Stromal gene signatures in large-B-cell lymphomas

Phase 2 study of alemtuzumab and dose-adjusted EPOCH-R in relapsed or refractory aggressive B-cell lymphomas

Immune cells within the lymphoma tumor microenvironment promote immune evasion and are rational therapeutic targets. Alemtuzumab targets CD52 expressed on malignant B-cells and infiltrating nonmalignant T-cells. We evaluated the safety and efficacy of alemtuzumab with DA-EPOCH-R in 48 patients with relapsed/refractory aggressive B-cell lymphoma. Febrile neutropenia occurred in 18% of cycles and serious infections in 21% of patients. Responses were observed in 30 (62%) patients, including 12 (80%) patients with classical HL and 3 (75%) patients with T-cell/histiocyte-rich large B-cell lymphoma (THRLCL). Seventeen (35%) patients achieved complete responses, and 12 (25%) were bridged to consolidation. The 2-year progression-free survival (PFS) and overall survival were 22.1% (95% CI, 11.5-34.7%) and 45.2% (95% CI, 34.3-58.9%), respectively. The 2-year PFS for HL and THRLCL patients was 35% and 50%, respectively. Alemtuzumab can be safely combined with DA-EPOCH-R in relapsed/refractory aggressive B-cell lymphomas and can induce durable responses in patients with T-cell-rich microenvironments.

Toll-like receptor 9 (TLR9) expression correlates with cell of origin and predicts clinical outcome in diffuse large B-cell lymphoma

BACKGROUND

Biological insights beyond the cell-of-origin (COO) classification can support clinical management in diffuse large B-cell lymphoma (DLBCL). We investigated if Toll-like receptor 9 (TLR9) expression could serve as a prognostic marker in DLBCL.

METHOD

TLR9 gene expression was analysed in four publicly available cohorts (n = 2474), and protein expression was investigated in germinal centre B-cell (GCB) and activated B-cell (ABC) DLBCL cell lines. Next, TLR9 protein expression was analysed in 120 diagnostic samples from R-CHOP-treated patients with relapsed/refractory disease (poor outcome, n = 50) or in complete remission (good outcome, n = 70). Associations were evaluated using logistic regression, estimating odds ratios (OR) and 95% confidence intervals (CI).

RESULTS

TLR9 gene expression was higher in ABC DLBCL compared to GCB DLBCL in external cohorts, and similar results were obtained for protein expression in cell lines. In patient samples, high TLR9 protein expression correlated with non-GCB type (p = 0.003) and poor outcome (p = 0.0016). High TLR9 expression remained associated with poor outcome in multivariable analysis after adjusting for COO and other clinical features (OR = 3.36, 95% CI 1.41-8.04). In exploratory analyses, a decrease of cell growth in ABC cell lines following inhibition of TLR9 activity with ODN4084-F was suggested.

CONCLUSION

We conclude that TLR9 correlates with ABC/non-GCB phenotype and is a potential predictor of poor prognosis in DLBCL.

Integrative genomic analysis of DLBCL identifies immune environments associated with bispecific antibody response

ABSTRACT

Most patients with diffuse large B-cell lymphoma (DLBCL) treated with immunotherapies such as bispecific antibodies (BsAbs) or chimeric antigen receptor (CAR) T cells fail to achieve durable treatment responses, underscoring the need for a deeper understanding of mechanisms that regulate the immune environment and response to treatment. Here, an integrative multiomics approach was applied to multiple large independent data sets to characterize DLBCL immune environments and to define their association with tumor cell-intrinsic genomic alterations and outcomes to CD19-directed CAR T-cell and CD20 × CD3 BsAb therapies. This approach effectively segregated DLBCLs into 4 immune quadrants (IQs) defined by cell-of-origin and immune-related gene set expression scores. These quadrants consisted of activated B cell-like (ABC) hot, ABC cold, germinal center B cell-like (GCB) hot, and GCB cold DLBCLs. Recurrent genomic alterations were enriched in each IQ, suggesting that lymphoma cell-intrinsic alterations contribute significantly to orchestrating unique DLBCL immune environments. For instance, SOCS1 loss-of-function mutations were significantly enriched among GCB hot DLBCLs, identifying a putative subset of inflamed DLBCLs that may be inherently susceptible to immunotherapy. In patients with relapsed/refractory DLBCL, DLBCL-IQ assignment correlated significantly with clinical benefit with a CD20 × CD3 BsAb (N = 74), but not with CD19-directed CAR T cells (Stanford, N = 51; Memorial Sloan Kettering Cancer Center, N = 69). Thus, DLBCL-IQ provides a new framework to conceptualize the DLBCL immune landscape and suggests the endogenous immune environment has a more significant impact on outcomes to BsAb than CAR T-cell treatment.

Downregulation of rRNA synthesis by BCL-2 induces chemoresistance in diffuse large B cell lymphoma

Overexpression of the antiapoptotic oncogene BCL-2 predicts poor prognosis in diffuse large B cell lymphoma (DLBCL) treated with anthracycline-based chemoimmunotherapy. Anthracyclines exert antitumor effects by multiple mechanisms including inhibition of ribosome biogenesis (RiBi) through rRNA synthesis blockade. RiBi inhibitors induce p53 stabilization through the ribosomal proteins-MDM2-p53 pathway, with stabilized p53 levels depending on baseline rRNA synthesis rate. We found that the BH3-mimetic venetoclax could not fully reverse BCL-2-mediated resistance to RiBi inhibitors in DLBCL cells. BCL-2 overexpression was associated with decreased baseline rRNA synthesis rate, attenuating p53 stabilization by RiBi inhibitors. Drugs stabilizing p53 irrespective of RiBi inhibition reversed BCL-2-induced resistance in vitro and in vivo, restoring p53 activation and apoptosis. A small nucleolar size, indicative of low baseline rRNA synthesis, correlated with high BCL-2 levels and poor outcomes in DLBCL patients. These findings uncover alternative BCL-2-dependent chemoresistance mechanisms, providing a rationale for specific combination strategies in BCL-2 positive lymphomas.

Single-cell sequencing and spatial transcriptomics reveal FAS+ T cell and autophagy-related signatures predicting chemoimmunotherapy response in diffuse large B-cell lymphoma patients

Current subtyping methods of diffuse large B-cell lymphoma (DLBCL) could not satisfy the clinical demands for risk assessment and prognostic prediction. We aimed to investigate the prognostic effect of autophagy-related genes (ARGs) in DLBCL. Transcriptomic data of 1,409 DLBCL patients, 531 healthy controls (HCs), and single-cell sequencing data of 4 DLBCL were included. Validation involved spatial transcriptomics from 10 DLBCL patients and 110 DLBCL proteomic data from a local cohort. We identified 153 differentially expressed ARGs between DLBCL patients (n=48) and HCs (n=531), classifying 414 DLBCL patients into two subtypes based on autophagy heterogeneity. Subtype I, characterized by upregulated T regulatory (Treg) cells (P<0.0001) and T follicular helper (Tfh) cells (P=0.0012), showed a superior prognosis (P=0.035). Eight prognostic ARGs were selected to construct an autophagy-related model, dividing patients into low- and high-risk groups. Kaplan-Meier survival analysis revealed significantly better outcomes for the low-risk group in both the discovery (P<0.0001) and validation cohorts (P=0.0041). High-risk patients exhibited elevated IDO1 (P=0.042) and LAG3 (P<0.001) levels. Among the eight signature proteins, higher FAS was further verified to indicate a better prognosis in the local cohort (n=110) using antibody array (P=0.0083). FAS was primarily expressed in T cells such as Treg and Tfh cells and was elevated in non-progressive disease patients. FAS-positive T cells showed increased interferon-gamma (normalized enrichment score (NES)=2.196, FDR<0.0001) and alpha (NES=1.836, FDR<0.01) response activities. We constructed an autophagy-related model and identified FAS as a prognostic biomarker. FAS+ Treg and Tfh cell-enriched TME indicated a favorable prognosis.

Advances in the Classification of Aggressive B-cell Lymphomas

Aggressive B-cell lymphomas are a biologically and clinically very heterogeneous group of tumors that may be related to different stages of B-cell differentiation development. This review aims to summarize recent advances in the understanding of these tumors with a focus on the practical approach to the diagnosis of these entities. We analyze the defining characteristics of the different subtypes of aggressive B-cell lymphomas, including nodal and extranodal diffuse large B-cell lymphoma, virus-associated lymphomas, terminally differentiated B-cell lymphomas, high-grade B-cell lymphomas, and Burkitt lymphoma. This review particularly explores the integration of morphologic, immunophenotypic, and genetic data that refine diagnostic accuracy and prognostic stratification, underscoring the necessity for a standardized approach in clinical practice. By synthesizing current knowledge, this review aims to enhance the understanding of aggressive B-cell lymphomas within the context of the evolving classification system, paving the way for future research and clinical advancements.

