Genomics of aggressive B-cell lymphoma

Cytogenomic and clinicopathological comparison of MYC-positive and MYC-negative High-grade B-cell lymphoma with 11q aberration in the context of other aggressive lymphomas with MYC rearrangement

According to the 2022 WHO classification, High-grade B-cell lymphoma with 11q aberration (HGBCL-11q) is a MYC-negative lymphoma with 11q duplication and terminal deletion as specific chromosomal aberrations for this neoplasm. However, there are a growing number of reports defying this definition describing cases with the co-occurrence of 11q aberration and MYC rearrangement (HGBCL-11q,MYCR). This research has two aims. First, to compare the unique HGBCL-11q,MYCR group of 9 cases with 26 HGBCL-11q cases on chromosomal, mutational and clinicopathological level. The second objective is to investigate the association of the new HGBCL-11q,MYCR group with HGBCL-11q and two other closely related MYC-positive aggressive lymphoma subtypes: Burkitt lymphoma (BL) (n=17) and High-grade B-cell lymphoma, not otherwise specified with MYC rearrangement (n=10). Genetic results were obtained by classical cytogenetics, fluorescence in situ hybridization, microarrays, and whole exome sequencing. In parallel histopathological/ immunohistochemical analyses (HP/IHC) with flow cytometry(FCM), in conjunction with clinical presentation and treatment outcomes are presented. Our findings reveal that HGBCL-11q,MYCR, exists as an independent nosological entity, distinct from BL and HGBCL-11q at the cytogenetic, molecular, and clinicopathological levels, although it contains common features of both lymphoma subtypes. Common features with BL include: MYC rearrangement with the immunoglobulin genes, patterns of secondary chromosomal aberrations like dup(1q), del(17p), high number of MYC and CCND3 mutations. Other BL features are: frequent extranodal abdominal presentation, morphology, GCB cell of origin determined by IHC and FCM, immunophenotypical features such as MYC(+)/LMO2(-) detected by flow cytometric features: CD45(+)weaker, more cases with CD43(+) and CD44(-) expression, only expression of IgD and IgM heavy chain and CD38(+)higher overexpression, which correlates with MYC rearrangement assessed by FCM. Similarity to HGBCL-11q includes the existence of 11q aberration, presence of DDX3X, ETS1, GNA13, NFRKB, KMT2D, and the lack of TCF3 and ID3 mutations. Additionally, frequent nodal and tonsillar presentation, morphology, GCB cell of origin, immunophenotypical features with flow cytometry measured CD56(+) expression, associated with NCAM duplication/amplification on 11q, and pathogenesis not associated with Epstein-Barr virus infection. The distinctive chromosomal change of HGBCL-11q,MYCR was the gain or amplification of 3q29. Our cohort of patients with HGBCL-11q,MYCR had similar relapse-free survival to that of patients with HGBCL-11q and BL, if treated with BL-directed regimens.

Applications of Multimodal Artificial Intelligence in Non-Hodgkin Lymphoma B Cells

Given advancements in large-scale data and AI, integrating multimodal artificial intelligence into cancer research can enhance our understanding of tumor behavior by simultaneously processing diverse biomedical data types. In this review, we explore the potential of multimodal AI in comprehending B-cell non-Hodgkin lymphomas (B-NHLs). B-cell non-Hodgkin lymphomas (B-NHLs) represent a particular challenge in oncology due to tumor heterogeneity and the intricate ecosystem in which tumors develop. These complexities complicate diagnosis, prognosis, and therapy response, emphasizing the need to use sophisticated approaches to enhance personalized treatment strategies for better patient outcomes. Therefore, multimodal AI can be leveraged to synthesize critical information from available biomedical data such as clinical record, imaging, pathology and omics data, to picture the whole tumor. In this review, we first define various types of modalities, multimodal AI frameworks, and several applications in precision medicine. Then, we provide several examples of its usage in B-NHLs, for analyzing the complexity of the ecosystem, identifying immune biomarkers, optimizing therapy strategy, and its clinical applications. Lastly, we address the limitations and future directions of multimodal AI, highlighting the need to overcome these challenges for better clinical practice and application in healthcare.

Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues

Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combining in situ polyadenylation and deterministic barcoding for spatial full coverage transcriptome sequencing, tailored for probing the diverse landscape of RNA species even in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish different malignant clones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA-mRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis trajectory. High resolution Patho-DBiT at the cellular level reveals a spatial neighborhood and traces the spatiotemporal kinetics driving tumor progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to study human tissue biology and aid in clinical pathology evaluation.

Accurate interpretation of p53 immunohistochemical patterns is a surrogate biomarker for TP53 alterations in large B-cell lymphoma

BACKGROUND

To clarify the relationship between p53 immunohistochemistry (IHC) staining and TP53 alterations (including mutations and deletions) in large B-cell lymphomas (LBCLs) and to explore the possibility of p53 IHC expression patterns as surrogate markers for TP53 alterations.

METHODS

A total of 95 patients diagnosed with LBCLs were selected, and paraffin samples were taken for TP53 gene sequencing, fluorescence in situ hybridization and p53 IHC staining. The results were interpreted by experienced pathologists and molecular pathologists.

RESULTS

Forty-three nonsynonymous TP53 mutations and p53 deletions were detected in 40 cases, whereas the remaining 55 cases had wild-type TP53 genes. The majority of TP53 mutations (34/43, 79.1%) occurred in exons 4-8, and R248Q was the most common mutation codon (4/43, 9.3%). The highest frequency single nucleotide variant was C > T (43.6%). p53 expression was interpreted as follows: Pattern A: p53 staining was positive in 0%-3% of tumor cells, Pattern B: p53 staining was positive in 4-65% of tumor cells, Pattern C: more than 65% of tumor cells were stained positive for p53. The p53 IHC expression patterns were associated with TP53 alterations. Gain of function variants and wild-type TP53 tended to exhibit type C and B p53 expression patterns, but loss of function variants were exclusively seen in type A cases. Additionally, interpretation of the staining by various observers produced significant reproducibility.

CONCLUSIONS

The p53 IHC expression patterns can be used to predict TP53 alterations and are reliable for diverse alteration types, making them possible surrogate biomarkers for TP53 alterations in LBCLs.

Intravascular large B-cell lymphoma with isolated bone marrow involvement

Introduction. Intravascular large B-cell lymphoma is a rare variant of large B-cell, highly invasive extranodal tumors of the lymphatic system. The pathogenesis of the disease lies in the ability of tumor cells to penetrate into small vessels and capillaries of various organs. The clinical presentation is atypical for diffuse large B-cell lymphoma. In the relevant literature, information on the diagnosis and treatment of this pathology is extremely rare, therefore each publication makes a significant contribution to expanding the horizons of hematologists and morphologists.

Aim – to present a case of diagnosing intravascular B-cell lymphoma.

Main findings. A clinical case of a 78-year-old patient who fell ill acutely is presented. At the onset of the disease, febrile fever was noted. In the general blood test: hemoglobin – 104 g/L; erythrocytes – 3.0 × 1012/L; ESR – 24 mm/h; platelets – 112 × 109/L, leukocytes – 4.9 × 109/L, 4 % of cells with lymphoblast morphology were found in the leukocyte formula. Blood serum tests revealed: an increase in uric acid concentrations – up to 639 μmol/L, LDH – up to 1885 U/L, beta-2-microglobulin – up to 8.9 mmol/L, C-reactive protein – up to 0.6 g/L, a decrease in the concentration of total protein – up to 45 g/L, an increase in the concentration of aspartate aminotransferase – up to 48 units/L at normal concentrations of bilirubin and alanine aminotransferase.

The histological and immunohistochemical picture, according to the study of bone biopsy, most corresponded to bone marrow damage by intravascular large B-cell lymphoma. Immunophenotyping was carried out – 15.7 % of blast cells with immunophenotype CD19+HLA/DR+CD24+CD37+CD20+CD10+IgM+ were detected. Cytogenetic studies revealed no karyotype abnormalities. The result of fluorescence in situ hybridization of the IGH locus (14q32) was normal. Based on the data obtained, the final clinical diagnosis was established: diffuse large B-cell lymphoma, stage IVB, intravascular variant with bone marrow involvement, aggressive course. The patient was prescribed the first line of therapy according to the R-CHOP scheme (rituximab, cyclophosphamide, vincristine, prednisolone). In the control study of the bone marrow, after the first course of therapy, the number of lymphoid elements was 3.6 %, laboratory parameters returned to normal.

