PhD Scientific Days 2023

Budapest, 22-23 June 2023

Pathology - Posters D

Genome-wide profiling of copy number alterations in primary cutaneous follicle center lymphoma using shallow whole-genome sequencing

Bence Bátai1, Laura Kiss1, Luca Varga1, Ákos Nagy1, Jacob Househam2, Jude Fitzgibbon3, Judit Csomor4, József Szakonyi5, Tamás Schneider6, Ágota Szepesi4* and Csaba Bödör1*

1 HCEMM-SU Molecular Oncohematology Research Group, Institute of Pathology and Experimental Cancer Research, Semmelweis University, Budapest; 2 Genomics and Evolutionary Dynamics Team, Centre for Evolution and Cancer, The Institute for Cancer, London; 3 Barts Cancer Institute, Queen Mary University of London, London; 4 Institute of Pathology and Experimental Cancer Research, Semmelweis University, Budapest; 5 Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest; 6 Department of Hematology and Lymphoma, National Institute of Oncology, Budapest; *shared corresponding authors

Text of the abstract

Introduction
Primary cutaneous follicle center lymphoma (PCFCL) has an excellent prognosis and in most cases the disease is manageable using local treatment. On the contrary, nodal follicular lymphoma (nFL), which can also present with cutaneous spread in a minority of the cases, often requires systemic therapy. Distinction of the two diseases based on histopathological criteria alone is not always feasible. Copy number alterations (CNAs) have never been investigated on a genome-wide resolution in PCFCL, yet they might serve as potential biomarkers during differential diagnosis.

Aims
Our aim was to analyze genome-wide CNAs in PCFCL in comparison to a nFL cohort in order to identify new diagnostic biomarkers of the disease.

Methods
We analyzed 23 PCFCL samples from 20 patients. DNA was isolated from formalin-fixed, paraffin-embedded tissue samples using QIAamp DNA FFPE Kit (Qiagen, Germany). Whole genome libraries were prepared using NEBNext Ultra II FS reagents (New England Biolabs, USA) and sequenced on the Illumina NextSeq2000 (Illumina, USA) platform to a target yield of 10 million single-end reads per sample. CNAs were called using QDNAseq (v. 1.34.0) and compared to process-matched diagnostic samples of a cohort of 66 nFL patients.

Results
The number of CNAs per sample showed no difference between PCFCL and nFL samples with median 4 (0-29) and 4 (0-32) alterations, respectively. At the chromosome arm level, 6q deletion was absent from diagnostic PCFCL samples (0/19 vs. 14/66, p=0.033), while 19p deletions were only identified in diagnostic PCFCL samples (2/19 vs. 0/66, p=0.048) compared to nFL cases. In one case, an additional focal deletion was identified in the 19p13.2-19p13.12 region spanning the location of SMARCA4 and NOTCH3, whereas no focal deletions were identified in nFL cases (3/19 vs. 0/66, p=0.010).

Conclusion
We identified CNAs which proved to be specific to PCFCL in comparison to nFL and point to potential differences in the underlying pathogenesis of these two diseases. After validation in a larger cohort, our findings could improve the differential diagnostic workflow of PCFCL.

Funding
The study was funded by the SE250+ Fellowship, the New National Excellence Programme (ÚNKP-22-3-II-SE-72), EFOP-3.6.3-VEKOP-16-2017-00009, H2020-739593, K21_137948, TKP2021-EGA-24, TKP2021-NVA-15, FK20_134253, MTA Bolyai Programme BO/125/22 and Elixir Hungary.