The Overexpression of Collagen Receptor DDR1 is Associated With Chromosome Instability and Aneuploidy in Diffuse Large B-Cell Lymphoma

Although chronic inflammation is implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL), the mechanisms responsible are unknown. We demonstrate that the overexpression of the collagen receptor, DDR1, correlates with reduced expression of spindle checkpoint genes, with three transcriptional signatures of aneuploidy and with a higher frequency of copy number alterations, pointing to a potential role for DDR1 in the acquisition of aneuploidy in DLBCL. In support of this, we found that collagen treatment of primary germinal centre B cells transduced with DDR1, not only partially recapitulated the aberrant transcriptional programme of DLBCL but also downregulated the expression of CENPE, a mitotic spindle that has a crucial role in preventing chromosome mis-segregation. CENPE expression was also downregulated following DDR1 activation in two B-cell lymphoma lines and was lost in most DDR1-expressing primary tumours. Crucially, the inhibition of CENPE and the overexpression of a constitutively activated DDR1 were able to induce aneuploidy in vitro. Our findings identify a novel mechanistic link between DDR1 signalling and chromosome instability in B cells and provide novel insights into factors driving aneuploidy in DLBCL.

Site-specific analysis of extranodal involvement in large B-cell lymphoma reveals distinct efficacy with chimeric antigen receptor T-cell therapy

Over 60% of relapsed/refractory large B-cell lymphoma (R/R LBCL) patients treated with chimeric antigen receptor (CAR) T-cells experience progressive disease. The impact of site-specific extranodal involvement on CAR-T outcomes has not been fully elucidated. This multicenter study included 516 R/R LBCL patients infused with CD19-targeted CAR T-cells; 177 (34%) had only-nodal (N), 66 (13%) only-extranodal (E) and 273 (53%) nodal and extranodal (NE) disease at time of CAR T-cells. The NE cohort included more patients with a poor performance status and high tumor burden. In the multivariable analysis, the NE group had a shorter progression-free survival (PFS) (HR 1.27 [95%CI 0.98-1.64], p = 0.07) and overall survival (HR 1.41 [95%CI 1.05-1.88], p = 0.02) compared to N. Conversely, we did not identify efficacy differences between N and E patients. A higher number of extranodal sites and specific organ involvement (liver, adrenal glands, pancreas), were associated with shorter PFS. Finally, extranodal involvement increased at time of relapse, displaying heterogeneous individual site clearance rates. In conclusion, patients with concomitant nodal and extranodal involvement at time of CAR-T had worse outcomes, but this cohort harbored high-risk baseline characteristics. An increasing number of extranodal sites and certain disease locations were associated with lower CAR-T efficacy.

Epigenetic Symphony in Diffuse Large B-Cell Lymphoma: Orchestrating the Tumor Microenvironment

DLBCL is a testament to the complexity of nature. It is characterized by remarkable diversity in its molecular and pathological subtypes and clinical manifestations. Despite the strides made in DLBCL treatment and the introduction of innovative drugs, around one-third of patients face a relapse or develop refractory disease. Recent findings over the past ten years have highlighted the critical interplay between the evolution of DLBCL and various epigenetic mechanisms, including chromatin remodeling, DNA methylation, histone modifications, and the regulatory roles of non-coding RNAs. These epigenetic alterations are integral to the pathways of oncogenesis, tumor progression, and the development of therapeutic resistance. In the past decade, the identification of dysregulated epigenetic mechanisms in lymphomas has paved the way for an exciting field of epigenetic therapies. Crucially, these epigenetic transformations span beyond tumor cells to include the sophisticated network within the tumor microenvironment (TME). While the exploration of epigenetic dysregulation in lymphoma cells is thriving, the mechanisms affecting the functions of immune cells in the TME invite further investigation. This review is dedicated to weaving together the narrative of epigenetic alterations impacting both lymphoma cells with a focus on their infiltrating immune companions.

A novel cancer-associated fibroblast-related gene signature for predicting diffuse large B cell lymphoma prognosis using weighted gene co-expression network analysis and machine learning

ObjectiveOur objective was to investigate a novel cancer-associated fibroblast-related gene signature for predicting clinical outcomes in patients with diffuse large B cell lymphoma.MethodsThe cancer-associated fibroblast-related module genes were identified from Gene Expression Omnibus datasets using weighted gene co-expression network analysis in our retrospective study. Least Absolute Shrinkage and Selection Operator Cox regression was applied to screen a minimal set of genes and construct a prognostic cancer-associated fibroblast-related gene signature for diffuse large B cell lymphoma. Kaplan-Meier plots and receiver operating characteristic curves were used to assess the prognostic performance of the prognostic cancer-associated fibroblast-related genes. A nomogram encompassing the clinical information and prognostic scores of the patients was constructed. Additionally, the relationships of the gene signature with the immune landscape and drug sensitivity were explored.ResultsCapitalizing on machine learning, we developed a prognostic cancer-associated fibroblast-related gene signature risk model, efficiently categorizing patients with diffuse large B cell lymphoma into high- and low-risk groups and exhibiting a more robust capacity for survival prediction. The nomogram showed stronger prognostic ability than the clinical factor-based model or the risk score alone. We also observed significant differences in immune cell profiles and therapeutic responses between the two groups, offering valuable insights for developing personalized treatments for diffuse large B cell lymphoma.ConclusionsWe developed a prognostic cancer-associated fibroblast-related gene-based genetic risk model to predict the prognosis of diffuse large B cell lymphoma, potentially aiding in treatment selection.

Senescence-associated lineage-aberrant plasticity evokes T-cell-mediated tumor control

Cellular senescence is a stress-inducible state switch relevant in aging, tumorigenesis and cancer therapy. Beyond a lasting arrest, senescent cells are characterized by profound chromatin remodeling and transcriptional reprogramming. We show here myeloid-skewed aberrant lineage plasticity and its immunological ramifications in therapy-induced senescence (TIS) of primary human and murine B-cell lymphoma. We find myeloid transcription factor (TF) networks, specifically AP-1-, C/EBPβ- and PU.1-governed transcriptional programs, enriched in TIS but not in equally chemotherapy-exposed senescence-incapable cancer cells. Dependent on these master TF, TIS lymphoma cells adopt a lineage-promiscuous state with properties of monocytic-dendritic cell (DC) differentiation. TIS lymphoma cells are preferentially lysed by T-cells in vitro, and mice harboring DC-skewed Eμ-myc lymphoma experience significantly longer tumor-free survival. Consistently, superior long-term outcome is also achieved in diffuse large B-cell lymphoma patients with high expression of a TIS-related DC signature. In essence, these data demonstrate a therapeutically exploitable, prognostically favorable immunogenic role of senescence-dependent aberrant myeloid plasticity in B-cell lymphoma.

Interaction between stromal cells and tumor cells promotes GCB-DLBCL cell survival via the CD40/RANK-KDM6B-NF-κB axis

The stromal cells as the main component of the tumor microenvironment in germinal center B cell-like diffuse large B cell lymphoma (GCB-DLBCL) probably is accountable for therapy resistance and relapse. To investigate the interaction between tumor cells and stromal cells, we established GCB-DLBCL patient-derived xenograft models to isolate primary tumor cells and coculture them with stromal cells. Additionally, we presented GCB-DLBCL cases with histopathologic confirmation and analyzed the online databases to explore the underlying mechanisms. We demonstrated that CD40 ligand (CD40L) expressed on stromal cells activated the CD40 pathway in GCB-DLBCL tumor cells, protecting tumor cells from apoptosis and up-regulating RANK ligand (RANKL). The RANKL expressed on tumor cells enhanced the expression of CD40L and BAFF in stromal cells, which in turn promoted tumor cells survival through activating NF-κB signaling. Significantly, the activation of CD40 pathway up-regulated KDM6B, a lysine-specific demethylase, and KDM6B further enhanced the transcription activity of NF-κB signaling, which has not been reported in B cells. Here, we provided compelling evidence that the interaction between stromal cells and tumor cells functions as a bona fide anti-apoptotic factor in GCB-DLBCL. This interaction mainly involves the CD40/RANK-KDM6B-NF-κB axis, which represents a promising therapeutic target for GCB-DLBCL.

Latent class analysis-derived classification improves the cancer-specific death stratification of lymphomas: A large retrospective cohort study

Lymphomas have diverse etiologies, treatment approaches, and prognoses. Accurate survival estimation is challenging for lymphoma patients due to their heightened susceptibility to non-lymphoma-related mortality. To overcome this challenge, we propose a novel lymphoma classification system that utilizes latent class analysis (LCA) and incorporates demographic and clinicopathological factors as indicators. We conducted LCA using data from 221,812 primary lymphoma patients in the Surveillance, Epidemiology, and End Results (SEER) database and identified four distinct LCA-derived classes. The LCA-derived classification efficiently stratified patients, thereby adjusting the bias induced by competing risk events such as non-lymphoma-related death. This remains effective even in cases of limited availability of cause-of-death information, leading to an enhancement in the accuracy of lymphoma prognosis assessment. Additionally, we validated the LCA-derived classification model in an external cohort and observed its improved prognostic stratification of molecular subtypes. We further explored the molecular characteristics of the LCA subgroups and identified potential driver genes specific to each subgroup. In conclusion, our study introduces a novel LCA-based lymphoma classification system that provides improved prognostic prediction by accounting for competing risk events. The proposed classification system enhances the clinical relevance of molecular subtypes and offers insights into potential therapeutic targets.

