Introduction: Splenic marginal zone B-cell lymphoma (SMZL) is a heterogeneous entity. The clinical course is variable, mutated genes are multiple with no unifying mechanism, essential regulatory pathways and surrounding microenvironments are diverse. We sought to provide a unifying view of SMZL by resolving its heterogeneity in subgroups sharing genomic abnormalities, pathway signatures and microenvironment compositions to uncover biomarkers and therapeutic vulnerabilities. Methods: We studied 303 pathologically confirmed SMZL spleen samples collected through the IELSG46 multicenter, international study (NCT02945319). The study cohort was representative of SMZL in terms of demographics, clinical features and outcome. We carried out a genetic and phenotypic analysis, defined self-organized signatures, validated them in independent primary tumors meta-data and in genetically modified mouse models, and correlated them with outcome data. Results: We identified and validated two prominent and self-aggregating genetic clusters in SMZL, termed NNK (58% of cases, from NF-kB, NOTCH and KLF2 modules) and DMT (32% of cases, from DNA-damage response, MAPK and TLR modules). NNK-SMZLs were dominated by mutations of NF-κB (e.g., TNFAIP3, TRAF3, BIRC3), NOTCH (e.g., NOTCH2, NOTCH1, SPEN) and KLF2. DMT-SMZLs were characterized by mutations in DNA damage response pathway genes (e.g., TP53, ATM). Mutations in MAPK (e.g., BRAF) and TLR genes (e.g., MYD88, all involving positions other than p.L265) were also enriched in DMT-SMZLs (Figure A and B). These genetic clusters have distinct underpinning biology. NNK-SMZLs were enriched of IGHV1-2*04 allele usage and of 7q deletion, while conversely DMT-SMZLs were depleted of both of them (Figure C). NNK-SMZL expressed significantly higher levels of genes belonging to NOTCH2 pathway and of genes that are activated by non-canonical NF-κB transcription factors. Conversely, DMT-SMZL had a signature of TP53 and apoptosis impairment (Figure D). Digital cytometry and in situ profiling segregated two basic types of SMZL immune microenvironment termed inflamed SMZL (50% of cases, associated with inflammatory cells and immune checkpoint activation) and non-inflamed SMZL (50% of cases) (Figure E and F). The combination of molecular and phenotypic profiling allowed to sort out a high risk clinical subset of patients whose tumor was characterized by having both NNK genotype and ‘’inflamed’’ microenvironment (Figure G). The research was funded by: Swiss Cancer League, ID 3746, 4395 4660, and 4705, Bern, Switzerland; Research Advisory Board of the Ente Ospedaliero Cantonale, ABREOC 2019-22514, Bellinzona, Switzerland; European Research Council (ERC) Consolidator Grant CLLCLONE, ID: 772051; Swiss National Science Foundation, ID 320030_169670/1, 310030_192439, 320036_179318, Berne, Switzerland; Fondazione Ticinese Contro il Cancro; Fondazione Fidinam, Lugano, Switzerland; Nelia & Amadeo Barletta Foundation, Lausanne, Switzerland; Fond’Action, Lausanne, Switzerland; The Leukemia & Lymphoma Society, Translational Research Program, ID 6594-20, New York; AFRI, Ente Ospedaliero Cantonale, Bellinzona, Switzerland; Fondazione Dr. Ettore Balli. Keywords: Diagnostic and Prognostic Biomarkers, Indolent non-Hodgkin lymphoma, Pathology and Classification of Lymphomas Conflicts of interests pertinent to the abstract P. Ghia Honoraria: AbbVie, ArQule/MSD, AstraZeneca, Beigene, Celgene/Juno(BMS, Gilead, Janssen, Loxo/Lilly, Roche Research funding: AbbVie, AstraZeneca, Gilead, Janssen, Sunesis G. Gritti Consultant or advisory role: Takeda, IQvia, Gilead Sciences Research funding: Gilead Sciences Educational grants: Roche, Abbvie, Gilead Sciences, Abbvie A. Moccia Consultant or advisory role: Roche, Janssen and Takeda L. Scarfó Honoraria: AbbVie, AstraZeneca and Janssen D. Rossi Honoraria: AbbVie, AstraZeneca, Janssen Research funding: AbbVie, AstraZeneca, Janssen
Splenic marginal zone B-cell lymphoma (SMZL) is a heterogeneous clinico-biological entity. The clinical course is variable, multiple genes are mutated with no unifying mechanism, and essential regulatory pathways and surrounding microenvironments are diverse. We sought to clarify the heterogeneity of SMZL by resolving different subgroups and their underlying genomic abnormalities, pathway signatures, and microenvironment compositions to uncover biomarkers and therapeutic vulnerabilities. We studied 303 SMZL spleen samples collected through the IELSG46 multicenter international study (NCT02945319) by using a multiplatform approach. We carried out genetic and phenotypic analyses, defined self-organized signatures, validated the findings in independent primary tumor metadata and in genetically modified mouse models, and determined correlations with outcome data. We identified 2 prominent genetic clusters in SMZL, termed NNK (58% of cases, harboring NF-κB, NOTCH, and KLF2 modules) and DMT (32% of cases, with DNA-damage response, MAPK, and TLR modules). Genetic aberrations in multiple genes as well as cytogenetic and immunogenetic features distinguished NNK- from DMT-SMZLs. These genetic clusters not only have distinct underpinning biology, as judged by differences in gene-expression signatures, but also different outcomes, with inferior survival in NNK-SMZLs. Digital cytometry and in situ profiling segregated 2 basic types of SMZL immune microenvironments termed immune-suppressive SMZL (50% of cases, associated with inflammatory cells and immune checkpoint activation) and immune-silent SMZL (50% of cases, associated with an immune-excluded phenotype) with distinct mutational and clinical connotations. In summary, we propose a nosology of SMZL that can implement its classification and also aid in the development of rationally targeted treatments.
