Michael Crump

TableS1. Patient characteristics of the CHL study training cohorts. Table S2. Gene list for the targeted sequencing panel and HLGen. Table S3 Patient Demographic and molecular alterations. Table S4. HLGen correlation with Age and EBV in Training and Validation cohort. Table S5. Antibodies used for immunohistochemistry staining. Table S6. Differential gene expression analysis followed by gene ontology analysis in L-428 model. Table S7. Differential gene expression analysis followed by gene ontology analysis in U-HO1 model + IL-3. Table S8 Differential gene expression analysis followed by gene ontology analysis in U-HO1 model + IL-5. Table S9 Gene expression changes across all three experimental models. Table S10. Classification methods for HLGen. Table S11 HLGen Prediction in Training cohort. Table S12 HLGen Prediction in Stanford cohort (Alig and colleagues, Nature 2024). Table S13. Antibodies used for immunohistochemistry staining. Table S14. IMC Clustering Strategy. Table S15. Antibodies used for flow cytometry staining. Table S16. Antibodies used for Western blotting.

Figure S1. Co-occurrence of mutation in CHL. Figure S2. STAT6 copy number gain. Figure S3. Frequent mutations according to key clinical features. Figure S4. Copy number alterations according to EB Virus (EBV) status on HRS cells. Figure S5. Multivariable analyses on thymic mutation. Figure S6. Coding mutation count according to key clinical features in CHL. Figure S7. Impact of molecular profile on survival in CHL. Figure S8. STAT6 mutations in CHL. Figure S9. Impact of molecular profile on survival in elderly CHL. Figure S10. MHC status on HRS cells and their molecular correlates. Figure S11. Molecular Subgroups of CHL. Figure S12. Correlation between molecular subtypes and key clinical features. Figure S13. Molecular subtype and progression free survival (PFS) in Hodgkin lymphoma. Figure S14. Overview of the imaging mass cytometry (IMC) analysis and panel. Figure S15. Spatial tumor-microenvironment correlates with molecular subtype in CHL. Figure S16. Membrane map depicting major immune cell populations in each molecular subgroup. Figure S17. Correlation between molecular subtypes and key features. Figure S18. Evidence of CSF2RB mutant allele expression at the protein level in L-1236 KO model. Figure S19. CSF2RB mutations confer cytokine-dependent gain-of-function signaling in the L-428 model. Figure S20. CSF2RB mutations promote activation of the STAT5 signaling pathway. Figure S21. Co-expression of CSF2RB-WT and E788* mutant enhances downstream cytokine responses. Figure S22. Characterization of extrinsic phenotypes of CSF2RB mutations. Figure S23. Tumor-microenvironment characterization with molecular subtype in CHL. Figure S24. Cohort and study design overview for the HLGen development. Figure S25. Oncoplot of the CHL samples from Stanford ctDNA cohort (n = 293), with clinical annotation according to molecular subtype. Figure S26. Impact of feature list reduction on HLGen classifier performance. Figure S27. Graphical summary of molecular subtypes and their clinical and tumor-microenvironment ecosystem correlates in classic Hodgkin lymphoma. Figure S28. GeoMx analyses on CD30+ HRS cells. Figure S29. Segmentation on Imaging Mass Cytometry. Figure S30. Gating Strategy of regulatory T cell population.

TableS1. Patient characteristics of the CHL study training cohorts. Table S2. Gene list for the targeted sequencing panel and HLGen. Table S3 Patient Demographic and molecular alterations. Table S4. HLGen correlation with Age and EBV in Training and Validation cohort. Table S5. Antibodies used for immunohistochemistry staining. Table S6. Differential gene expression analysis followed by gene ontology analysis in L-428 model. Table S7. Differential gene expression analysis followed by gene ontology analysis in U-HO1 model + IL-3. Table S8 Differential gene expression analysis followed by gene ontology analysis in U-HO1 model + IL-5. Table S9 Gene expression changes across all three experimental models. Table S10. Classification methods for HLGen. Table S11 HLGen Prediction in Training cohort. Table S12 HLGen Prediction in Stanford cohort (Alig and colleagues, Nature 2024). Table S13. Antibodies used for immunohistochemistry staining. Table S14. IMC Clustering Strategy. Table S15. Antibodies used for flow cytometry staining. Table S16. Antibodies used for Western blotting.