NPM: latent batch effects correction of omics data by nearest-pair matching

MOTIVATION

Batch effects (BEs) are a predominant source of noise in omics data and often mask real biological signals. BEs remain common in existing datasets. Current methods for BE correction mostly rely on specific assumptions or complex models, and may not detect and adjust BEs adequately, impacting downstream analysis and discovery power. To address these challenges we developed NPM, a nearest-neighbor matching-based method that adjusts BEs and may outperform other methods in a wide range of datasets.

RESULTS

We assessed distinct metrics and graphical readouts, and compared our method to commonly used BE correction methods. NPM demonstrates the ability in correcting for BEs, while preserving biological differences. It may outperform other methods based on multiple metrics. Altogether, NPM proves to be a valuable BE correction approach to maximize discovery in biomedical research, with applicability in clinical research where latent BEs are often dominant.

AVAILABILITY AND IMPLEMENTATION

NPM is freely available on GitHub (https://github.com/bigomics/NPM) and on Omics Playground (https://bigomics.ch/omics-playground). Computer codes for analyses are available at (https://github.com/bigomics/NPM). The datasets underlying this article are the following: GSE120099, GSE82177, GSE162760, GSE171343, GSE153380, GSE163214, GSE182440, GSE163857, GSE117970, GSE173078, and GSE10846. All these datasets are publicly available and can be freely accessed on the Gene Expression Omnibus repository.

CAMKIIδ Reinforces Lipid Metabolism and Promotes the Development of B Cell Lymphoma

The most prevalent types of lymphomas are B cell lymphomas (BCL). Newer therapies for BCL have improved the prognosis for many patients. However, approximately 30% with aggressive BCL either remain refractory or ultimately relapse. These patients urgently need other options. This study shows how calcium/calmodulin-dependent protein kinase II delta (CAMKIIδ) is pivotal for BCL development. In BCL cells, ablation of CAMKIIδ inhibits both lipolysis from lipid droplets and oxidative phosphorylation (OXPHOS). With lipolysis blocked, BCL progression is markedly suppressed in two distinct BCL mouse models: MYC-driven EµMyc mice and Myc/Bcl2 double-expressed mice. When CAMKIIδ is present, it destabilizes transcription factor Forkhead Box O3A (FOXO3A) by phosphorylating it at Ser7 and Ser12. This then permits transcription of downstream gene IRF4 - a master transcription factor of lipid metabolism. The CAMKIIδ/FOXO3A axis bolsters lipid metabolism, mitochondrial respiration, and tumor fitness in BCL under metabolic stress. This study also evaluates Tetrandrine (TET), a small molecule compound, as a potent CAMKIIδ inhibitor. TET attenuates metabolic fitness and elicits therapeutic responses both in vitro and in vivo. Collectively, this study highlights how CAMKIIδ is critical in BCL progression. The results also pave the way for innovative therapeutic strategies for treating aggressive BCL.

N-glycosylation of ephrin B1 modulates its function and confers therapeutic potential in B-cell lymphoma

Given the pivotal role of the Eph-Ephrin signaling pathway in tumor progression, agonists or antagonists targeting Eph-Ephrin have emerged as promising anticancer strategies. However, the implications of glycosylation modifications within Eph-Ephrin and their targeted protein therapeutics remain elusive. Here, we identify that N-glycosylation within the receptor-binding domain (RBD) of ephrin B1 (EFNB1) is indispensable for its functional repertoire. Notably, compared with wildtype EFNB1, the glycosylation-deficient N139D mutant drastically diminishes the sensitivity of tumor cells with chemotherapeutic agents, suggesting the existence of both glycosylation-dependent and -independent effects mediated by EFNB1. Transcriptomic analysis highlights immune response and oxidative phosphorylation as the primary signaling pathways modulated by glycosylation modifications. In coculture systems, the EFNB1-RBD-Fc recombinant protein, while inhibiting B-lymphoma cells, also exerts differential impacts on stromal cells depending on their glycosylation status. Furthermore, the efficacy of both glycosylated and nonglycosylated EFNB1-RBD-Fc is influenced by the endogenous EFNB1 levels within tumor cells. Taking together, this study demonstrates the complexity and multifaceted roles of glycosylation in modulating EFNB1 function. These findings underscore the need for a nuanced understanding of glycosylation patterns in Eph-Ephrin-targeted therapies to optimize their therapeutic potential.

Spatial transcriptomics reveals prognostically LYZ+ fibroblasts and colocalization with FN1+ macrophages in diffuse large B-cell lymphoma

BACKGROUND

Diffuse large B-cell lymphoma (DLBCL) is a clinically heterogeneous malignancy with diverse patient outcomes, largely influenced by the tumor microenvironment (TME). Understanding the roles of fibroblasts and macrophages within the TME is essential for developing personalized therapeutic strategies in DLBCL.

METHODS

This study is a multi-omics approach, integrating spatial transcriptomics (n = 11), bulk transcriptomics (n = 2,499), immunohistochemistry (IHC, n = 37), multiplex immunofluorescence (mIF, n = 56), and plasma samples (n = 240) to identify and characterize fibroblast and tumor-associated macrophage subtypes in the TME. Hub genes for LYZ+ fibroblasts and FN1+ macrophages were selected through univariate Cox regression and random forest analyses. Their prognostic significance was validated using IHC, mIF, and autoantibody assays in DLBCL patients treated with R-CHOP and in non-small cell lung cancer (NSCLC) patients receiving immune checkpoint inhibitors (ICIs).

RESULTS

Fibroblasts and macrophages were classified into two distinct subtypes. Patients with higher LYZ+ fibroblasts infiltration demonstrated superior prognosis, which was associated with increased infiltration of FN1+ macrophages. Key hub genes identified for LYZ+ fibroblasts included LYZ, ANPEP, CSF3R, C15orf48, LILRB4, CLEC7A, and COL7A1, while hub FN1+ macrophages genes included COL1A1, FN1, APOE, DCN, MMP2, SPP1, COL3A1, and COL1A2. Independent prognostic markers in DLBCL treated with R-CHOP and NSCLC treated with ICIs were identified, including LYZ and LILRB4 at both protein and mRNA levels, and COL1A2 autoantibodies (p < 0.05). In DLBCL patients treated with R-CHOP, FN1 mRNA and autoantibody levels were also prognostic markers (p < 0.05). In NSCLC treated with ICIs, COL3A1 autoantibody was prognostic marker (p < 0.05).

CONCLUSIONS

This study identified a prognostically relevant LYZ+ fibroblasts and FN1+ macrophages in DLBCL. The hub genes associated with these subtypes represent potential biomarkers, providing insights into improving patient outcomes in DLBCL.

Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers

Genes involved in the regulation of chromatin structure are frequently disrupted in cancer, contributing to an aberrant transcriptome and phenotypic plasticity. Yet, therapeutics targeting mutant forms of chromatin-modifying enzymes have yielded only modest clinical utility, underscoring the difficulty of targeting the epigenomic underpinnings of aberrant gene regulatory networks. Here, we sought to identify novel epigenetic vulnerabilities in diffuse large B-cell lymphoma (DLBCL). Through phenotypic screens and biochemical analysis, we demonstrated that inhibition of the H3K9 demethylases KDM4A and KDM4C elicits potent, subtype-agnostic cytotoxicity by antagonizing transcriptional networks associated with B-cell identity and epigenetically rewiring heterochromatin. KDM4 demethylases associated with the KRAB zinc finger ZNF587, and their enzymatic inhibition led to DNA replication stress and DNA damage-einduced cGAS-STING activation. Broad surveys of transcriptional data from patients also revealed KDM4 family dysregulation in several other cancer types. To explore this potential therapeutic avenue, we performed high-throughput small molecule screens with H3K9me3 nucleosome substrates and identified novel KDM4 demethylase inhibitors. AI-guided protein-ligand binding predictions suggested diverse modes of action for various small molecule hits. Our findings underscore the relevance of targeting fundamental transcriptional and epigenetic mechanisms for anti-cancer therapy.

Overexpression of ornithine decarboxylase 1 mediates the immune-deserted microenvironment and poor prognosis in diffuse large B-cell lymphoma

Background

Previous researches mainly focused on whether cancer stem cells exist in diffuse large B-cell lymphoma (DLBCL). However, subgroups with dismal prognosis and stem cell-like characteristics have been overlooked.

Methods

Using large scale data (n = 2133), we conducted machine learning algorithms to identify a high risk DLBCL subgroup with stem cell-like features, and then investigated the potential mechanisms in shaping this subgroup using transcriptome, genome and single-cell RNA-seq data, and in vitro experiments.