Introduction: Current prognostic models of classic Hodgkin lymphoma (cHL) incorporate pre-treatment clinical and laboratory parameters, but have low discrimination capacity and limited clinical utility. Circulating tumor DNA (ctDNA) is a sensitive cancer biomarker, but its clinical validity in cHL is unknown. Here we tested whether pre-treatment ctDNA qualification and quantification is prognostic in cHL. Methods: The IOSI-EMA-003 (NCT03280394) is a prospective, observational, multicentric, international, non-interventional trial in which liquid biopsy samples were collected from newly diagnosed cHL patients at the following time points: baseline, interim and end of treatment PET/CT assessments. The LyV4.0 ctDNA CAPP-seq assay (sensitivity: 0.1%) was used to qualify and quantify ctDNA. Clinical data quality was assured through remote medical monitoring. Baseline, interim and end of treatment PET/CT are undergoing central review. Results: A total of 135 patients were recruited. Baseline characteristics were those expected in unelected, previously untreated cHL. After a median follow-up of 33 months, 25 patients had progression events, accounting for 3-year progression free survival (PFS) of 80.0%. At baseline, ctDNA was detected in 90% of patients, with an average of 27 somatic mutation reporters per case. A summary of genes affected by nonsynonymous, synonymous, and noncoding somatic mutations is shown in Figure A. Median ctDNA load was 358.5 hGE/mL of plasma (range 0-16572.4), and correlated (p = 0.004) with clinical proxies of the tumor volume (Figure B). None of the genes mutated in ≥5% of patients, including TP53, stratified PFS (Figure C). By recursive partitioning, ctDNA load in baseline samples stratified PFS with an optimized threshold of 1500 hGE/mL of plasma (Figure D). Patients with high pre-treatment levels of ctDNA had significantly inferior rates of 3-year PFS (44.4% vs 86.9% p = 0.000006) than those with low levels (Figure E). High pre-treatment levels of ctDNA occurred: i) in 0% of early, 12.2% of intermediate and 15.9% of advanced cHL; and ii) in 6.0% of 0-2 international prognostic score (IPS) and 27.3% of >3 IPS cHL. Levels of pre-treatment ctDNA marked patients’ outcome, irrespective of whether they presented in intermediate or advanced stage. The combination of high pre-treatment ctDNA and poor IPS risk >3 allowed to sort out upfront poor risk cHL showing a 3-year PFS of only 33.3% (Figure F). In multivariable analysis, the interaction between pre-treatment ctDNA and IPS remained prognostic for PFS (HR 7.3, 95% CI 3.0-17.5, p = 0.00009) when controlling for GHSG risk. PFS prediction metrics (c-index) were 64.9% for ctDNA, 66.2% for IPS and 69.8% for IPS combined to ctDNA. The research was funded by: -Fond’Action, Lausanne, Switzerland; -Translational Research Program, No. 6594-20, The Leukemia & Lymphoma Society, New York Keywords: Diagnostic and Prognostic Biomarkers, Hodgkin lymphoma Conflicts of interests pertinent to the abstract A. Moccia Consultant or advisory role: Roche, Janssen and Takeda D. Rossi Honoraria: AbbVie, AstraZeneca, Janssen Research funding: AbbVie, AstraZeneca, Janssen.
