Comprehensive analysis of TP53 mutation characteristics and identification of patients with inferior prognosis and enhanced immune escape in diffuse large B cell lymphoma

Abstract Background: Diffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous lymphatic malignancy. The role of TP53 gene alterations in DLBCL remains unclear. Methods: We performed a comprehensive analysis of the genomic characteristics of TP53 through targeted next-generation sequencing (n=176), RNA-sequencing (n=152), and circulating tumor DNA sequencing (n=38). Results: TP53 was frequently mutated in DLBCL; most TP53 mutations occurred in the DNA-binding domain (DBD). However, TP53 alone is insufficient to effectively differentiate the risk of DLBCL, even when only considering mutations in the DBD region. However, CD58 mutations, which are mutually exclusive from TP53 mutations, in combination with TP53 mutations, could significantly differentiate the prognosis of DLBCL. The survival of patients with either one of the mutually exclusive mutation patterns, namely, TP53MUT&CD58WT or TP53WT&CD58MUT, was inferior to those harboring both wild-type TP53 and CD58. Notably, patients with the TP53WT&CD58MUT mutation pattern had the worst outcome and were characterized by an enhanced immune escape, including features such as the abundant infiltration of inflammatory cells and upregulation of inhibitory immunomodulatory molecules; these patients represent the candidate populations for immune therapy. Conclusions: Our findings indicated that the mutation patterns of TP53 and CD58 accurately stratified patients with DLBCL to permit the optional immunotherapy.

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Comprehensive Analysis of TP53 Mutation Characteristics and Identification of Patients with Inferior Prognosis and Enhanced Immune Escape in Diffuse Large B Cell Lymphoma

Blood ◽

10.1182/blood-2021-149899 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 4485-4485

Author(s):

Tingting Zhang ◽

Yue Fei ◽

Bin Meng ◽

Qiongli Zhai ◽

Xiubao Ren ◽

...

Keyword(s):

Tp53 Mutation ◽

Immune Escape ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Comprehensive Analysis ◽

Dna Binding Domain ◽

Tp53 Mutations ◽

Large B Cell Lymphoma ◽

Mutation Pattern ◽

Large B Cell

Abstract Background: Diffuse large B-cell lymphoma (DLBCL) is a highly heterogeneous lymphatic malignancy from both the clinical and molecular standpoints. TP53 mutations have been observed in DLBCL with high frequency mutations, which play a crucial role in lymphomagenesis. Considering the complex pathophysiological mechanisms involved in DLBCL, we herein assume that the interaction of TP53 with other genetic variants together promote the development of DLBCL. We also explore that these genetic interactions shape the discrepant immune landscape in DLBCL. Methods: We performed a comprehensive analysis of TP53 mutations in the DNA-binding domain (DBD) region. Genome alterations that were mutually exclusive or co-occurring with TP53 mutations were identified, and their potential value in prognosis and possible relationships with tumor microenvironment (TME) were further examined using targeted next-generation sequencing (n=176), transcriptome sequencing (n=152) and circulating tumor DNA sequencing (n=38). Results: TP53 was frequently mutated in DLBCL with a rate of 30% (53 of 176). The occurrence of TP53 mutations was skewed toward the early stages of DLBCL pathogenesis. Among these variants of TP53, 74% were missense mutations, and the remaining were inactivating frameshift indels, nonsense mutations, coding sequencing indels and splicing mutations. Importantly, most mutations (87.5%) occurred in exons 5-8, which encoded the DNA-binding domain (DBD) region of TP53. Codons 175, 273, and 248 of the p53 protein had the highest mutation frequency, which are also the hot spots of TP53 mutation found in most human cancers. However, TP53 alone is insufficient to effectively differentiate the risk of DLBCL, even when only considering mutations in the DBD region. CD58 mutations, which are mutually exclusive from TP53 mutations, in combination with TP53 mutations, could significantly differentiate the prognosis of DLBCL. The survival of patients with either one of the mutually exclusive mutation patterns, namely, TP53MUT&CD58WT or TP53WT&CD58MUT, was inferior to those harboring both wild-type TP53 and CD58. Notably, patients with TP53WT&CD58MUT mutation pattern had the worst outcome and were characterized by a higher overall tumor mutation burden (TMB) and immune score. An enhanced immune escape feature, including the abundant infiltration of inflammatory cells and upregulation of inhibitory immunomodulatory molecules such as PD-1, TIM3, LAG3, KLRC1, KLRC3, KLRD1, IDO1, IDO2 and TDO2, was observed in these patients with TP53WT&CD58MUT mutation pattern. A larger number of terms related to cytokine and chemokine and inflammatory pathways were enriched in the TP53WT&CD58MUT group, including cytokine and chemokine production, binding and activity, and interferon-γ pathway. Additionally, GSEA demonstrated that interferon-α and -γ responses and IL-6/JAK/STAT3 signaling enriched in the TP53WT&CD58MUT group. These patients with TP53WT&CD58MUT mutation pattern represent the candidate populations for immune therapy. Conclusions: Our findings indicated that the mutation patterns of TP53 and CD58 accurately stratified patients with DLBCL to permit the optional immunotherapy. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