Results

We identified a high-risk subgroup (25.6 % of DLBCL) with stem cell-like characteristics and dismal prognosis. This high-risk group (HRG) was featured by upregulation of key enzyme (ODC1) in polyamine metabolism and cold tumor microenvironment (TME), and had a poor prognosis with lower 3-year overall survival (OS) (54.3 % vs. 83.6 %, P < 0.0001) and progression-free survival (PFS) (42.8 % vs. 74.7 %, P < 0.0001) rates compared to the low-risk group. HRG also exhibited malignant proliferative phenotypes similar to Burkitt lymphoma. Patients with MYC rearrangement, double-hit, double-expressors, or complete remission might have either favorable or poor prognosis, which could be further distinguished by our risk stratification model. Genomic analysis revealed widespread copy number losses in the chemokine and interferon coding regions 8p23.1 and 9p21.3 in HRG. We identified ODC1 as a therapeutic vulnerability for HRG-DLBCL. Single-cell analysis and in vitro experiments demonstrated that ODC1 overexpression enhanced DLBCL cell proliferation and drove macrophage polarization towards the M2 phenotype. Conversely, ODC1 inhibition reduced DLBCL cell proliferation, induced cell cycle arrest and apoptosis, and promoted macrophage polarization towards the M1 phenotype. Finally, we developed a comprehensive database of DLBCL for clinical application.

Conclusions

Our study effectively advances the precise risk stratification of DLBCL and reveals that ODC1 and immune-deserted microenvironment jointly shape a group of DLBCL patients with stem cell-like features. Targeting ODC1 regulates immunotherapies in DLBCL, offering new insights for DLBCL treatment.

T Cells Spatially Regulate B Cell Receptor Signaling in Lymphomas through H3K9me3 Modifications

Activated B cell-like diffuse large B-cell lymphoma (ABC-DLBCL) is a subtype associated with poor survival outcomes. Despite identifying therapeutic targets through molecular characterization, targeted therapies have limited success. New strategies using immune-competent tissue models are needed to understand how DLBCL cells evade treatment. Here, synthetic hydrogel-based lymphoma organoids are used to demonstrate how signals in the lymphoid tumor microenvironment (Ly-TME) can alter B cell receptor (BCR) signaling and specific histone modifications, tri-methylation of histone 3 at lysine 9 (H3K9me3), dampening the effects of BCR pathway inhibition. Using imaging modalities, T cells increase DNA methyltransferase 3A expression and cytoskeleton formation in proximal ABC-DLBCL cells, regulated by H3K9me3. Expansion microscopy on lymphoma organoids reveals T cells increase the size and quantity of segregated H3K9me3 clusters in ABC-DLBCL cells. Findings suggest the re-organization of higher-order chromatin structures that may contribute to evasion or resistance to therapy via the emergence of novel transcriptional states. Treating ABC-DLBCL cells with a G9α histone methyltransferase inhibitor reverses T cell-mediated modulation of H3K9me3 and overcomes T cell-mediated attenuation of treatment response to BCR pathway inhibition. This study emphasizes the Ly-TME's role in altering DLBCL fate and suggests targeting aberrant signaling and microenvironmental cross-talk that can benefit high-risk patients.

Prognostic value of the controlling nutritional status (CONUT) score in patients with diffuse large B-cell lymphoma: a meta-analysis

BACKGROUND

The significance of the controlling nutritional status (CONUT) score in predicting the prognostic outcomes of diffuse large B-cell lymphoma (DLBCL) has been widely explored, with conflicting results. Therefore, the present meta-analysis aimed to identify the prognostic significance of the CONUT in DLBCL by aggregating current evidence.

METHODS

The Web of Science, PubMed, Embase, CNKI and Cochrane Library databases were searched for articles from inception to October 15, 2024. The prognostic value of CONUT for DLBCL was analyzed by determining the pooled hazard ratios (HRs) with 95% confidence intervals (CIs). The Newcastle-Ottawa Scale (NOS) was used to analyze study quality.

RESULTS

Eight studies including 2687 cases were included in this work. The NOS scores of these studies were 7-9 (median, 8), demonstrating high quality. Our analyses revealed that an elevated CONUT score significantly predicted poor overall survival (OS) (HR = 1.63, 95%CI = 1.29-2.05, p < 0.001) and inferior progression-free survival (PFS) (HR=1.22, 95%CI = 1.12-1.33, p < 0.001) in patients with DLBCL. Further, the elevated CONUT score showed a significant correlation with the following clinicopathological factors in DLBCL: Ann Arbor stage III-IV, Eastern Cooperative Oncology Group Performance Status (ECOG PS) of 2-4, presence of extranodal disease, ≥high intermediate National Comprehensive Cancer Network International Prognostic Index (NCCN IPI), presence of B symptoms, elevated lactose dehydrogenase (LDH) levels, and presence of bone marrow infiltration.

CONCLUSIONS

An increased CONUT score was dramatically associated with poor OS and PFS in patients with DLBCL, as well as with clinicopathological characteristics representing DLBCL tumor development.

Metabolic Heterogeneity in Diffuse Large B-Cell Lymphoma Cells Reveals an Innovative Antimetabolic Combination Strategy

Background/Objectives: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma, characterized by aggressive and heterogeneous tumors originating from B-cells. Especially in patients with relapsed or refractory (R/R) disease, DLBCL remains a challenging cancer to treat. Metabolic reprogramming is a hallmark of malignant cells. Our research focuses on developing strategies to enhance clinical outcomes for R/R DLBCL patients by targeting metabolic vulnerabilities. Methods: We investigated the effects of combining metformin and L-asparaginase, two FDA-approved antimetabolic drugs, on DLBCL cell metabolism and survival. Nuclear magnetic resonance (NMR) spectroscopy was employed to assess metabolic disturbances induced by the drug combination. The impact on lipid metabolism, glycolysis, glutaminolysis, the tricarboxylic acid (TCA) cycle, and antioxidant responses was examined. Induction of apoptosis was evaluated by FACS analysis. Results: The combination of metformin and L-asparaginase strongly sensitized DLBCL cells to apoptosis, independently of their oxidative phosphorylation (OxPhos) or BCR/glycolytic status. NMR spectroscopy revealed that this combination induces broader metabolic disturbances than either drug alone. It disrupts lipid metabolism by altering levels of phospholipids, cholesterol, and fatty acids. Additionally, it counteracts the pro-glycolytic effect of metformin, decreases glycolysis, and reduces glutaminolysis. It also affects the TCA cycle and antioxidant responses, critical for cellular energy production and redox balance. Furthermore, this combination interferes with two key cancer survival pathways, mTORC1 and MAPK signaling. Importantly, proof of principle for its beneficial effect was demonstrated in DLBCL patients. Conclusions: Combining metformin and L-asparaginase affects DLBCL cell survival by targeting multiple metabolic pathways and may represent a novel therapeutic approach for R/R DLBCL patients.

The Role of the Tumor Microenvironment in T-Cell Redirecting Therapies of Large B-Cell Lymphoma: Lessons Learned from CAR-T to Bispecific Antibodies

T-cell redirecting therapies, which include chimeric antigen receptor T-cells (CAR-Ts) and bispecific antibodies (BSAs), have revolutionized the treatment of relapsed\refractory large B-cell lymphoma (LBCL). Expanding clinical experience with these advanced therapies shows the potential for the optimization of their use with combination or consolidation strategies, which necessitates the prognostic stratification of patients. While traditional clinical prognostic factors identified in the era of chemotherapy are characterized by limited value, the tumor microenvironment (TME) is becoming a new prognostic cluster. We examine how the heterogeneity of LBCL, characterized by variations in tumor parameters and differences in TME immune cell composition, immune checkpoint expression, and cytokine milieu, correlates with both positive responses and resistance to treatment. While classical parameters such as histological subtype, cell of origin, and target antigen expression lack proven prognostic value for T-cell redirecting therapies, the density and functional state of tumor-infiltrating lymphocytes, tumor-associated macrophages, and immune checkpoint molecules are shown to be critical determinants of therapeutic success, particularly in CAR-T therapy. We identify several gaps in the current knowledge and suggest that the insights gained from CAR-T experience could be instrumental in refining BSA applications. This report also highlights limitations in the current knowledge, as TME data derive from a limited number of registrational trials with varying methodologies, complicating cross-study comparisons and often focusing on immediate response metrics rather than long-term outcomes. By dissecting the complex interactions within the TME, this review aims to identify new prognostic factors and targets, ultimately fostering more effective and tailored treatment strategies for LBCL patients.