Copy Number Alteration and Mutational Profile of High-Grade B-Cell Lymphoma with MYC and BCL2 and/or BCL6 Rearrangements, Diffuse Large B-Cell Lymphoma with MYC-Rearrangement, and Diffuse Large B-Cell Lymphoma with MYC-Cluster Amplification

Diffuse large B-cell lymphoma (DLBCL) with MYC alteration is classified as high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (double/triple-hit lymphoma; DHL/THL), DLBCL with MYC rearrangement (single-hit lymphoma; SHL) and DLBCL with MYC-cluster amplification (MCAD). To elucidate the genetic features of DHL/THL, SHL, and MCAD, 23 lymphoma cases from Tokai University Hospital were analyzed. The series included 10 cases of DHL/THL, 10 cases of SHL and 3 cases of MCAD. The analysis used whole-genome copy number microarray analysis (OncoScan) and a custom-made next-generation sequencing (NGS) panel of 115 genes associated with aggressive B-cell lymphomas. The copy number alteration (CNA) profiles were similar between DHL/THL and SHL. MCAD had fewer CNAs than those of DHL/THL and SHL, except for +8q24. The NGS profile characterized DHL/THL with a higher "mutation burden" than SHL (17 vs. 10, p = 0.010), and the most relevant genes for DHL/THL were BCL2 and SOCS1, and for SHL was DTX1. MCAD was characterized by mutations of DDX3X, TCF3, HLA-A, and TP53, whereas MYC was unmutated. In conclusion, DHL/THL, SHL, and MCAD have different profiles.

Outcome of aggressive B-cell lymphoma with TP53 alterations administered with CAR T-cell cocktail alone or in combination with ASCT

TP53 gene alteration confers inferior prognosis in refractory/relapse aggressive B-cell non-Hodgkin lymphoma (r/r B-NHL). From September 2016 to September 2020, 257 r/r B-NHL patients were assessed for eligibility for two trials in our center, assessing anti-CD19 and anti-CD22 chimeric antigen receptor (CAR19/22) T-cell cocktail treatment alone or in combination with autologous stem cell transplantation (ASCT). TP53 alterations were screened in 123 enrolled patients and confirmed in 60. CAR19/22 T-cell administration resulted in best objective (ORR) and complete (CRR) response rate of 87.1% and 45.2% in patients with TP53 alterations, respectively. Following a median follow-up of 16.7 months, median progression-free survival (PFS) was 14.8 months, and 24-month overall survival (OS) was estimated at 56.3%. Comparable ORR, PFS, and OS were determined in individuals with or without TP53 alterations, and in individuals at different risk levels based on functional stratification of TP53 alterations. CAR19/22 T-cell treatment in combination with ASCT resulted in higher ORR, CRR, PFS, and OS, but reduced occurrence of severe CRS in this patient population, even in individuals showing stable or progressive disease before transplantation. The best ORR and CRR in patients with TP53 alterations were 92.9% and 82.1%, respectively. Following a median follow-up of 21.2 months, 24-month PFS and OS rates in patients with TP53 alterations were estimated at 77.5% and 89.3%, respectively. In multivariable analysis, this combination strategy predicted improved OS. In conclusion, CAR19/22 T-cell therapy is efficacious in r/r aggressive B-NHL with TP53 alterations. Combining CAR-T cell administration with ASCT further improves long-term outcome of these patients.

Molecular Update and Evolving Classification of Large B-Cell Lymphoma

Diffuse large B-cell lymphomas (DLBCLs) are aggressive B-cell neoplasms with considerable clinical, biologic, and pathologic diversity. The application of high throughput technologies to the study of lymphomas has yielded abundant molecular data leading to the identification of distinct molecular identities and novel pathogenetic pathways. In light of this new information, newly refined diagnostic criteria have been established in the fourth edition of the World Health Organization (WHO) consensus classification of lymphomas, which was revised in 2016. This article reviews the histopathological and molecular features of the various aggressive B-cell lymphoma subtypes included in the updated classification.