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Prognostic impact of TP53 mutation in newly diagnosed diffuse large B‐cell lymphoma patients treated in the FIL‐DLCL04 trial

British Journal of Haematology ◽

10.1111/bjh.17971 ◽

2021 ◽

Author(s):

Annalisa Chiappella ◽

Fary Diop ◽

Claudio Agostinelli ◽

Mattia Novo ◽

Luca Nassi ◽

...

Keyword(s):

B Cell ◽

Tp53 Mutation ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Prognostic Impact ◽

Newly Diagnosed ◽

Large B Cell Lymphoma ◽

Large B Cell

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PD-L1 gene alterations identify a subset of diffuse large B-cell lymphoma harboring a T-cell–inflamed phenotype

Blood ◽

10.1182/blood-2018-10-879015 ◽

2019 ◽

Vol 133 (21) ◽

pp. 2279-2290 ◽

Cited By ~ 28

Author(s):

James Godfrey ◽

Sravya Tumuluru ◽

Riyue Bao ◽

Michael Leukam ◽

Girish Venkataraman ◽

...

Keyword(s):

T Cell ◽

B Cell ◽

Immune Escape ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Data Set ◽

Large B Cell Lymphoma ◽

Programmed Death ◽

Large B Cell ◽

Gene Alterations

Abstract Programmed death-ligand 1 (PD-L1) expression on malignant cells is a dominant immune escape mechanism across a variety of human cancers. A unique genetic mechanism underlying PD-L1 upregulation has been uncovered in classical Hodgkin lymphoma (cHL), in which copy gains of the chromosomal region (9p24.1) containing the programmed death-1 (PD-1) ligands PD-L1 and PD-L2 are recurrently observed. While chromosome 9p24.1 copy-number alterations are ubiquitous in cHL, they also occur in diffuse large B-cell lymphoma (DLBCL), albeit with a lower incidence. Here, fluorescence in situ hybridization was used to identify DLBCLs harboring PD-L1 gene alterations, thereby enabling a characterization of the immunogenomic landscape of these lymphomas. Among 105 DLBCL cases analyzed, PD-L1 alterations were identified in 27%. PD-L1 alterations were highly enriched among non–germinal center DLBCLs and exhibited robust PD-L1 protein expression. These lymphomas were heavily infiltrated by clonally restricted T cells and frequently downregulated human leukocyte antigen expression. RNA sequencing of PD-L1–altered DLBCLs revealed upregulation of genes involved in negative T-cell regulation and NF-κB pathway activation, while whole-exome sequencing identified frequent mutations in genes involved in antigen presentation and T-cell costimulation. Many of these findings were validated in a large external data set. Interestingly, DLBCL patients with PD-L1 alterations had inferior progression-free survival following front-line chemoimmunotherapy; however, in the relapsed/refractory setting, PD-L1 alterations were associated with response to anti-PD-1 therapy. Collectively, our results indicate that PD-L1 alterations identify a unique biological subset of DLBCL in which an endogenous antilymphoma immune response has been activated, and that is associated with responsiveness to PD-1 blockade therapy.

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A limited role for TP53 mutation in the transformation of follicular lymphoma to diffuse large B-cell lymphoma

Leukemia ◽

10.1038/sj.leu.2403802 ◽

2005 ◽

Vol 19 (8) ◽

pp. 1459-1465 ◽

Cited By ~ 44

Author(s):

A J Davies ◽

A M Lee ◽

C Taylor ◽

A J Clear ◽

L K Goff ◽

...