Successful Treatment of a Patient Presenting with Simultaneous Diffuse Large B-Cell Lymphoma and Hodgkin Lymphoma: A Case Report

BACKGROUND Simultaneously occuring diffuse large B-cell lymphoma (DLBCL) and Hodgkin lymphoma (HL) is extremely rare. Generally, patients with CD20-positive DLBCL receive rituximab, cyclophosphamide, vincristine, doxorubicin, prednisone (R-CHOP) regimen, while those with HL receive brentuximab vedotin, doxorubicin, vinblastine, dacarbazine (A-AVD) regimen as first-line therapy. Establishing a strategy for treating both lymphoma subtypes concurrently is thus very difficult. We report successful treatment of a patient simultaneously diagnosed with advanced DLBCL and HL. CASE REPORT A 20-year-old man visited the Hematology Department of Kyungpook National University Hospital after the diagnosis of germinal center B-cell DLBCL in the kidney and HL (nodular sclerosis type) in the neck lymph node. His DLBCL was classified as Ann Arbor stage IV with an International Prognostic Index score of 4, a high-risk group. Six cycles of R-CHOP therapy were planned, and central nervous system prophylaxis with intrathecalmethotrexate was added because of the high-risk features of central nervous system involvement. After completing 6 cycles of chemotherapy, without significant adverse events (Deauville score of 1), complete remission was confirmed. Then, the patient decided to undergo consolidative autologous stem cell transplantation (auto-SCT). He received busulfan, cyclophosphamide, and etoposide conditioning regimen, after which auto-SCT was conducted in April 2021. After auto-SCT, the patient was undergoing regular check-ups and doing well, without obvious disease relapse or specific symptoms. He maintained a disease-free status for 40 months to date. CONCLUSIONS Our case showed that R-CHOP regimen was effective not only for DLBCL but also for HL. Notably, consolidative upfront auto-SCT should be considered for a deeper response.

Molecular Features of Diffuse Large B-Cell Lymphoma Associated With Primary Treatment Resistance

Diffuse large B-cell lymphoma (DLBCL) patients that fail to achieve a complete metabolic response with frontline immunochemotherapy have a poor prognosis. Genomic profiling has led to a broader understanding of the molecular drivers in DLBCL, but it is unknown how well current classifiers identify patients that will experience primary treatment resistance (PTR). Using whole exome and RNA sequencing data from newly diagnosed DLBCL patients, we evaluated the genomic landscape of PTR and compared it to that of non-PTR DLBCL. We found a significant increase in the frequency of TP53 (34% vs. 15%, p = 0.005) and ARID1A mutations (21% vs. 7%, p = 0.007) in PTR cases, with pathway analysis further demonstrating a downregulation of TP53 and an increase in chromatin modifying pathways. These results suggest that TP53 and ARID1A may be key mediators of PTR and important pathways contributing to the poor outcomes. We found that the current molecular classifiers were unable to identify PTR cases at diagnosis. However, our newly identified high-risk signature identified 46% of PTR cases at diagnosis. Overall, these results contribute to our understanding of the genomic landscape of patients with primary treatment resistance.

Prognostic model based on M2 macrophage-related signatures for predicting outcomes, enhancing risk stratification, and providing therapeutic insights in diffuse large B-cell lymphoma

Purpose

The tumor microenvironment (TME) in lymphoma is influenced by M2 macrophages. This research proposes an novel predictive model that leverages M2 macrophage-associated genes to categorize risk, forecast outcomes, and evaluate the immune profile in patients with newly diagnosed diffuse large B-cell lymphoma (DLBCL) undergoing R-CHOP therapy.

Methods

Gene expression data and clinical information from DLBCL patients were retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Co-expressed genes linked to M2 macrophage in DLBCL were analyzed using CIBERSORT. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to explore associated signaling pathways. The M2 macrophage-related gene prognostic model was developed and validated using Cox and LASSO regression. Prognostic signature genes were verified by single-cell RNA-seq analysis.

Results

92 M2 macrophage-related genes were identified based on bulk-seq data. MS4A4A, CCL13, LTB, CCL23, CCL18, XKR4, IL22RA2, and FOLR2 were used to construct the risk model. AUC values for 1-, 3-, and 5-year survival were 0.74, 0.72, and 0.72, respectively. High-risk patients demonstrated elevated immune scores and poorer overall survival. The high-risk subgroup also exhibited greater sensitivity to both chemotherapeutic agents and immune checkpoint inhibitors.

Conclusion

This study presents an accurate and reliable M2 macrophage-related risk model, enhancing understanding of distinct prognostic subsets in DLBCL. It offers potential novel drug options for future treatments.

Improving Cure Rates for Patients with Newly Diagnosed Large B-Cell Lymphomas: Targeted Therapies for High-Risk Pathologic Subgroups as Defined by Clinical Laboratory Testing

BACKGROUND/OBJECTIVES

Diffuse large B-cell lymphoma (DLBCL) and high-grade B cell lymphoma (HGBL) comprise the majority of large B-cell lymphomas (LBCL), and approximately two-thirds of patients diagnosed with these LBCLs are cured following treatment with first-line immunochemotherapy. While the International Prognostic Index (IPI) score is a validated prognostic tool used for patients treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP), there is a growing body of evidence that suggests that LBCL tumor features, which can be detected by clinical laboratory testing, can predict patient survival following first-line immunochemotherapy.

CONCLUSIONS

Clinical laboratory testing may also allow for rational identification of targeted agents that can be added to first-line immunochemotherapy for high-risk, pathologically defined subsets of LBCL patients, and this approach may result in better survival outcomes for the entire LBCL patient population as compared with adding pathologically "agnostic" agents for those defined as high risk by IPI score.

Sequencing of therapy for patients with diffuse large B-cell lymphoma in the era of novel drugs

Diffuse large B-cell lymphoma (DLBCL) is the most common aggressive lymphoma, accounting for ~40% of all cases in adults. Whilst approximately two-thirds of DLBCL patients can be cured by first-line therapy, one-third of patients are primary refractory or relapse after an initial response (r/r DLBCL). Recent advances in the treatment of DLBCL have been achieved by a plethora of novel drugs, such as monoclonal antibodies, antibody-drug conjugates (ADC), bi-specific T-cell engagers (BITEs), and CD-19 directed chimeric antigen receptor (CAR)-T-cell therapies. The increasing number of therapeutic options significantly improved the outcome of patients; however, the therapeutic algorithm has become increasingly complex. In this review, we provide an overview of novel therapies for DLBCL patients and potential treatment sequencing from first to second, third, and later lines.

EZB-type diffuse large B-cell lymphoma cell lines have superior migration capabilities compared to MCD-type

Diffuse large B-cell lymphoma (DLBCL) represents the most prevalent aggressive B-cell lymphoma. The group is heterogeneous and the outcome is variable. A variety of approaches have been employed with the objective of improving the stratification of DLBCL patients according to their prognosis, based on the cell of origin. Recently, distinct genetic subtypes of DLBCL have been identified. Given the importance of cell migration in immune cells, the objective of this study was to ascertain whether different genetic subtypes of DLBCL exhibit disparate migration abilities. MCD- and EZB-type DLBCL cell lines were subjected to testing to ascertain their basal velocity in straight microchannels and their ability to overcome tight constrictions of 2 μm. The EZB-type cell lines showed superior basal migration velocity and constriction passage time, and a similar trend was observed in live cell imaging of native human DLBCL tissue. In addition, MCD-type DLBCL exhibited significantly elevated levels of nuclear lamin A/C, which is responsible for the stiffness of the nuclear envelope and could thus explain the disparate migration behaviours observed among these subtypes. Our study suggests that different genetic subtypes of DLBCL may not only influence the outcome after therapy but also the motility of the tumour cells.

Tumour-associated macrophages in diffuse large B-cell lymphoma: the prognostic and therapeutic impact in a South African centre with high HIV seroprevalence

Diffuse large B-cell lymphoma (DLBCL) is a common malignancy among people living with HIV. Macrophage enrichment of the tumour microenvironment (TME) is a prognostic factor in DLBCL among immunocompetent people, with some studies reporting that macrophage enrichment predicts a superior response to rituximab therapy. The macrophage phenotype is also important, with reportedly poorer outcomes with enrichment of anti-inflammatory (M2) macrophages. To date, the relationship between the type/number of tumour macrophages and outcomes in HIV-associated DLBCL (HIV-DLBCL) has been poorly explored. In this study, we assessed tumour macrophage numbers in a South African cohort of patients with DLBCL and a high HIV-seropositivity rate. Immunohistochemistry for CD68 and CD163 was performed on the diagnostic biopsies of 79 patients with DLBCL. Relevant information was documented from the clinical records, including disease stage, international-prognostic index score, HIV-related parameters, C-reactive protein, ferritin levels and immune cell numbers (monocytes, lymphocytes and neutrophils). Survival analysis was performed using Kaplan-Meier survival estimates, and the correlation between tumour macrophage numbers and a variety of immunological parameters was assessed using Spearman's rho. Of the 79 patients included, 87.2% were living with HIV, and rituximab therapy was used in 46.9%. Tumour macrophage numbers were not related to HIV status, but low pro-inflammatory (M1) macrophage numbers (CD68 + CD163 -) were significantly associated with poorer outcomes (HR 2.02, p = 0.03). M2 macrophage (CD68 + CD163 +) enrichment was not predictive of survival but was associated with improved response to rituximab therapy (HR 0.19; p = 0.002). Macrophage numbers were marginally correlated with ferritin levels, which showed modest performance as a peripheral blood biomarker of the TME macrophage status (AUC 0.6 at a level of 374 µg/L), and high ferritin levels were associated with a superior response to rituximab-therapy (HR 0.28, p = 0.034). Pro-inflammatory macrophages are important in tumour control in HIV-DLBCL, while M2 macrophage enrichment improves the response to rituximab therapy. Ferritin shows promise as a biomarker for identifying patients more likely to benefit from rituximab therapy.

