Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma

Advances in Hodgkin lymphoma research

Hodgkin lymphoma (HL) has been and still is the most enigmatic lymphoid malignancy in humans. Since the first molecular analysis of isolated Hodgkin and Reed-Sternberg (HRS) tumor cells of classic HL 30 years ago, substantial advances in our understanding of HL have been made. This review describes the cellular origin of HL, summarizes the current knowledge about the genetic lesions in HRS cells, and highlights the role of Epstein-Barr virus (EBV) in HL pathogenesis. Moreover, the pathobiological roles of altered gene expression and deregulated signaling pathways are discussed and key aspects of the HL microenvironment are presented.

The art of war: using genetic insights to understand and harness radiation sensitivity in hematologic malignancies

It is well established that hematologic malignancies are often considerably radiosensitive, which enables usage of far lower doses of therapeutic radiotherapy. This review summarizes the currently known genomic landscape of hematologic malignancies, particularly as it relates to radiosensitivity and the field of radiation oncology. By tracing the historical development of the modern understanding of radiosensitivity, we focus on the discovery and implications of pivotal mutated genes in hematologic malignancies such as TP53, ATM, and other genes critical to DNA repair pathways. These genetic insights have contributed significantly to the advancement of personalized medicine, aiming to enhance treatment precision and outcomes, and there is an opportunity to extend these insights to personalized radiotherapy. We explore the transition from early discoveries to the current efforts in integrating comprehensive genomic data into clinical practice. Specific examples from Hodgkin lymphoma, non-Hodgkin lymphoma, and plasma cell neoplasms illustrate how genetic mutations could influence radiosensitivity and impact subsequent radiotherapeutic response. Despite the advancements, challenges remain in translating these genetic insights into routine clinical practice, particularly due to the heterogeneity of alterations and the complex interactions within cancer signaling pathways. We emphasize the potential of radiogenomics to address these challenges by identifying genetic markers that predict radiotherapy response and toxicity, thereby refining treatment strategies. The need for robust decision support systems, standardized protocols, and ongoing education for healthcare providers is critical to the successful integration of genomic data into radiation therapy. As research continues to validate genetic markers and explore novel therapeutic combinations, the promise of personalized radiotherapy becomes increasingly attainable, offering the potential to significantly improve outcomes for patients with hematologic malignancies.

Molecular profiling of cell-free DNA from classic Hodgkin lymphoma patients identifies potential prognostic clusters and corresponds with disease dynamics

Cell-free DNA (cfDNA) analysis has advantages over tissue analysis for molecular profiling of classic Hodgkin lymphoma (cHL) at diagnosis and offers additional opportunities for sensitive non-invasive disease tracking during treatment. The aim of this study is to correlate cfDNA based molecular profiling with disease characteristics including serum Thymus and Activation Regulated Chemokine (TARC) levels and FDG-PET imaging, which are established markers of disease assessment. cfDNA isolated from plasma samples of 42 cHL patients was analyzed using low coverage whole genome and targeted next-generation sequencing. Patients were clustered in three groups based on Epstein-Barr virus (EBV) and SOCS1 mutational status. Patients in the EBV-negative (EBV-) & SOCS1 mutated (m) cluster had more extensive disease based on significantly higher serum TARC (sTARC) levels, higher metabolic tumor volume and increased risk of treatment failure. Additionally, the median variant allele frequency and mutational load was highest in the EBV- & SOCS1m cluster, which was validated in two external cohorts. The estimated tumor fraction and median variant allele frequency of the single nucleotide variants correlated with sTARC levels. Disease tracking over time demonstrated cfDNA level dynamics that partly resembled sTARC levels and imaging results. In conclusion, we show that cfDNA based clustering on EBV status and SOCS1 mutational status correlates with adverse disease characteristics and increased risk of treatment failure. CfDNA-based disease tracking has the potential to serve as a sensitive tool that can complement existing response assessment methods in cHL patients.

Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors

A key challenge in cancer research is to identify the secreted factors that contribute to tumor cell survival. Nowhere is this more evident than in Hodgkin lymphoma, where malignant Hodgkin Reed Sternberg (HRS) cells comprise only 1-5% of the tumor mass, the remainder being infiltrating immune cells that presumably are required for the survival of the HRS cells. Until now, there has been no way to characterize the complex Hodgkin lymphoma tumor microenvironment at genome scale. Here, we performed genome-wide transcriptional profiling with spatial and single-cell resolution. We show that the neighborhood surrounding HRS cells forms a distinct niche involving 31 immune and stromal cell types and is enriched in CD4+ T cells, myeloid and follicular dendritic cells, while being depleted of plasma cells. Moreover, we used machine learning to nominate ligand-receptor pairs enriched in the HRS cell niche. Specifically, we identified IL13 as a candidate survival factor. In support of this hypothesis, recombinant IL13 augmented the proliferation of HRS cells in vitro. In addition, genome-wide CRISPR/Cas9 loss-of-function studies across more than 1,000 human cancer cell lines showed that IL4R and IL13RA1, the heterodimeric partners that constitute the IL13 receptor, were uniquely required for the survival of HRS cells. Moreover, monoclonal antibodies targeting either IL4R or IL13R phenocopied the genetic loss of function studies. IL13-targeting antibodies are already FDA-approved for atopic dermatitis, suggesting that clinical trials testing such agents should be explored in patients with Hodgkin lymphoma.