Keyword(s):

Follicular Lymphoma ◽

B Cell ◽

Tp53 Mutation ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Large B Cell Lymphoma ◽

Limited Role ◽

Large B Cell

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Genomic and Transcriptional Characterization of Primary Mediastinal Large B Cell Lymphoma

Blood ◽

10.1182/blood-2021-149745 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 2398-2398

Author(s):

Rebecca J Leeman-Neill ◽

Devang Thakkar ◽

Sarah L. Ondrejka ◽

Eric D. Hsi ◽

Amy Chadburn ◽

...

Keyword(s):

B Cells ◽

B Cell ◽

Research Funding ◽

Immune Escape ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Dna And Rna ◽

Large B Cell Lymphoma ◽

Recurrent Mutations ◽

Large B Cell

Abstract Introduction: Primary mediastinal large B-cell lymphoma (PMBL) is a rare non-Hodgkin lymphoma subtype that occurs predominantly in young adults, with an overall favorable prognosis. The cell of origin is presumed to be thymic medullary B-cells and the gene expression profile of PMBL is similar to classic Hodgkin lymphoma. Recent studies have begun unravelling the genomic alterations underlying PMBL. Frequent, recurrent mutations (e.g. B2M, TNFAIP3, SOCS1, STAT6, GNA13) have been reported, but most of the studies have analyzed a small number of cases. To gain further insights into disease biology, we recruited 63 cases of PMBL as part of the Atlas of Blood Cancer Genomes (ABC-G) initiative, a consortium consisting of 25 institutions. Methods: Formalin-fixed paraffin-embedded (FFPE) biopsies and clinical data were collected. All cases were subjected to centralized review by an experienced panel of hematopathologists to ensure accurate diagnosis. Whole-exome DNA and RNA sequencing was performed using the Illumina platform and the DNA and RNA reads aligned to the GRCh38 genome and transcriptome respectively. Exonic variants were filtered using a set of paired normal samples and population-based databases to identify putative driver mutations, which were then aggregated at the gene level. Mutational analysis was performed on 56 samples that passed quality filtering and expression analysis on 45 samples. RNAseq data was normalized using DESeq2. Results: The cohort included samples from 16 males and 24 females, with a median age of 33 years (range 16 - 72) at the time of diagnosis. The majority of patients were treated with R-CHOP (47%) or R-EPOCH (43%), with 93% of patients surviving through the end of follow-up (median follow-up: 60.1 months). Besides the known recurrent mutations involving the JAK-STAT (STAT6 -21%, SOCS1 - 26%), NFKB (TNFAIP3 - 27%, NFKB1A - 7%), immune escape (B2M - 20%, LTB - 11%, IRF8 - 9%, IRF4 -9%), and chromatin modification (ZNF217 - 16%, CREBBP - 11%, KMT2D -11%) pathways , we discovered recurrent somatic variants in novel candidate driver genes in this disease, including NOTCH4 (7%), DICER1 (11%), MCL1 (7%), amongst others. EZH2, EP300, and XPO1 mutations were not detected. CIITA mutations and fusions were observed in 14% and 11% of cases, respectively, with novel partner genes (IGHA2, IGHG1, CDC6) detected in 67% of the fusion positive cases. Copy number alterations included gains at 2p16.1 (REL - 20%) and 9p24.2 (JAK2/PDL1/PDL2 - 24%), as well as loci not previously implicated in PMBL, 8q24.3 and 9q34.3 (each in 20%). Of note, CIITA alterations and 9p24 gains were virtually mutually exclusive, highlighting diverse mechanisms of immune escape in this entity. The transcriptomes of cases harboring CIITA alterations demonstrated differential enrichment of genes involved in protein glycosylation. The PMBLs in our series showed significant enrichment of the reported PMBL genetic classifier score, compared to nodal diffuse large B cell lymphoma (DLBCL) (p=0.0003). Finally, the gene expression profile of thymic B cells was more similar to that of PMBL than nodal DLBCL (p=0.0144). Conclusions: Our study, representing one of the largest comprehensive genomic and transcriptomic analyses of PMBL, expands the mutational landscape of PMBL, provides evidence for biologically distinct disease subsets and suggests an origin of PMBLs from thymic B-cells. Disclosures Hsi: AbbVie: Research Funding; Eli Lilly: Research Funding; Cytomx: Honoraria; Seattle Genetics: Honoraria. McKinney: BTG: Consultancy; Celgene: Consultancy, Research Funding; Epizyme: Consultancy; Genetech: Consultancy, Honoraria, Research Funding; Incyte: Research Funding; Kite/Gilead: Honoraria, Speakers Bureau; Molecular Templates: Consultancy, Research Funding; Nordic Nanovector: Research Funding; Novartis: Research Funding; Pharmacyclics: Consultancy; Verastem: Consultancy; Beigene: Research Funding; ADC Therapeutics: Consultancy, Speakers Bureau. Jaye: Stemline Therapeutics: Honoraria. Cohen: Genentech, Takeda, BMS/Celgene, BioInvent, LAM, Astra Zeneca, Novartis, Loxo/Lilly: Research Funding; Janssen, Adaptive, Aptitude Health, BeiGene, Cellectar, Adicet, Loxo/Lilly, AStra ZenecaKite/Gilead: Consultancy. Behdad: Lilly: Speakers Bureau; Roche/Foundation Medicine: Speakers Bureau; Thermo Fisher: Speakers Bureau. Dave: Data Driven Bioscience: Current equity holder in publicly-traded company.