Decreased PU.1 expression in mature B cells induces lymphomagenesis

Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of lymphoma, accounting for 30% of non-Hodgkin lymphomas. Although comprehensive analysis of genetic abnormalities has led to the classification of lymphomas, the exact mechanism of lymphomagenesis remains elusive. The Ets family transcription factor, PU.1, encoded by Spi1, is essential for the development of myeloid and lymphoid cells. Our previous research illustrated the tumor suppressor function of PU.1 in classical Hodgkin lymphoma and myeloma cells. In the current study, we found that patients with DLBCL exhibited notably reduced PU.1 expression in their lymphoma cells, particularly in the non-germinal center B-cell-like (GCB) subtype. This observation suggests that downregulation of PU.1 may be implicated in DLBCL tumor growth. To further assess PU.1's role in mature B cells in vivo, we generated conditional Spi1 knockout mice using Cγ1-Cre mice. Remarkably, 13 of the 23 knockout mice (56%) showed splenomegaly, lymphadenopathy, or masses, with some having histologically confirmed B-cell lymphomas. In contrast, no wild-type mice developed B-cell lymphoma. In addition, RNA-seq analysis of lymphoma cells from Cγ1-Cre Spi1F/F mice showed high frequency of each monoclonal CDR3 sequence, indicating that these lymphoma cells were monoclonal tumor cells. When these B lymphoma cells were transplanted into immunodeficient recipient mice, all mice died within 3 weeks. Lentiviral-transduced Spi1 rescued 60% of the recipient mice, suggesting that PU.1 has a tumor suppressor function in vivo. Collectively, PU.1 is a tumor suppressor in mature B cells, and decreased PU.1 results in mature B-cell lymphoma development.

Virtual tissue expression analysis

MOTIVATION

Bulk RNA expression data are widely accessible, whereas single-cell data are relatively scarce in comparison. However, single-cell data offer profound insights into the cellular composition of tissues and cell type-specific gene regulation, both of which remain hidden in bulk expression analysis.

RESULTS

Here, we present tissueResolver, an algorithm designed to extract single-cell information from bulk data, enabling us to attribute expression changes to individual cell types. When validated on simulated data tissueResolver outperforms competing methods. Additionally, our study demonstrates that tissueResolver reveals cell type-specific regulatory distinctions between the activated B-cell-like (ABC) and germinal center B-cell-like (GCB) subtypes of diffuse large B-cell lymphomas (DLBCL).

AVAILABILITY AND IMPLEMENTATION

R package available at https://github.com/spang-lab/tissueResolver (archived as 10.5281/zenodo.14160846).Code for reproducing the results of this article is available at https://github.com/spang-lab/tissueResolver-docs archived as swh:1:dir:faea2d4f0ded30de774b28e028299ddbdd0c4f89).

Development and Validation of a Novel Four Gene-Pairs Signature for Predicting Prognosis in DLBCL Patients

Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin's lymphoma. Because individual clinical outcomes of DLBCL in response to standard therapy differ widely, new treatment strategies are being investigated to improve therapeutic efficacy. In this study, we identified a novel signature for stratification of DLBCL useful for prognosis prediction and treatment selection. First, 408 prognostic gene sets were selected from approximately 2500 DLBCL samples in public databases, from which four gene-pair signatures consisting of seven prognostic genes were identified by Cox regression analysis. Then, the risk score was calculated based on these gene-pairs and we validated the risk score as a prognostic predictor for DLBCL patient outcomes. This risk score demonstrated independent predictive performance even when combined with other clinical parameters and molecular subtypes. Evaluating external DLBCL cohorts, we demonstrated that the risk-scoring model based the four gene-pair signatures leads to stable predictive performance, compared with nine existing predictive models. Finally, high-risk DLBCL showed high resistance to DNA damage caused by anticancer drugs, suggesting that this characteristic is responsible for the unfavorable prognosis of high-risk DLBCL patients. These results provide a novel index for classifying the biological characteristics of DLBCL and clearly indicate the importance of genetic analyses in the treatment of DLBCL.

First-Line Combination of R-CHOP with the PDE4 Inhibitor Roflumilast for High-Risk DLBCL

BACKGROUND

Diffuse large B-cell lymphoma (DLBCL) is a common and often fatal malignancy. The standard-of-care immunochemotherapy, R-CHOP, cures only about 60% of DLBCL patients. Improving this cure rate will likely require the effective translation of basic biology knowledge into clinical activities. We previously identified the cyclic-AMP/phosphodiesterase 4 (PDE4) axis as an important modulator of lymphomagenic processes. We also showed that the FDA-approved PDE4 inhibitor roflumilast can suppress B-cell receptor (BCR) signals, phosphoinositide 3-kinase (PI3K) activity and angiogenesis. These data suggested that combining roflumilast with R-CHOP may be beneficial in DLBCL.

METHODS

We conducted a single-center, single-arm, open-label, phase 1 study of roflumilast in combination with the standard of care, R-CHOP (Ro+R-CHOP), in pathologically proven, treatment-naïve, high-risk DLBCL patients.

RESULTS

Ro+R-CHOP was safe, and at a median follow-up time of 44 months, 70% of patients were alive and disease free (median OS not reached, PFS 44% (95% CI, 21-92). In this pilot series, we found that the addition of roflumilast suppressed PI3K activity in peripheral blood mononuclear cells, and VEGF-A secretion in the urine. We also encountered preliminary evidence to suggest that the Ro+R-CHOP combination may be particularly beneficial to patients diagnosed with high-risk genetic subtypes of DLBCL, namely MCD and A53.

CONCLUSIONS

These initial findings suggest that roflumilast may be an alternative agent able to inhibit BCR/PI3K activity and angiogenesis in DLBCL, and that the testing of Ro+R-CHOP in a larger series of genetically characterized tumors is warranted. This study was registered at ClinicalTrials.gov, number NCT03458546.

Identification of Immune-Related Gene Pair Signature to Predict Prognosis of Diffuse Large B-Cell Lymphoma Based on Bioinformatics Analyses

Since over one-third of DLBCL patients experience relapse or refractory after standard therapy, high-risk patients must be predicted. We developed a prognostic immune-related gene pairs (IRGPs) signature for DLBCL patients using bioinformatics analyses. This signature can predict the prognosis of these patients adequately, either alone or in combination with other clinical parameters. It hopes to improve the stratification and management of these patients for broad clinical applications.

Wogonin induces mitochondrial apoptosis and synergizes with venetoclax in diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is among the most aggressive hematological malignancies and patients are commonly treated with combinatorial immunochemotherapies such as R-CHOP. Till now, the prognoses are still variable and unsatisfactory, depending on the molecular subtype and the treatment response. Developing effective and tolerable new agents is always urgently needed, and compounds from a natural source have gained increasing attentions. Wogonin is an active flavonoid extracted from the traditional Chinese herbal medicine Scutellaria baicalensis Georgi and has shown extensive antitumor potentials. However, the therapeutic effect of wogonin on DLBCL remains unknown. Here, we found that treatment with wogonin dose- and time-dependently reduced the viability in a panel of established DLBCL cell lines. The cytotoxicity of wogonin was mediated through apoptosis induction, along with the loss of mitochondrial membrane potential and the downregulation of BCL-2, MCL-1, and BCL-xL. In terms of the mechanism, wogonin inhibited the PI3K and MAPK pathways, as evidenced by the clear decline in the phosphorylation of AKT, GSK3β, S6, ERK, and P38. Furthermore, the combination of wogonin and the BCL-2 inhibitor venetoclax elicited synergistically enhanced killing effect on DLBCL cells regardless of their molecular subtypes. Finally, administration of wogonin significantly impeded the progression of the DLBCL tumor in a xenograft animal model without obvious side effects. Taken together, the present study suggests a promising potential of wogonin in the treatment of DLBCL patients either as monotherapy or an adjuvant for venetoclax-based combinations.

Diffuse large B-cell lymphoma

Large B-cell lymphoma, the prototype of aggressive non-Hodgkin lymphomas, is both the most common lymphoma and accounts for the highest global burden of lymphoma-related deaths. For nearly 4 decades, the goal of treatment has been "cure", first based on CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone), and subsequently with rituximab plus CHOP. However, there is significant clinical, pathologic, and biologic heterogeneity, and not all patients are cured. Understanding and incorporating this biologic heterogeneity into treatment decisions unfortunately is not yet standard of care. Despite this gap, we now have significant advances in frontline, relapsed, and refractory settings. The POLARIX trial shows, for the first time, improved progression-free survival in a prospective randomized phase 3 setting. In the relapsed and refractory settings, there are now many approved agents/regimens, and several bispecific antibodies poised to join the arsenal of options. While chimeric antigen receptor T-cell therapy is discussed in detail elsewhere, it has quickly become an excellent option in the second-line setting and beyond. Unfortunately, special populations such as older adults continue to have poor outcomes and be underrepresented in trials, although a new generation of trials aim to address this disparity. This brief review will highlight the key issues and advances that offer improved outcomes to an increasing portion of patients.

