Background: We leveraged advanced ctDNA analytic methods to present an in-depth overview of the genetic landscape of classic Hodgkin lymphoma (cHL) and its connection to disease pathophysiology and clinical course. Methods: cHL cases (N=297) from the IOSI-EMA003-NCT03280394 and FIL-RougeBIO-NCT05066555 studies were assessed by LyV4.0 ctDNA CAPP‐seq.
Results: An expression quantitative trait locus (seQTL) of the BCL6-intragenic super-enhancer (SE) was identified in 30% of cHL, and impeded the binding of PRDM1 to BCL6. The BCL6 seQTL aligns with an area of accessible chromatin and heightened H3K27 acetylation in cHL, which was nominated a SE in cHL cell lines expressing BCL6. Notably, the BCL6 seQTL was found to co-occur with BCL6 expression in cHL cell lines and HRS cells of primary biopsies, despite the co-expression of PRDM1. BCL6 expression ranging from weak to strong was detected in the nucleus of HRS cells of 68% of primary biopsies. The core set of genes that are directly bound and regulated by BCL6 exhibited similar expression levels and chromatin accessibility in GCB cells and in BCL6 expressing cHL cell lines. BCL6 protein degradation was observed with BI-3802 in cell lines expressing BCL6. After BCL6 degradation, the core set of BCL6 genes was similarly derepressed in cHL cell lines as in DLBCL cell line. Compared to the BI-5372 control molecule, treatment with BI-3802 significantly decreased proliferation in all cell lines where BCL6 degradation was observed. Whole genome duplication (WGD) was prevalent in cHL (24%) and independently and reproducibly linked to a lower PFS after initial treatment (30-months PFS: 63% in the training and 65% in the validation cohorts). The endoreduplication-tolerance CCNE1 gene was amplified in 13% cHL and associated with WGD. Genetic clustering identified two subgroups, with C1 (32%) exhibiting a higher proportion of EBV infection, minimal STAT6 mutations, and limited aneuploidy. “Macrophage” (52%) and a “T-cell” (48%) microenvironments were deconvoluted by RNA-seq and orthogonally validated by tissue microarrays. The number of predicted MHC-I/MHC-II neoantigens was higher in patients with “macrophage” than with “T-cell” microenvironment, consistent with the selective pressures exerted by T-cells.
Conclusion: This study broadens the understanding of known oncogenic mechanisms in cHL development and identifies novel deregulated gene targets (BCL6) relevant to therapy and prognostic biomarkers (WGD).
Maria Cristina Pirosa, Matin Salehi, Alessio Bruscaggin, Lodovico Terzi di Bergamo, Federico Jauk, Gabriela Forestieri, Simone Bocchetta, Deborah Piffaretti, Riccardo Moia, Vanessa Cristaldi, Martina di Trani, Georgia Alice Galimberti, Katia Pini, Valeria Spina, Claudia Giordano, Adalgisa Condoluci, Salvatore Annunziata, Fabrizio Bergesio, Renzo Boldorini, Eugenio Borsatti, Pietro Bulian, Stephane Chauvie, Marco Cuzzocrea, Bernhard Gerber, Michał Kurlapski, Luigi Maria Larocca, Andrea Rinaldi, Marcello Rodari, Grzegorz Romanowicz, Gian Mauro Sacchetti, Anastasios Stathis, Georg Stüssi, Ilaria Zangrilli, Eleonora Calabretta, Francesco Corrado, Antonio Pinto, Luca Mazzucchelli, Valter Gattei, Jan Maciej Zaucha, Armando Santoro, Stefan Hohaus, Franco Cavalli, Emanuele Zucca, Gianluca Gaidano, Carmelo Carlo‐Stella, Alexandar Tzankov, Luca Ceriani, Davide Rossi