Figure S1. Co-occurrence of mutation in CHL. Figure S2. STAT6 copy number gain. Figure S3. Frequent mutations according to key clinical features. Figure S4. Copy number alterations according to EB Virus (EBV) status on HRS cells. Figure S5. Multivariable analyses on thymic mutation. Figure S6. Coding mutation count according to key clinical features in CHL. Figure S7. Impact of molecular profile on survival in CHL. Figure S8. STAT6 mutations in CHL. Figure S9. Impact of molecular profile on survival in elderly CHL. Figure S10. MHC status on HRS cells and their molecular correlates. Figure S11. Molecular Subgroups of CHL. Figure S12. Correlation between molecular subtypes and key clinical features. Figure S13. Molecular subtype and progression free survival (PFS) in Hodgkin lymphoma. Figure S14. Overview of the imaging mass cytometry (IMC) analysis and panel. Figure S15. Spatial tumor-microenvironment correlates with molecular subtype in CHL. Figure S16. Membrane map depicting major immune cell populations in each molecular subgroup. Figure S17. Correlation between molecular subtypes and key features. Figure S18. Evidence of CSF2RB mutant allele expression at the protein level in L-1236 KO model. Figure S19. CSF2RB mutations confer cytokine-dependent gain-of-function signaling in the L-428 model. Figure S20. CSF2RB mutations promote activation of the STAT5 signaling pathway. Figure S21. Co-expression of CSF2RB-WT and E788* mutant enhances downstream cytokine responses. Figure S22. Characterization of extrinsic phenotypes of CSF2RB mutations. Figure S23. Tumor-microenvironment characterization with molecular subtype in CHL. Figure S24. Cohort and study design overview for the HLGen development. Figure S25. Oncoplot of the CHL samples from Stanford ctDNA cohort (n = 293), with clinical annotation according to molecular subtype. Figure S26. Impact of feature list reduction on HLGen classifier performance. Figure S27. Graphical summary of molecular subtypes and their clinical and tumor-microenvironment ecosystem correlates in classic Hodgkin lymphoma. Figure S28. GeoMx analyses on CD30+ HRS cells. Figure S29. Segmentation on Imaging Mass Cytometry. Figure S30. Gating Strategy of regulatory T cell population.

The tissue architecture of classic Hodgkin lymphoma (cHL) is unique among cancers and is characterized by rare malignant Hodgkin and Reed–Sternberg cells that coevolve with a complex ecosystem of immune cells in the tumor microenvironment (TME). The lack of a comprehensive systems-level interrogation has hindered the description of disease heterogeneity and clinically relevant molecular subtypes. In this study, we employed an integrative, multimodal approach to characterize cHL tumors using malignant cell sequencing, spatial transcriptomics, and imaging mass cytometry. We identified four molecular subtypes (CST, CN913, STB, and CN2P), each characterized by distinct clinical features, mutational patterns, malignant cell gene expression profiles, and spatial architecture involving immune cell populations. Functional modeling of CSF2RB mutations, a characteristic feature of the CST subtype, revealed dysregulated oncogenic signaling and unique TME cross-talk. These findings highlight the significance of multidimensional profiling in elucidating patterns of molecular alterations that drive immune ecosystems and underlie therapeutically exploitable vulnerabilities. Significance: Our systematic and comprehensive genomic and spatially resolved profiling of Hodgkin lymphoma revealed a paradigmatic link between a genetic disease subtype and TME composition and function. Insights into mutation-driven mechanisms of deregulated cytokine signaling will pave the way for therapeutic interventions that interfere with oncogenic signaling and cellular ecosystems in cancer.