Tumor Biology Hides Novel Therapeutic Approaches to Diffuse Large B-Cell Lymphoma: A Narrative Review

Diffuse large B-cell lymphoma (DLBCL) is a malignancy of immense biological and clinical heterogeneity. Based on the transcriptomic or genomic approach, several different classification schemes have evolved over the years to subdivide DLBCL into clinically (prognostically) relevant subsets, but each leaves unclassified samples. Herein, we outline the DLBCL tumor biology behind the actual and potential drug targets and address the challenges and drawbacks coupled with their (potential) use. Therapeutic modalities are discussed, including small-molecule inhibitors, naked antibodies, antibody-drug conjugates, chimeric antigen receptors, bispecific antibodies and T-cell engagers, and immune checkpoint inhibitors. Candidate drugs explored in ongoing clinical trials are coupled with diverse toxicity issues and refractoriness to drugs. According to the literature on DLBCL, the promise for new therapeutic targets lies in epigenetic alterations, B-cell receptor and NF-κB pathways. Herein, we present putative targets hiding in lipid pathways, ferroptosis, and the gut microbiome that could be used in addition to immuno-chemotherapy to improve the general health status of DLBCL patients, thus increasing the chance of being cured. It may be time to devote more effort to exploring DLBCL metabolism to discover novel druggable targets. We also performed a bibliometric and knowledge-map analysis of the literature on DLBCL published from 2014-2023.

The prognostic value of hydroxybutyrate dehydrogenase in diffuse large B cell lymphoma

In our investigation, we examined biochemical parameters and identified hydroxybutyrate dehydrogenase (HBDH) as a significant predictor for diffuse large B cell lymphoma (DLBCL) patients. A group of 100 patients was used to explore potential biomarkers related to progression-free survival (PFS). Subsequently, an independent cohort of 404 patients from a separate hospital was recruited to validate our findings. Our results revealed a strong association between elevated HBDH levels and poor PFS. Furthermore, although overexpression of LDHB, but not LDHA, was notably linked to poorer outcomes, HBDH expression emerged as a more robust predictor of clinical prognosis compared to LDH expression. Our investigations, which included metabolic and genetic pathway enrichment analyses, indicated that patients exhibiting heightened HBDH expression were characterized by distinct pathways related to energy metabolism and lymphoma progression. In conclusion, elevated HBDH levels were correlated with adverse survival and might serve as an independent parameter for evaluating patient outcomes.

Cell of Origin Classification of Diffuse Large B-Cell Lymphoma

Context

Diffuse large B-cell lymphoma (DLBCL) is a neoplasm of medium-to-large B lymphoid cells with diffuse growth patterns. Although it is a potentially curable disease, around 40% of the cases are either refractory to primary treatment or relapse. Based on gene expression profiling (GEP), DLBCL can be classified as germinal center B-cell subtype (GCB) and activated B-cell subtype (ABC). About 10%-15% of cases do not convincingly fall into either of the two subtypes and hence remain unclassified. Most widely used and suggested by WHO is Hans algorithm comprising immunohistochemical markers CD10, B-cell lymphoma6 (BCL6), and IRF4/MUM1, which classifies CD10+ and CD10-/BCL6+/MUM1-DLBCL as GCB, while CD10-/BCL6+/MUM1 + and BCL6-DLBCL as non-GCB.

Aims

The aim of this study was to classify DLBCL into GCB and non-GCB subtypes using Hans Algorithm.

Settings and Design

This was a retrospective study.

Materials and Methods

Twenty-eight histologically diagnosed cases of nodal (71.4%), as well as extranodal (28.6%) DLBCL, were taken over the period of 2 years with age ranging between 10 and 65 years with 19 males and 9 females. M: F = 2.1:1. Depending upon the site involved, a primary panel of immunohistochemistry (IHC) markers, namely CD20, CD3, LCA, EMA, and CK, followed by a secondary panel comprising CD10, CD19, CD30, LMP1, BCL2, BCL6, MUM1, MYC, and FOXP1 was used.

Results

In this study, it was found that the non-GCB subtype was more common than the GCB subtype in Indian population.

Conclusions

Although the gold standard of GEP to assign cells of origin is using RNA microarray analysis, however, due to resource constraints and other limitations such as long turnaround times, IHC is the next acceptable alternative.

Exploring the Potential of Enhanced Prognostic Performance of NCCN-IPI in Diffuse Large B-Cell Lymphoma by Integrating Tumor Microenvironment Markers: Stromal FOXC1 and Tumor pERK1/2 Expression

BACKGROUND

FOXC1 and ERK1-2 are proteins implicated in aggressive biological behavior of various malignancies including lymphomas.

MATERIAL AND METHODS

We investigate the additive prognostic value of stromal FOXC1 expression and tumor phosphorylated ERK1-2 (pERK1-2) expression to the established National Comprehensive Cancer Network International Prognostic Index (NCCN-IPI), in 92 diffuse large B-cell lymphoma (DLBCL) cases. Multidimensional analysis using statistics and machine learning (ML) models assessed prognostic value of established clinicopathologic variables with stromal FOXC1 and tumor pERK1-2 expressions.

RESULTS

Both high FOXC1 stroma group and high pERK1-2 tumor group were significantly associated with shorter progression-free survival (PFS) and overall survival (OS) compared with low group (p = 0.015, 0.034 and p = 0.025, 0.025 each respectively). In multivariable analysis, high FOXC1 stromal expression was an independent prognostic factor of OS (p = 0.037). The addition of stromal FOXC1 and tumor pERK1-2 to the NCCN-IPI score significantly improved prediction of time to death compared with NCCN-IPI score alone (Harrell's C-index = 0.801 vs. 0.764; p = 0.030). ML models reconfirmed the addition of stromal FOXC1 expression and tumor pERK1-2 to NCCN-IPI score had the highest C-index (0.952) among combinations. Stromal FOXC1 and tumor pERK1-2 were determinants of DLBCL prognosis, whose addition significantly improved prognostic performance of the NCCN-IPI.

Natural killer cell-associated prognosis model characterizes immune landscape and treatment efficacy of diffuse large B cell lymphoma

PURPOSE

NK cells are essential for the detection, identification and prediction of cancer. However, so far, there is no prognostic risk model based on NK cell-related genes to predict the prognosis and treatment outcome of DLBCL patients. This study aimed to explore a risk assessment model that could accurately predict the prognosis and treatment efficacy of DLBCL.

METHODS

Bioinformatics analysis of the expression profiles of DLBCL samples in the GEO database was performed. Cox regression and LASSO regression analysis were used to determine NK cell-related genes associated with patient's prognosis. Based on these genes, a risk assessment model was constructed to predict the prognosis of patients and the effectiveness of treatment. Finally, qRT-PCR was used to verify the expression of gene tags in clinical samples.

RESULTS

We identified seven prognosis-related NK cell-related genes (MAP2K1, PRKCB, TNFRSF10B, IL18, LAMP1, RASGRP1, and SP110), and DLBCL patients were divided into low- and high-risk groups based on these genes. Survival analysis showed that the prognosis of patients with low-risk group was better. Pathway enrichment analysis showed that the differentially expressed genes between the two risk groups were related to immune response pathways. Compared with the high-risk group, the low-risk group had higher infiltration of immune cells in tumor tissues. Besides, compared with high-risk group, low-risk patients by immunotherapy or other commonly used anti-tumor drugs might have better efficacy after treatment. In addition, qRT-PCR showed that the expression of risk genes including TNFRSF10B, IL18 and LAMP1 were significantly increased in most DLBCL samples compared to control samples, while the expression of protective genes including MAP2K1, PRKCB, RASGRP1 and SP110 were significantly decreased.

CONCLUSION

The NK cell-related gene signatures were proved to be a reliable indicator of the success of immunotherapy in patients with DLBCL, thus providing a unique evaluation method.

Characterizing the Cell-Free Transcriptome in a Humanized Diffuse Large B-Cell Lymphoma Patient-Derived Tumor Xenograft Model for RNA-Based Liquid Biopsy in a Preclinical Setting

The potential of RNA-based liquid biopsy is increasingly being recognized in diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma. This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n = 171) derived from a DLBCL PDTX model, including 27 humanized (HIS) PDTX, 8 HIS non-PDTX, and 21 non-HIS PDTX non-obese diabetic (NOD)-scid IL2Rgnull (NSG) mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP), CD20-targeted human IFNα2-based AcTaferon combined with CHOP (huCD20-Fc-AFN-CHOP), or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform. RNA sequencing data of the formalin-fixed paraffin-embedded (FFPE) tissue and blood plasma samples of the original patient were included. Flow cytometry was performed on immune cells isolated from whole blood, spleen, and bone marrow. Bulk deconvolution was performed using the Tabula Sapiens v1 basis matrix. Both R-CHOP and huCD20-Fc-AFN-CHOP were able to control tumor growth in most mice. Xenograft tumor volume was strongly associated with circulating tumor RNA (ctRNA) concentration (p < 0.001, R = 0.89), as well as with the number of detected human genes (p < 0.001, R = 0.79). Abundance analysis identified tumor-specific biomarkers that were dynamically tracked during tumor growth or treatment. An 8-gene signature demonstrated high accuracy for assessing therapy response (AUC 0.92). The tumoral gene detectability in the ctRNA of the PDTX-derived plasma was associated with RNA abundance levels in the patient's tumor tissue and blood plasma (p < 0.001), confirming that tumoral gene abundance contributes to the cell-free RNA (cfRNA) profile. Decomposing the transcriptome, however, revealed high inter- and intra-mouse variability, which was lower in the HIS PDTX mice, indicating an impact of human engraftment on the stability and profile of cfRNA. Immunochemotherapy resulted in B cell depletion, and tumor clearance was reflected by a decrease in the fraction of human CD45+ cells. Lastly, bulk deconvolution provided complementary biological insights into the composition of the tumor and circulating immune system. In conclusion, the blood plasma-derived transcriptome serves as a biomarker source in a preclinical PDTX model, enables the assessment of biological pathways, and enhances the understanding of cfRNA dynamics.