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Genomic Complexity in Diffuse Large B-Cell Lymphoma Is Associated with p53 Expression and Inferior Survival

Blood ◽

10.1182/blood.v124.21.3023.3023 ◽

2014 ◽

Vol 124 (21) ◽

pp. 3023-3023

Author(s):

Charles Ma ◽

Imran N Siddiqi ◽

Yi Xie ◽

Anil Tulpule ◽

Jane Houldsworth

Keyword(s):

B Cell ◽

Tp53 Mutation ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Stock Option ◽

P53 Expression ◽

Genomic Complexity ◽

Large B Cell Lymphoma ◽

Gain Loss ◽

Large B Cell

Abstract Genomic complexity in diffuse large-B-cell lymphoma has recently been reported to have strong prognostic value in patients with diffuse large B-cell lymphoma (DLBCL) treated with rituximab-based immunochemotherapy (PMID:22975378). In that study, the presence of the respective gain/loss of at least one of nine genomic markers along the CDKN2A-TP53-RB-E2F axis was used to define cases with “complex” genomes. Genomic imbalance at these specific loci were suggested to functionally contribute toward cell cycle deregulation resulting in increased overall genomic instability. Other clinicopathologic studies have clearly demonstrated that inferior survival is also associated with elevated expression of p53, which serves as a surrogate for TP53 mutation. To date, there have been very few studies, if any, that have examined the relationship between genomic imbalance and complexity, and clinicopathologic features in DLBCL, in particular with relevance to TP53. To this end, DNA was extracted from either sections of formalin-fixed paraffin-embedded biopsies with greater than 70% tumor burden or tumor-enriched cores of 85 DLBCL specimens from patients treated at a single institution (with IRB approval). DNAs from 39 specimens have been blindly submitted to array-CGH to date, using a targeted array (Agilent Technologies). The design permitted assessment at 50 loci commonly gained/lost in DLBCL (arising within 36 minimal common regions [MCRs]) using well defined scoring criteria. Specimens were classified as “complex” if any one of the following aberrations were detected: gain of 1q23, 6p21, 7q22, 12q15, or 19p13, or loss of 9p21, 13q14, 16q12, or 17p13. For all cases, expression of p53, MYC, BCL2, Ki-67, and Epstein-Barr virus (EBV) had previously been examined and reported (PMID:24619762) as was the COO subtype. Correlative analyses with overall survival (OS) were tested using the Kaplan Meier method and log rank statistic. Significance of pathogenomic correlations were examined using the Fisher’s exact t-test (P<0.05 was considered significant). Of the 39 cases evaluated to date, IPI was available for 34. For the preliminary analysis comprising 39 cases, genomic complexity (observed for 22 cases) did not significantly correlate with IPI, consistent with the prior report where genomic complexity associated with inferior survival independent of IPI (PMID:22975378). However, genomic complexity did portend shortened survival within the preliminary 39 patients studied to date (P<0.01) and a trend was observed for the 29 who received RCHOP or RCHOP-like therapy (P=0.05) (for the remaining 10 cases, treatment status was unknown for 7 and 3 received palliative care). Genomic complexity based on absolute number of aberrations for the entire 50 assessed (>1), did not exhibit significant association with outcome. Fourteen of 18 cases with p53 expression (>30%) had complex genomes, which was significantly enriched compared with cases with low or no p53 expression (P <0.03). No significant correlation was found between genomic complexity and BCL2 (>70%) and MYC (45%) expression, nor with COO subtype. Specifically for TP53, loss of 17p13 was detected in 7/39 cases, and positively correlated with adverse outcome both for the entire dataset (P=0.05) and for RCHOP-treated patients (P=0.02). Interestingly, of those with loss, 3 were not positive for p53 expression and overall, p53 expression did not correlate with 17p loss. Previous analyses in this dataset had also revealed that co-expression of p53 and MYC, but not BCL2 had an enhanced negative effect on outcome. Only one of 5 cases with co-expression of p53 and MYC also displayed 17p loss. Overall then, p53 expression was associated with underlying genomic complexity but specific loss of the TP53 locus appeared to mark another smaller subset of DLBCL patients with inferior survival, independent of p53 expression. Expansion of the study to include the additional 46 cases is currently ongoing to confirm these emerging correlative patterns, as is determination of the TP53 mutation status of each specimen. Additional correlative pathogenomic studies will also be afforded with the larger dataset, examining the role of the 8 other loci of genomic gain/loss suggested to underlie genomic complexity in DLBCL. Disclosures Ma: Cancer Genetics, Inc.: Employment, Stock option holder Other. Houldsworth:Cancer Genetics, Inc: Employment, Stock and stock option holder Other.

