABC) Type of Diffuse Large B Cell Lymphoma (DLBCL): Analysis of Molecular Predictors, Signatures, Cell Cycle State and Patient Survival

Aiming to find key genes and events, we analyze a large data set on diffuse large B-cell lymphoma (DLBCL) gene-expression (248 patients, 12196 spots). Applying the loess normalization method on these raw data yields improved survival predictions, in particular for the clinical important group of patients with medium survival time. Furthermore, we identify a simplified prognosis predictor, which stratifies different risk groups similarly well as complex signatures. We identify specific, activated B cell-like (ABC) and germinal center B cell-like (GCB) distinguishing genes. These include early (e.g. CDKN3) and late (e.g. CDKN2C) cell cycle genes. Independently from previous classification by marker genes we confirm a clear binary class distinction between the ABC and GCB subgroups. An earlier suggested third entity is not supported. A key regulatory network, distinguishing marked over-expression in ABC from that in GCB, is built by: ASB13, BCL2, BCL6, BCL7A, CCND2, COL3A1, CTGF, FN1, FOXP1, IGHM, IRF4, LMO2, LRMP, MAPK10, MME, MYBL1, NEIL1 and SH3BP5. It predicts and supports the aggressive behaviour of the ABC subgroup. These results help to understand target interactions, improve subgroup diagnosis, risk prognosis as well as therapy in the ABC and GCB DLBCL subgroups.

Distinctive Patterns of BCL6 Molecular Alterations in Different Subsets of Diffuse Large B-Cell Lymphoma and Their Functional Consequences.

Gene expression profiling of diffuse large B-cell lymphoma (DLBCL) has revealed biologically and prognostically distinct subgroups: germinal center B-cell-like (GCB), activated B cell-like (ABC), and primary mediastinal (PM) DLBCL. The BCL6 gene on chromosome 3q27 is a transcriptional repressor and is required for GC formation and function. Two molecular alterations involving the BCL6 gene are commonly observed in DLBCL: chromosomal translocations and mutations in the 5′ non-coding region.The functional consequences of BCL6 translocation and mutation have not been studied in the context of DLBCL subgroups. Therefore, we examined the frequency of translocations and the spectrum of BCL6 mutations in exon 1 and intron 1 in different DLBCL subgroups. We correlated these findings with BCL6 mRNA and protein expression, as well as the expression of BCL6 target genes. Fluorescence in situ hybridization (FISH) using a break-apart probe detected BCL6 translocations in 24 of 112 (21%) DLBCL cases. Surprisingly, the frequency of BCL6 translocation was higher in the ABC subgroup than the GCB subgroup (10 of 40; 25% vs 5 of 44; 11%, respectively) and the PM subgroup had the highest incidence (4 of 8; 50%). Expression of BCL6 protein was detected by immunohistochemistry in 75 of 138 cases (54%), including 15 of 44 (34%) in the ABC subgroup, 46 of 57 (80%) in the GCB subgroup and 4 of 10 (40%) in the PM subgroup. A good correlation of protein and mRNA expression, as assessed by cDNA microarrays (NEJM 346:1937–47; 2002) was observed in the GCB subgroup but not in the other subgroups. BCL6 mutations were detected in 71 of 128 cases (55%) of DLBCL with a higher frequency in the GCB subgroup (34 of 50; 68%) and PM subgroup (10 of 12; 90%) than the ABC subgroup (14 of 43; 32%). Interestingly, there was a distinctive pattern of distribution of BCL6 mutations in the DLBCL subgroups. For example, 11 of 100 (11%) of the mutations targeted exon 1 and 8 of these 11 mutants were observed in the GCB subgroup. They preferentially affected the BCL6, STAT1 or predicted CEBP binding sites. High BCL6 mRNA and protein expression was generally associated with mutants affecting the 3′ BCL6 binding sites. We also examined the expression of 25 known BCL6 target genes in the different subgroups of DLBCL and observed the repression of this set of genes mainly in the GCB but not in the ABC subgroup, and the presence of a translocation did not correlate with target gene suppression.In conclusion, the frequency of BCL6 translocation and mutation is distinctly different in the DLBCL subgroups and BCL6 expression has different regulatory influences on target genes in different subgroups of DLBCL. Exon 1 mutations preferentially occur in the GCB subgroup and affect transcription factor binding sites. However, BCL6 translocations did not show good correlation with BCL6 expression or functional repression of target genes. The influence of the reciprocal partner genes in the translocations on the pathogenesis of DLBCL warrants further investigation.

Gene Expression Profiling of Diffuse Large B-Cell Lymphoma

Initial gene expression profiling studies of diffuse large B-cell lymphoma (DLBCL) revealed that this single diagnosis actually encompasses two distinct diseases that differ in the expression of hundreds of genes. One subtype, germinal center B-cell-like (GCB) DLBCL, strongly resembles normal germinal center B-cells and has a good prognosis following chemotherapy, whereas activated B-cell-like (ABC) DLBCL resembles mitogenically activated blood B cells and has a poor outcome. An expanded analysis of 274 DLBCL cases confirmed the existence of the GCB and ABC subgroups, but demonstrated that additional subgroups exist. Furthermore, two recurrent oncogenic events in DLBCL, t(14;18) and amplification of the c-rel locus on chromosome 2p, were only observed in GCB DLBCL, whereas constitutive activation of NF-κB was seen in ABC DLBCL, showing that the gene expression subgroups represent pathogenetically distinct diseases. Gene expression profiling has also been used to identify individual genes that predict overall survival in DLBCL, the majority coming from gene expression signatures that reflect the cell of origin, proliferation rate, and host immune response to the tumor. A multivariate model including 17 genes representing these biological features divided patients with DLBCL into quartiles with strikingly distinct 5-year survival rates, ranging from 73% to 15%. The use of gene expression profiling should eventually lead to an integration of molecular diagnosis and consequent selection of the most appropriate treatment.