In Vivo and Ex Vivo Patient-Derived Tumor Xenograft Models of Lymphoma for Drug Discovery

In the hemato-oncology field, remarkable scientific progress has been achieved, primarily propelled by the discovery of new technologies, improvement in genomics, and novel in vitro and in vivo models. The establishment of multiple cell line collections and the development of instrumental mouse models enhanced our ability to discover effective therapeutics. However, cancer models that faithfully mimic individual cancers are still imperfect. Patient-derived tumor xenografts (PDTXs) have emerged as a powerful tool for identifying the mechanisms which drive tumorigenesis and for testing potential therapeutic interventions. The recognition that PDTXs can maintain many of the donor samples' properties enabled the development of new strategies for discovering and implementing therapies. Described in this article are protocols for the generation and characterization of lymphoma PDTXs that may be used as the basis of shared procedures. Universal protocols will foster the model utilization, enable the integration of public and private repositories, and aid in the development of shared platforms. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Tissue handling and cryopreservation of primary and PDTX samples Basic Protocol 2: Performing tumor implant in immunocompromised mice PDTX models Alternate Protocol 1: Intra-medullary femoral injection Alternate Protocol 2: Intravenous injection Alternate Protocol 3: Intraperitoneal injection Support Protocol 1: Phenotypical characterization of PDTXs by flow cytometry Support Protocol 2: Biological and molecular characterization of PDTX tumors by PCR detection of IGK, IGH, and TCR rearrangements Basic Protocol 3: Harvesting PDTX-derived tumor cells for ex vivo experiments Basic Protocol 4: In vivo testing of multiple compounds in a PDTX mouse model.

Targeted massively parallel sequencing of mature lymphoid neoplasms: assessment of empirical application and diagnostic utility in routine clinical practice

Massively parallel sequencing (MPS) has become a viable diagnostic tool to interrogate genetic profiles of numerous tumors but has yet to be routinely adopted in the setting of lymphoma. Here, we report the empirical application of a targeted 40-gene panel developed for use in mature lymphoid neoplasms (MLNs) and report our experience on over 500 cases submitted for MPS during the first year of its clinical use. MPS was applied to both fresh and fixed specimens. The most frequent diagnoses were diffuse large B-cell lymphoma (116), chronic lymphocytic leukemia/small lymphocytic lymphoma (60), marginal zone lymphoma (52), and follicular lymphoma (43), followed by a spectrum of mature T-cell neoplasms (40). Of 534 cases submitted, 471 generated reportable results in MLNs, with disease-associated variants (DAVs) detected in 241 cases (51.2%). The most frequent DAVs affected TP53 (30%), CREBBP (14%), MYD88 (14%), TNFRSF14 (10%), TNFAIP3 (10%), B2M (7%), and NOTCH2 (7%). The bulk of our findings confirm what is reported in the scientific literature. While a substantial majority of mutations did not directly impact diagnosis, MPS results were utilized to either change, refine, or facilitate the final diagnosis in ~10.8% of cases with DAVs and 5.5% of cases overall. In addition, we identified preanalytic variables that significantly affect assay performance highlighting items for specimen triage. We demonstrate the technical viability and utility of the judicious use of a targeted MPS panel that may help to establish general guidelines for specimen selection and diagnostic application in MLNs in routine clinical practice.

RNA-Based next generation sequencing complements but does not replace fluorescence in situ hybridization studies for the classification of aggressive B-Cell lymphomas

Aggressive B-cell lymphomas are currently classified based in part upon the presence or absence of translocations involving BCL2, BCL6, and MYC. Most clinical laboratories employ fluorescence in situ hybridization (FISH) analysis for the detection of these rearrangements. The potential role of RNA-based sequencing approaches in the evaluation of malignant lymphoma is currently unclear. In this study, we performed RNA sequencing (RNAseq) in 37 cases of aggressive B-cell lymphomas using a commercially available next generation sequencing assay and compared results to previously performed FISH studies. RNAseq detected 1/7 MYC (14%), 3/8 BCL2 (38%) and 4/8 BCL6 (50%) translocations identified by FISH. RNAseq also detected 1 MYC/IGH fusion in a case not initially tested by FISH due to low MYC protein expression and 2 BCL6 translocations that were not detected by FISH. RNAseq identified the partner gene in each detected rearrangement, including a novel EIF4G1-BCL6 rearrangement. In summary, RNAseq complements FISH for the detection of rearrangements of BCL2, BCL6 and MYC in the evaluation and classification of aggressive B-cell lymphomas by detecting rearrangements that may be cryptic by FISH methods and by identifying the rearrangement partner genes. Detection of these clinically important translocations may be optimized by combined use of FISH and RNAseq.