Unmet Needs in the First-Line Treatment of Diffuse Large B-cell Lymphoma: Expert Recommendations From the Asia-Pacific Region With a Focus on the Challenging Subtypes

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma, accounting for around 30-60% of all cases. The management of DLBCL in Asia has several unmet needs due to the diversity of the population, the heterogeneity of local clinical guidelines for DLBCL and the wide disparity in resources and healthcare systems across different regions. Rituximab combined with cyclophosphamide, doxorubicin, vincristine, and prednisone (RCHOP) is widely recognized as the standard first-line treatment for DLBCL; however, alternative regimens are required to improve patient outcomes in challenging subtypes, such as patients with high International Prognostic Index scores, old/frail patients, and patients with double-hit and double-expressor DLBCL or concurrent central nervous system disease. This review article draws from the expertise of practicing hematologists/oncologists in the region, with the aim of integrating data from current scientific evidence to address the unmet needs and unique socioeconomic challenges faced by challenging high risk patient groups in the Asia-Pacific region.

Advances in biology, diagnosis and treatment of DLBCL

Diffuse large B-cell lymphoma (DLBCL), with approximately 150,000 new cases worldwide each year, represent nearly 30% of all cases of non-Hodgkin lymphoma (NHL) and are phenotypically and genetically heterogeneous. A gene-expression profile (GEP) has identified at least three major subtypes of DLBCL, each of which has distinct clinical, biological, and genetic features: activated B-cell (ABC)-like DLBCL, germinal-center B-cell (GCB)-like DLBCL, and unclassified. Different origins are associated with different responses to chemotherapy and targeted agents. Despite DLBCL being a highly heterogeneous disease, more than 60% of patients with DLBCL can be cured after using rituximab combined with cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) to inhibit the growth of cancer cells while targeting the CD20 receptor. In recent decades, the improvement of diagnostic levels has led to a refinement classification of DLBCL and the development of new therapeutic approaches. The objective of this review was to summarize the latest studies examining genetic lesions and therapies for DLBCL.

Heterogeneity or change in cell of origin in diffuse large B-cell lymphomas determined using hans algorithm

This study aimed to analyze the heterogeneity or change in cell of origin (COO) in diffuse large B-cell lymphoma (DLBCLs) using the Hans algorithm including 156 patients with multiple DLBCL specimens. COO was detected via immunohistochemical staining for CD10, BCL6, and MUM1. The COO of the main tumor at initial diagnosis was germinal center B-cell (GCB) and non-GCB type in 50 (32%) and 106 (68%) patients, respectively. It did not change in 126 patients (81%). However, it changed in 30 patients (19%), from GCB to non-GCB in 12 patients and vice versa in 18 patients. The COO was heterogeneous or changed in 14% of simultaneous samples at other sites during the initial diagnosis, in 7% of primary refractory sites, and in 20% of samples obtained in the relapse phase other than the primary site. Changes in CD10, BCL6, and MUM1 expression were observed in 15%, 23%, and 24% samples, respectively. A low incidence of change in COO was observed in DLBCL with CD10+/BCL6+/MUM1- (4%), CD10-/BCL6-/MUM1+ (3%), and CD10-/BCL6-/MUM1- (0%) patterns, whereas DLBCL with other patterns showed COO changes at rates of 20-37%. In conclusion, COO was heterogeneous or changed in 19% of DLBCL cases. The COO should be re-examined in other biopsy samples to determine the optimal treatment.

PI3K inhibitor idelalisib enhances the anti-tumor effects of CDK4/6 inhibitor palbociclib via PLK1 in B-cell lymphoma

Relapsed or refractory diffuse large B cell lymphoma (DLBCL) and mantle cell lymphoma (MCL) patients still faced with poor survival, representing an unmet clinical need. In-depth research into the disease's pathogenesis and the development of targeted treatment strategies are urgently needed. Here, we conducted a comprehensive bioinformatic analysis of gene mutation and expression using data from our center and public databases. Cell cycle-related genes especially for CDKN2A/B-CDK4/6/CCND1 machinery altered frequently in DLBCL and MCL. Clinically, high CDK4 and CDK6 expression were correlated with poor prognosis of DLBCL and MCL patients. Furthermore, we also validated the pharmacological efficacy of CDK4/6 inhibitor palbociclib and its synergy effect with PI3K inhibitor idelalisib utilizing in vitro cell lines and in vivo cell-derived xenograft (CDX) and patient-derived xenograft (PDX) mouse models. Our results provided sufficient pre-clinical evidence to support the potential combination of palbociclib and idelalisib for DLBCL and MCL patients.

PD-L1+ macrophage and tumor cell abundance and proximity to T cells in the pretreatment large B-cell lymphoma microenvironment impact CD19 CAR-T cell immunotherapy efficacy

CD19-targeted chimeric antigen receptor T-cell (CAR-T) immunotherapy has transformed the management of relapsed/refractory large B-cell lymphoma (LBCL), yet durable remissions are observed in less than half of treated patients. The tumor microenvironment (TME) is a key and understudied factor impacting CD19 CAR-T therapy outcomes. Using NanoString nCounter transcriptome profiling (n = 24) and multiplex immunohistochemistry (mIHC, n = 15), we studied the TME in pretreatment biopsies from patients with LBCL undergoing CD19 CAR-T therapy. Patients who achieved complete response (CR) after CAR-T therapy demonstrated higher expression of genes associated with T-cell trafficking and function, whereas those who did not achieve CR had higher expression of genes associated with macrophages and T-cell dysfunction. Distinct patterns of immune infiltration and fibrosis in the TME were associated with CAR-T therapy outcomes, and these findings were corroborated using artificial intelligence-assisted image analyses. Patients who achieved CR had a lower proportion of the biopsy occupied by an interspersed immune infiltrate and a higher proportion of hypocellular/fibrotic regions. Furthermore, mIHC revealed lower density of CD4+ T cells and higher densities of both macrophages and tumor cells expressing PD-L1 in non-CR patients. Spatial analysis revealed that PD-1+ T cells were in close proximity to PD-L1+ macrophages or PD-L1+ tumor cells in patients who did not compared to those who did achieve CR after CAR-T therapy. These findings suggest that morphologic patterns in the TME and engagement of the PD-1/PD-L1 axis in pretreatment biopsies may impact CD19 CAR-T immunotherapy response in patients with LBCL.

Long noncoding RNA XIST: a novel independent prognostic biomarker for patients with ABC-DLBCL receiving R-CHOP treatment

Approximately one-third of activated B-cell-like diffuse large B-cell lymphoma (ABC-DLBCL) cases were unresponsive to standard first-line therapy; thus, identifying biomarkers to evaluate therapeutic efficacy and assessing the emergence of drug resistance is crucial. Through early-stage screening, long noncoding RNA (lncRNA) X-inactive specific transcript (XIST) was found to be correlated with the R-CHOP treatment response. This study aimed to clarify the characteristics of XIST in ABC-DLBCL. The expression level of XIST in 161 patients with ABC-DLBCL receiving R-CHOP therapy was examined via RNA in situ hybridization, and the association between XIST expression and clinicopathological features, treatment response and prognosis was analyzed in the study cohort and validated in the Gene Expression Omnibus cohort. Cell biological experiments and bioinformatics analyses were conducted to reveal aberrant signaling. The proportion of complete response in patients with high XIST expression was lower than that in patients with low XIST expression (53.8% versus 77.1%) (P = 0.002). High XIST expression was remarkably associated with the characteristics of tumor progression and was an independent prognostic element for overall survival (P = 0.039) and progression-free survival (P = 0.027) in ABC-DLBCL. XIST was proven to be involved in m6A-related methylation and ATF6-associated autophagy. XIST knockdown repressed ABC-DLBCL cellular proliferation by regulating Raf/MEK/ERK signaling. High XIST expression was associated with ABC-DLBCL tumorigenesis and development and contributed to R-CHOP treatment resistance. XIST may be a promising signal to predict ABC-DLBCL prognosis.