WHOLE GENOME SEQUENCING OF SERIAL FL BIOPSIES FROM 96 PATIENTS WITH FOLLICULAR LYMPHOMA REVEAL TREATMENT-SPECIFIC PATTERNS OF TUMOUR EVOLUTION

Introduction: Follicular lymphoma (FL) is a heterogeneous disease in terms of clinical course, treatment landscape, and molecular features. Patients presenting with limited stage disease may be treated with radiation therapy (RT), which is effectively curative in over 50% of patients, while those with disseminated disease may be observed or treated with a range of systemic therapies depending on symptoms and extent of disease. Sequencing of serial FL biopsies has demonstrated the existence of a population of cells ancestral to the diagnostic tumour and subsequent FL progression and transformation. We hypothesized that different presentations, and treatments thereof, would have distinct effects on the genomic evolution of FL.

Methods: Paired biopsies and matched constitutional DNA from 96 FL patients who experienced either FL progression (pFL) or histological transformation (tFL) to aggressive lymphoma were profiled with whole genome sequencing (WGS). 21 patients with limited-stage disease received RT with curative intent, and all but 3 relapses occurred outside of the RT field. For the remaining patients with advanced stage, 39 were treated with (immuno)chemotherapy and 36 were observed as the management between biopsies. The median time between biopsies was 2.6 y and was not significantly different between treatment groups. Within the RT group, the second biopsy was tFL in 6 patients (29%), compared to 16 (41%) and 12 (30%) in the systemic therapy and observation cohorts, respectively. Somatic variants were identified with an ensemble variant calling approach.

Results: There were no significant differences in mutation frequencies of any known FL genes when comparing diagnosis versus relapse, pFL versus tFL, or treatment. Mutations in KMT2D and the CREBBP lysine acetyltransferase (KAT) domain were significantly more likely to be ancestral (identical variants in both tumours), while mutations in BCR were more likely to be divergent (exclusive to one tumour; FDR < 0.1; Figure A). We quantified degree of divergence between tumours as the percentage of mutations exclusive to one time point. Both diagnostic and relapsed tumours were significantly more divergent in patients treated with RT, and there were no significant differences in divergence between patients who were observed versus received systemic therapy (p < 0.05; Figure B). Divergence correlated with time between biopsies only in patients treated with RT (R 0.4–0.5, p < 0.05).

Conclusions: Leveraging data from patients who experience lymphoma after curative-intent RT, the inferred ancestral clone is sparser in terms of mutation burden compared to advanced stage patients. These data suggest that the ancestor of relapses in these patients is more likely to be a pre-malignant precursor cell, reflecting the effectiveness of RT in eradicating the fully-developed FL in limited-stage patients.

Research funding declaration: Terry Fox Research Institute, Genome BC, Genome Canada, Marathon of Hope Cancer Centre Network, Canadian Institutes of Health Research, BC Cancer Foundation, Provincial Health Services Authority

Keywords: bioinformatics; computational and systems biology; genomics, epigenomics, and other -omics; indolent non-Hodgkin lymphoma

Potential sources of conflict of interest:

A. C. Lo

Consultant or advisory role: Need

J. W. Craig

Consultant or advisory role: Bayer

Honoraria: BeiGene

C. L. Freeman

Consultant or advisory role: BMS, Seattle Genetics, Celgene, Abbvie, Sanofi, Incyte, Amgen, ONK therapeutics, Janssen

Other remuneration: Research funding from BMS, Janssen, Roche/Genentech

A. S. Gerrie

Honoraria: AbbVie, AstraZeneca, Janssen, and Beigene

Other remuneration: Research funding from AbbVie, AstraZeneca, Janssen, Roche, and Loxo Oncology

D. Villa

Honoraria: AbbVie, Janssen, Kite/Gilead, AstraZeneca, Roche, BeiGene, Bristol Myers Squibb/Celgene, Merck, Zetagen

Other remuneration: Research funding from AstraZeneca and Roche

K. J. Savage

Consultant or advisory role: Data Safety Monitoring Committee for Regeneron

Honoraria: SeaGen, Bristol Myers Squibb, Merck, and AbbVie

Other remuneration: Research funding from Bristol Myers Squibb, Roche, Merck, Seagen, Viracta, and AstraZeneca

L. H. Sehn

Honoraria: AbbVie, Acerta, Amgen, Apbiologix, AstraZeneca, Celgene, Chugai, Gilead, Incyte, Janssen, Kite, Karyopharm, Lundbeck, Merck, Morphosys, Roche/Genentech, Sandoz, Seattle Genetics, Servier, Takeda, Teva, TG Therapeutics, and Verastem

Other remuneration: Research funding from Roche/Genentech and Teva

C. Steidl

Consultant or advisory role: Bayer, Eisai

Other remuneration: Research funding from Epizyme and Trillium Therapeutics Inc.

D. W. Scott

Consultant or advisory role: AbbVie, AstraZeneca, GenMab, Incyte, Roche, and Veracyte

Other remuneration: Research funds from Janssen and Roche/Genentech; and named inventor on a patent describing the use of gene expression to subtype aggressive B-cell lymphomas, one of which is licensed to nanoString Technologies