Burkitt-Like Lymphoma with 11q Aberration: A Case Report and Review of a Rare Entity

Burkitt-like lymphoma with 11q aberration is a rare diagnostic entity commonly occurring in children and young adults with a nodal presentation. This entity shares many similar morphologic and immunophenotypic features with conventional Burkitt lymphoma and other aggressive B-cell lymphomas, making its recognition challenging. However, the presence of its characteristic 11q gain/loss pattern is helpful in the diagnosis. We report a case of Burkitt-like lymphoma presenting as a right neck mass in a 17-year-old female patient that demonstrated no improvement with antibiotic therapy. The neoplasm displayed a diffuse proliferation of intermediate-sized atypical lymphoid cells with prominent nucleoli in a background of apoptotic debris, morphologically raising concern for conventional Burkitt lymphoma. Subsequent immunohistochemical and cytogenetic studies established the most likely diagnosis of Burkitt-like lymphoma with 11q aberration. Though rare, Burkitt-like lymphoma exhibits significant morphologic overlap with other high-grade B-cell lymphomas, making it an important entity to consider on the differential diagnosis of these lesions.

Eμ-TCL1xMyc: A Novel Mouse Model for Concurrent CLL and B-Cell Lymphoma

PURPOSE

Aberrant Myc expression is a major factor in the pathogenesis of aggressive lymphoma, and these lymphomas, while clinically heterogeneous, often are resistant to currently available treatments and have poor survival. Myc expression can also be seen in aggressive lymphomas that are observed in the context of CLL, and we sought to develop a mouse model that could be used to study therapeutic strategies for aggressive lymphoma in the context of CLL.

EXPERIMENTAL DESIGN

We crossed the Eμ-TCL1 mouse model with the Eμ-Myc mouse model to investigate the clinical phenotype associated with B-cell-restricted expression of these oncogenes. The resulting malignancy was then extensively characterized, from both a clinical and biologic perspective.

RESULTS

Eμ-TCL1xMyc mice uniformly developed highly aggressive lymphoid disease with histologically, immunophenotypically, and molecularly distinct concurrent CLL and B-cell lymphoma, leading to a significantly reduced lifespan. Injection of cells from diseased Eμ-TCL1xMyc into WT mice established a disease similar to that in the double-transgenic mice. Both Eμ-TCL1xMyc mice and mice with disease after adoptive transfer failed to respond to ibrutinib. Effective and durable disease control was, however, observed by selective inhibition of nuclear export protein exportin-1 (XPO1) using a compound currently in clinical development for relapsed/refractory malignancies, including CLL and lymphoma.

CONCLUSIONS

The Eμ-TCL1xMyc mouse is a new preclinical tool for testing experimental drugs for aggressive B-cell lymphoma, including in the context of CLL.

Novel therapies for relapsed/refractory aggressive lymphomas

Most patients with aggressive non-Hodgkin lymphoma will be cured with initial chemoimmunotherapy; however, most patients with relapsed disease will not be cured and will die as a result of their disease. In these cases, continued treatment with conventional chemotherapy is typically not of benefit and can contribute to significant toxicities and decreased quality of life for patients. Fortunately, a number of therapies are currently available or under investigation for this group of patients, ranging from oral tyrosine kinase inhibitors targeting multiple pathways within the malignant cells to adoptive cellular therapies that harness the patient's immune system to fight disease. Additionally, many agents that are modestly effective as monotherapies can be safely combined with additional novel and conventional therapies to improve response rates and duration. Chimeric antigen receptor T cells are among the most promising group of therapies and provide the potential for cure for patients with relapsed/refractory lymphoma. In this chapter, we will review the currently available novel treatments as well as those still under investigation and discuss the most appropriate approach to patients with relapsed/refractory aggressive lymphoma. We will highlight the challenges associated with these therapies, as well as potential toxicities, and the need for additional clinical trials evaluating combinations and newer treatments.