Overlaying TP53 loss and aneuploidy with distinct diffuse large B-cell lymphoma subtypes refines tumor classification and enhances risk stratification
Authors
Andrey Suponin¹, Pavel Zemskiy¹, Dmitrii Snitkin¹, Mark Meerson¹, Alexander Bagaev¹, Alexander Nesmelov¹, Konstantin Chernyshov¹, Nikita Kotlov¹, Louis Staudt²
- BostonGene Corporation, Waltham, MA, USA
- National Cancer Institute Bethesda, Maryland, USA
Abstract
Background:
Genetic subtypes are widely used to stratify diffuse large B-cell lymphoma (DLBCL). Yet, patients within the same subtype often exhibit heterogeneous outcomes. While chromosome number alteration (CNA)-driven subtypes such as A53 and C2 capture genomic instability, they encompass tumors with variable degrees of aneuploidy. Loss-of-function (LOF) TP53 alterations and aneuploidy have each been associated with adverse prognosis, but their independent and combined effects in DLBCL remain insufficiently defined.
Aims: To refine genomic stratification of DLBCL by disentangling the effects of TP53 loss and quantitative aneuploidy, we introduced two novel genomic instability statuses into Lymphly, our previously developed DLBCL genetic subtype classification framework. These statuses are TP53+/−, denoting TP53 LOF alterations, and A+/−, an aneuploidy-based status. This approach explicitly distinguishes TP53 loss from aneuploidy within Lymphly subtypes.
Methods:
We analyzed 1,123 DLBCL samples with genome-wide CNA profiling. Survival data were available for 579 samples. The aneuploidy score was defined as the number of chromosome arms deviating from average ploidy (excluding acentric arms). The distribution was bimodal (range 0–39), with a nadir at ~15. K-means clustering defined A+ tumors as those with >14 arm-level CNAs. TP53+ status was defined as TP53 LOF mutation or deletion. We also analyzed previously assigned A53/C2 cases to assess the concordance of these existing CNA-based subtypes with the Lymphly statuses. To evaluate the utility of the Lymphly statuses, we characterized their expression profiles and assessed their ability to stratify patients based on survival outcomes.
Results:
TP53+ tumors had significantly higher aneuploidy scores than TP53− tumors (p<0.0001). However, many individual tumors in the two groups had similar aneuploidy values. A+ cases comprised 20.7% of the analyzed samples and were evenly distributed across TP53 strata: 11.7% TP53+/A+ and 9.1% TP53−/A+. TP53+/A− and TP53−/A− cases made up 23.3% and 55.9%, respectively. Together, TP53+/− and A+/− statuses captured most of the A53/C2 cases analyzed, demonstrating the ability of these two Lymphly statuses to delineate the sample composition and underlying biology of the A53 and C2 subtypes.
Biologically, A+ tumors were enriched for the germinal center B-cell–like cell-of-origin (GCB COO), exhibited reduced B-cell content, and showed altered DNA replication and repair programs. Clinically, TP53+ was associated with primary refractoriness and inferior survival, whereas A+ was associated with improved prognosis, particularly among TP53+ tumors.
Summary/Conclusion:
TP53 loss and high aneuploidy represent independent and clinically meaningful genomic dimensions in DLBCL, in addition to Lymphly subtypes. Their integration into Lymphly refines the existing A53/C2 classification and improves risk stratification based on biologically grounded, actionable insights. Our findings provide a robust framework for patient stratification based on genomic features, offering potential benefits for trial design, patient selection, and treatment decision-making.
Genetic subtypes are widely used to stratify diffuse large B-cell lymphoma (DLBCL). Yet, patients within the same subtype often exhibit heterogeneous outcomes. While chromosome number alteration (CNA)-driven subtypes such as A53 and C2 capture genomic instability, they encompass tumors with variable degrees of aneuploidy. Loss-of-function (LOF) TP53 alterations and aneuploidy have each been associated with adverse prognosis, but their independent and combined effects in DLBCL remain insufficiently defined.
Aims: To refine genomic stratification of DLBCL by disentangling the effects of TP53 loss and quantitative aneuploidy, we introduced two novel genomic instability statuses into Lymphly, our previously developed DLBCL genetic subtype classification framework. These statuses are TP53+/−, denoting TP53 LOF alterations, and A+/−, an aneuploidy-based status. This approach explicitly distinguishes TP53 loss from aneuploidy within Lymphly subtypes.
Methods:
We analyzed 1,123 DLBCL samples with genome-wide CNA profiling. Survival data were available for 579 samples. The aneuploidy score was defined as the number of chromosome arms deviating from average ploidy (excluding acentric arms). The distribution was bimodal (range 0–39), with a nadir at ~15. K-means clustering defined A+ tumors as those with >14 arm-level CNAs. TP53+ status was defined as TP53 LOF mutation or deletion. We also analyzed previously assigned A53/C2 cases to assess the concordance of these existing CNA-based subtypes with the Lymphly statuses. To evaluate the utility of the Lymphly statuses, we characterized their expression profiles and assessed their ability to stratify patients based on survival outcomes.
Results:
TP53+ tumors had significantly higher aneuploidy scores than TP53− tumors (p<0.0001). However, many individual tumors in the two groups had similar aneuploidy values. A+ cases comprised 20.7% of the analyzed samples and were evenly distributed across TP53 strata: 11.7% TP53+/A+ and 9.1% TP53−/A+. TP53+/A− and TP53−/A− cases made up 23.3% and 55.9%, respectively. Together, TP53+/− and A+/− statuses captured most of the A53/C2 cases analyzed, demonstrating the ability of these two Lymphly statuses to delineate the sample composition and underlying biology of the A53 and C2 subtypes.
Biologically, A+ tumors were enriched for the germinal center B-cell–like cell-of-origin (GCB COO), exhibited reduced B-cell content, and showed altered DNA replication and repair programs. Clinically, TP53+ was associated with primary refractoriness and inferior survival, whereas A+ was associated with improved prognosis, particularly among TP53+ tumors.
Summary/Conclusion:
TP53 loss and high aneuploidy represent independent and clinically meaningful genomic dimensions in DLBCL, in addition to Lymphly subtypes. Their integration into Lymphly refines the existing A53/C2 classification and improves risk stratification based on biologically grounded, actionable insights. Our findings provide a robust framework for patient stratification based on genomic features, offering potential benefits for trial design, patient selection, and treatment decision-making.
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