Computational pathology identifies a low B-cell content in the tumour microenvironment as a predictor of adverse outcome in patients with classic Hodgkin lymphoma treated with ABVD

AIMS

The prognostic impact of B lymphocytes surrounding Hodgkin and Reed Sternberg (HRS) cells in classic Hodgkin lymphoma (cHL) and pathogenic variants in genes associated with apoptosis regulation remains undefined.

METHODS

We have quantified the proportion of B lymphocytes in tumour microenvironment (TME) in 220 diagnostic slides from 110 cHL patients applying computational pathology (CP) and sequenced cases using a targeted panel including 47 genes recurrently mutated in mature B-cell neoplasms. Kaplan-Meier estimators and multivariate Cox regression on overall survival (OS) and progression-free survival (PFS) were assessed following the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis guidelines.

RESULTS

The mean percentage of B lymphocytes was 45.1 (SD: 24.8). Genes recurrently affected by nonsynonymous somatic mutations in 25% or more of patients included EP300, NOTCH and ABL1. A lower number of mutations were discovered in Epstein-Barr virus-positive cHL (21.1% vs 78.8%) reinforcing the notion that viral infection could functionally replace the need for genomic aberrations. Classic Hodgkin lymphoma (cHL) patients that jointly presented a reduction in the number of B lymphocytes in TME (<8%) and the absence of mutations in apoptosis-associated genes (ABL1, BIRC3, CASP8 and FAS) presented a lower OS (mean OS: 31.5 months, 95% CI: 0 to 69.7 months) in comparison with patients without this event (mean OS: 84.7 months, 95% CI: 61.9 to 107.5 months) (p=0.01). This high-risk cHL subgroup also presented a significantly lower PFS (mean PFS: 8.5 months, 95% CI: 7.5 to 9.5 months) in comparison with B-cell-enriched or apoptosis-mutated cHL (mean PFS: 55.2 months; 95% CI: 42.4 to 68 months) (p<0.001).

CONCLUSIONS

This study expands previous data on the value of CP in cHL, and specifically, the distribution of B cells, identifying patients with an increased risk of treatment failure and progression. Furthermore, immune escape by apoptosis dysregulation during clonal selection occurring in germinal centres constitutes a landmark of cHL. These results could be the basis for further development of targeted therapies directed against apoptosis modulators in cHL.

Genetic and immunological features of immune deficiency and dysregulation-associated lymphoproliferations and lymphomas as a basis for classification

Immune deficiency and dysregulation-associated lymphoproliferative disorders and lymphomas (IDD-LPDs) encompass a heterogeneous clinical and pathological spectrum of disorders that range from indolent lymphoproliferations to aggressive lymphomas. They arise in a variety of clinical settings and are associated with oncogenic viruses such as the Epstein-Barr virus (EBV) and Kaposi sarcoma-associated herpesvirus/human herpes virus (KSHV/HHV8) in some, but not all, cases. The recognition of IDD-LPDs as distinct from LPDs in immune competent patients is essential to tailor clinical management options for affected patients. The 5th edition of the World Health Organisation classification has introduced an integrated classification of IDD-LPDs with the goal of standardising diagnoses among different settings to enhance clinical decision support. In parallel, new knowledge in the field, particularly surrounding the role of oncogenic viruses and the tumour microenvironment, has led to clearer understanding of the complex pathogenesis of IDD-LPDs and how these features can be precisely harnessed for therapeutic purposes. In this perspective, we highlight the need for multidisciplinary decision-making to augment patient care as well as key areas where evolving concepts offer challenges and opportunities for clinical management, research and future iterations of the classification.

Targeted mutational profiling of Epstein Barr virus-positive mucocutaneous ulcer: Implications for differential diagnosis with EBV-positive diffuse large B-cell lymphoma

Epstein Barr Virus-positive mucocutaneous ulcer (EBVMCU) can be difficult to distinguish from EBV-positive diffuse large B cell lymphoma (DLBCL). We used targeted next-generation sequencing (NGS) to explore genetic alterations in EBVMCU to aid in this diagnostic challenge. Ten cases of EBVMCU were evaluated by a targeted NGS panel of 164 genes. Targeted NGS identified 18 variants in 15 genes in eight cases of EBVMCU. Loss of function TET2 variants were most frequently identified (3 of 10 cases, 30 %). One TET2 variant occurred at low variant allele frequency (VAF) of 3 %, which may be suggestive of clonal hematopoiesis of indeterminate potential. One case harbored a loss of function DNMT3A variant at low VAF. Two cases demonstrated missense variants in the IRF8 gene. Both variants occurred at a VAF close to 50 % and with an estimated high burden of disease (75 %). Two cases of mucosal gastrointestinal involvement had no reportable variants. Mutational profiling of EBVMCU identified TET2 loss of function variants at an elevated frequency in our cohort; however, the findings are not specific and its clinical significance cannot be completely elucidated. Further studies are needed to confirm the findings in an independent and larger cohort of EBVMCU, to determine the cell of origin of the variants, and to further assess their significance in the pathogenesis of this disorder.