Background and Aims: Immunosuppression can cause hepatitis B virus (HBV) reactivation, leading to severe outcomes in patients with “resolved” HBV infection. This multicenter, randomized, placebo-controlled trial assessed the efficacy of preemptive antiviral therapy in HBsAg-negative, anti–HBc-positive patients receiving rituximab-based chemotherapy for non-Hodgkin lymphoma (NHL). Methods: Patients were randomized 1:1 to tenofovir alafenamide (TAF)/placebo across 3 phases: chemotherapy plus TAF/placebo (phase 1), TAF/placebo post-chemotherapy (phase 2), and follow-up after therapy cessation (phase 3). The primary endpoint was HBsAg reverse seroconversion. HBsAg and ALT were monitored every 3–12 weeks, depending on treatment phase, and HBV DNA was measured post hoc. ClinicalTrials.gov (NCT02186574). Results: Among 42 patients (median age 65.2 years, 52.4% male, 52.4% aggressive lymphoma, 73.8% anti-HBs positive), 20 received TAF and 22 received a placebo. Median ALT was 20.0 U/L (IQR: 15.0–28.0) at baseline. Median follow-up was 69.4 weeks (IQR: 63.7–166), with 6.1 weeks (IQR: 4.7–8.3) between visits. During follow-up, 2 patients in the TAF arm, but none receiving placebo, experienced HBsAg reverse seroconversions: occurring in phase 3 at 62.3 weeks from baseline, and in phase 1 at 20.0 weeks from baseline. Neither patient experienced ALT >2× ULN. HBV DNA >1000 IU/mL was observed in 8 instances among 6 patients, 3 in each arm, with no associated hepatitis. Low-level DNA (<1000 IU/mL) was not indicative of reverse seroconversion, DNA increases, or ALT elevations. Conclusions: The use of preemptive TAF therapy did not reduce the risk of HBsAg reverse seroconversion; however, the findings should be interpreted with caution as the study was underpowered due to slow enrolment leading to early termination. Low-level HBV DNA elevations were not associated with HBV reactivation. Thus, close HBsAg and ALT monitoring are adequate in HBsAg-negative patients undergoing rituximab-based chemotherapy.

Summary: Adult T‐cell leukaemia/lymphoma (ATLL) is a rare, aggressive haematological malignancy linked to human T‐cell leukaemia virus type I (HTLV‐1) and associated with poor outcomes. Despite its higher prevalence in HTLV‐1‐endemic regions, the relationship between clinical characteristics and patients' sociocultural background remains underexplored. We retrospectively analysed 79 ATLL patients treated at our institution (1993–2023). The median age at diagnosis was 47 years, and 72% of patients were of Caribbean origin. Median progression‐free and overall survival were 10.2 and 16.2 months, respectively, with only five patients receiving allogeneic stem cell transplantation. Central nervous system (CNS) involvement at diagnosis occurred in 22% of patients and was associated with worse outcomes, while 14% experienced CNS relapse within a median of 4.9 months. Using the Ontario Marginalization Index, we found higher levels of material, household/dwelling and racialized/newcomer‐related marginalization compared to the general Greater Toronto Area population, though these factors were not linked to poorer outcomes. Our findings reveal that ATLL patients in this cohort were predominantly of Caribbean descent, presented at a young age and faced significant CNS involvement and poor survival outcomes, underscoring ATLL as an unmet clinical need.

In the LY.17 randomized phase II clinical trial, adults with relapsed and refractory diffuse large B-cell lymphoma treated with ibrutinib-R-GDP (IR-GDP) for up to three cycles had more documented bacterial and fungal infections, without improvement in overall response, compared with R-GDP. CR, complete response; DLBCL, diffuse large B-cell lymphoma; PD, progressive disease; PR, partial response; R/R, relapsed/refractory; SD, stable disease.