To advance the use of circulating tumor DNA (ctDNA) applications, their broad clinical validity must be tested in different treatment settings, including targeted therapies. Using the prespecified longitudinal systematic collection of plasma samples in the phase 1/2a LYM1002 trial (registered on www.clinicaltrials.gov as NCT02329847), we tested the clinical validity of ctDNA for baseline mutation profiling, residual tumor load quantification, and acquisition of resistance mutations in patients with lymphoma treated with ibrutinib+nivolumab. Inclusion criterion for this ancillary biological study was the availability of blood collected at baseline and cycle 3, day 1. Overall, 172 ctDNA samples from 67 patients were analyzed by the LyV4.0 ctDNA Cancer Personalized Profiling Deep Sequencing Assay. Among baseline variants in ctDNA, only TP53 mutations (detected in 25.4% of patients) were associated with shorter progression-free survival; clones harboring baseline TP53 mutations did not disappear during treatment. Molecular response, defined as a >2-log reduction in ctDNA levels after 2 cycles of therapy (28 days), was achieved in 28.6% of patients with relapsed diffuse large B-cell lymphoma who had ≥1 baseline variant and was associated with best response and improved progression-free survival. Clonal evolution occurred frequently during treatment, and 10.3% new mutations were identified after 2 treatment cycles in nonresponders. PLCG2 was the topmost among genes that acquired new mutations. No patients acquired the C481S BTK mutation implicated in resistance to ibrutinib in CLL. Collectively, our results provide the proof of concept that ctDNA is useful for noninvasive monitoring of lymphoma treated with targeted agents in the clinical trial setting.
Background: Overall, ten independent retrospective studies addressed the question of the tolerability of ibrutinib in the real-world setting. Discontinuation rates ranged from 5% to 29%. Such heterogeneity may reflect differences in the case mix, follow up and accessibility to next treatments. Dose reduction/transient interruption rates ranged from 22% to 32%. The impact of intolerance on ibrutinib effectiveness according to baseline CLL biology is largely unknown. We assessed whether outcomes of patients with high-risk CLL is affected by ibrutinib discontinuation, interruption, or dose reduction due to intolerance. Methods: The IOSI-EMA-001 and the IOSI-EMA-003 observational prospective studies (NCT02827617; NCT03280394) enrolled patients with CLL treated with ibrutinib according to prescribing indications in Switzerland and Italy. Pre-treatment demographics, disease data, mutation analysis by LyV4.0 CAPP-seq assay, information on treatment discontinuation, interruption and dose reduction, and efficacy outcomes were collected. Results: In stotal, 90 patients were included in the per protocol population. Baseline features include age >65 years in 71% of cases, male gender in 61%, previous treatment in 47%, beta-2-microglobulin >5 mg/L in 40%, lactate dehydrogenase >ULN in 55%, TP53 disruption in 83%, and unmutated IGHV in 78%. Baseline mutations of SF3B1 (30%), NOTCH1 (28%), ATM (15%), EGR2 (13%), MGA (11%), POT1 (11%), and BIRC3 (10%) were reported in ≥10% of cases. The median follow-up of patients was 2.8 years. Median time on ibrutinib was 29 months. Discontinuation of ibrutinib due to any reason except progressive disease (PD) was reported in 21% of patients and their median time on ibrutinib was 17 months. Median time to discontinuation due to any reason except PD was 16 months. At least 1 interruption was reported in 31% of patients, and 6% interrupted treatment >1 time. The median consecutive days of interruption was 28 and the median total days of interruption was 38. Dose reduction was required by 25% of patients, including 5% who reduced to 140 mg/d. Median dose intensity (proportion of administered vs planned doses of ibrutinib 420 mg/d) was 93.4%. Three-years PFS of the per protocol cohort was 80.3% (CI 69.9-92.2). Early discontinuation due to any reason except PD, treatment interruption, regardless of duration (≥1, ≥8, ≥14 and ≥21 consecutive days), and dose reduction had no impact on PFS. By recursive partitioning, PFS stratification based on the best cut-off for dose intensity did not show a negative outcome, indicating no compounded effect of both dose reduction and interruption. Conclusions: Ibrutinib treatment modifications seem not to have major impact on PFS in patients with high-risk CLL. The impact of ibrutinib dose intensity during the first months of therapy on PFS, and the impact of ibrutinib tolerability on time to next treatment will be explored in this dataset. Keywords: Tumor Biology and Heterogeneity, Diagnostic and Prognostic Biomarkers, Ongoing Trials Conflicts of interests pertinent to the abstract E. Zucca Honoraria: AbbVie; AstraZeneca; Janssen Research funding: AbbVie; AstraZeneca; Janssen D. Rossi Honoraria: AstraZeneca; AbbVie; Janssen Research funding: AstraZeneca; AbbVie; Janssen