Infant with diffuse large B-cell lymphoma identified postmortem with homozygous founder Slavic RAG1 variant: a case report and literature review

Background and aims

There is an increased risk of lymphomas in inborn errors of immunity (IEI); however, germline genetic testing is rarely used in oncological patients, even in those with early onset of cancer. Our study focuses on a child with a recombination-activating gene 1 (RAG1) deficiency who was identified through a screening program for Slavic founder genetic variants among patients who died with malignancy at an early age in Belarus.

Results

We identified one homozygous founder RAG1 variant out of 24 available DNA samples from 71 patients who developed lymphoma aged <3 years from the Belarusian cancer registry between 1986 and 2023. Our patient had an episode of pneumonia at 3 months of age and was hospitalized for respiratory distress, candida-positive lung disease, and lymphadenopathy at 14 months of age. The diagnosis of Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) was established. The patient had a normal lymphocyte count that decreased over time. One month after chemotherapy initiation, the patient died due to sepsis and multiple organ failure without a genetic diagnosis. In a retrospective analysis, T-cell receptor excision circles (TRECs) and kappa-deleting recombination excision circles (KRECs) were undetectable in peripheral blood.

Conclusions

A targeted screening program designed to detect a Slavic founder variant in the RAG1 gene among children revealed a 14-month-old Belarusian male infant with low TREC levels who died of EBV-driven DLBCL and complications of chemotherapy including infections. This case highlights how patients with IEI and recurrent infections may develop serious non-infectious complications, such as fatal malignancy. It also emphasizes the importance of early identification, such as newborn screening for severe combined immune deficiency. Earlier diagnosis of RAG deficiency could have prompted hematopoietic stem cell transplant well before the DLBCL occurrence. This likely would impact the onset and/or management strategies for the cancer.

Pathogenic Variants Associated with Epigenetic Control and the NOTCH Pathway Are Frequent in Classic Hodgkin Lymphoma

Classic Hodgkin lymphoma (cHL) constitutes a B-cell neoplasm derived from germinal center lymphocytes. Despite high cure rates (80-90%) obtained with the current multiagent protocols, a significant proportion of cHL patients experience recurrences, characterized by a lower sensitivity to second-line treatments. The genomic background of chemorefractory cHL is still poorly understood, limiting personalized treatment strategies based on molecular features. In this study, using a targeted next-generation sequencing (NGS) panel specifically designed for cHL research, we compared chemosensitive and chemorefractory diagnostic tissue samples of cHL patients. Furthermore, we longitudinally examined paired diagnosis-relapsesamples of chemorefractory cHL in order to define patterns of dynamic evolution and clonal selection. Pathogenic variants in NOTCH1 and NOTCH2 genes frequently arise in cHL. Mutations in genes associated with epigenetic regulation (CREBBP and EP300) are particularly frequent in relapsed/refractory cHL. The appearance of novel clones characterized by mutations previously not identified at diagnosis is a common feature in cHL cases showing chemoresistance to frontline treatments. Our results expand current molecular and pathogenic knowledge of cHL and support the performance of molecular studies in cHL prior to the initiation of first-line therapies.

Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling

The scarcity of malignant Hodgkin and Reed-Sternberg cells hampers tissue-based comprehensive genomic profiling of classic Hodgkin lymphoma (cHL). By contrast, liquid biopsies show promise for molecular profiling of cHL due to relatively high circulating tumour DNA (ctDNA) levels1-4. Here we show that the plasma representation of mutations exceeds the bulk tumour representation in most cases, making cHL particularly amenable to noninvasive profiling. Leveraging single-cell transcriptional profiles of cHL tumours, we demonstrate Hodgkin and Reed-Sternberg ctDNA shedding to be shaped by DNASE1L3, whose increased tumour microenvironment-derived expression drives high ctDNA concentrations. Using this insight, we comprehensively profile 366 patients, revealing two distinct cHL genomic subtypes with characteristic clinical and prognostic correlates, as well as distinct transcriptional and immunological profiles. Furthermore, we identify a novel class of truncating IL4R mutations that are dependent on IL-13 signalling and therapeutically targetable with IL-4Rα-blocking antibodies. Finally, using PhasED-seq5, we demonstrate the clinical value of pretreatment and on-treatment ctDNA levels for longitudinally refining cHL risk prediction and for detection of radiographically occult minimal residual disease. Collectively, these results support the utility of noninvasive strategies for genotyping and dynamic monitoring of cHL, as well as capturing molecularly distinct subtypes with diagnostic, prognostic and therapeutic potential.