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Comprehensive analysis of differentially expressed profiles of lncRNAs and mRNAs reveals ceRNA networks in the transformation of diffuse large B‑cell lymphoma

Oncology Letters ◽

10.3892/ol.2018.8722 ◽

2018 ◽

Cited By ~ 5

Author(s):

Lu Tian ◽

Yangyan He ◽

Hongkun Zhang ◽

Ziheng Wu ◽

Donglin Li ◽

...

Keyword(s):

B Cell ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Comprehensive Analysis ◽

Differentially Expressed ◽

Large B Cell Lymphoma ◽

Large B Cell

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Spatial Signatures Identify Immune Escape via PD-1 as a Defining Feature of T-cell/Histiocyte-rich Large B-cell Lymphoma

Blood ◽

10.1182/blood.2020006464 ◽

2020 ◽

Cited By ~ 1

Author(s):

Gabriel K. Griffin ◽

Jason L. Weirather ◽

Margaretha Roemer ◽

Mikel Lipschitz ◽

Alyssa Kelley ◽

...

Keyword(s):

T Cell ◽

B Cells ◽

B Cell ◽

Immune Escape ◽

Cell Lymphoma ◽

B Cell Lymphoma ◽

Spatially Resolved ◽

Large B Cell Lymphoma ◽

Immune Signatures ◽

Large B Cell

T-cell/histiocyte-rich large B cell lymphoma (TCRLBCL) is an aggressive variant of diffuse large B cell lymphoma (DLBCL) characterized by rare malignant B cells within a robust but ineffective immune cell infiltrate. The mechanistic basis of immune escape in TCRLBCL is poorly defined and not targeted therapeutically. We performed a genetic and quantitative spatial analysis of the PD-1/PD-L1 pathway in a multi-institutional cohort of TCRLBCLs and found that malignant B cells harbor PD-L1/PD-L2 copy gain or amplification in 64% of cases, which is associated with increased PD-L1 expression (p = 0.0111). By directed and unsupervised spatial analyses of multi-parametric cell phenotypic data within the tumor microenvironment, we found that TCRLBCL is characterized by tumor-immune 'neighborhoods' in which malignant B cells are surrounded by exceptionally high numbers of PD-L1-expressing TAMs and PD-1-positive T cells. Further, unbiased clustering of spatially-resolved immune signatures distinguished TCRLBCL from related subtypes of B-cell lymphoma, including classic Hodgkin lymphoma (cHL) and DLBCL-NOS. Finally, we observed clinical responses to PD-1 blockade in three of five patients with relapsed/refractory TCRLBCL who were enrolled in clinical trials for refractory hematologic malignancies, including two complete responses and one partial response. Taken together, these data implicate PD-1 signaling as an immune escape pathway in TCRLBCL, and also support the potential utility of spatially-resolved immune signatures to aid the diagnostic classification and immunotherapeutic prioritization of diverse tumor types.

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