Molecular Profiling and Disease Tracking of Post-Transplant Lymphoproliferative Diseases Using Cell-Free DNA

• Published in: Blood 2024-11, Vol.144 (Supplement 1), p.6234-6234
• Main Authors: Veltmaat, Nick, Zhong, Yujie, Montes De Jesus, Filipe, Bult, Johanna, Mutsaers, Pim, Stevens, Wendy B.C., Mous, Rogier, van der Poel, Marjolein W.M., Chamuleau, Martine E.D., Noordzij, Walter, Verschuuren, Erik A.M., Kluiver, Joost L., Diepstra, Arjan, Plattel, Wouter, van den Berg, Anke, Nijland, Marcel
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood-2024-210000

Introduction. Post-transplant lymphoproliferative disorder (PTLD) comprises a spectrum of hematological malignancies that develop after solid organ transplantation (SOT). Unlike diffuse large B-cell lymphoma (DLBCL), initial treatment of PTLD patients starts with rituximab monotherapy. Identifying patients who do not respond to rituximab is essential to prevent delay in administering chemotherapy. We previously showed that cell-free tumor DNA (ctDNA) isolated from plasma represents a promising approach to profile PTLD at diagnosis [PID 37705050]. The use of ctDNA as biomarker has shown feasible in DLBCL, but has not yet been established for PTLD. We aimed to explore the feasibility of ctDNA for genomic profiling and response assessment in PTLD. Methods. Plasma samples of 28 PTLD patients were collected in this prospective observational multi-center cohort study in the Netherlands (National trial registry 7402). Low-coverage whole genome sequencing (lcWGS) was performed for detection of copy number variants (CNVs). Ultra deep (median ~15.000x target coverage) targeted next generation sequencing (NGS) was performed for the detection of single nucleotide variants (SNVs). The targeted panel contained 117 genes (comprising 391 kb) known to be recurrently mutated in B-cell lymphomas. SNVs were called using an in-house pipeline, optimized for detecting small somatic variants with low variant allele frequencies (VAFs) [PID 37705050]. For baseline samples, the VAF cutoff was set to >0.5%. For follow-up timepoints, this cutoff was removed to further increase sensitivity. ctDNA concentrations based on the VAF of SNVs were expressed as haploid genomic equivalent per milliliter (hGE/mL) of plasma. IchorCNA was used to call CNVs. Results. Median age of patients was 57 years (range 29-74), with 68% presenting with Ann Arbor stage III - IV. Median time between SOT and PTLD was 68 months (range 3-379). SOT consisted of kidney (n=17, 61%), liver (n=7, 25%), lung (n=3, 11%) and hematopoietic stem cell transplant (n=1, 4%). Pathology review showed DLBCL (19/24), Burkitt like (1/24), polymorphic PTLD (1/24) and undetermined B-cell lymphomas (3/24). EBV was negative for 10 (45%), positive for 12 (55%) and unknown for 2 cases. Out of 28 patients, 21 (75%) started initial treatment with rituximab, 6 (21%) initiated R-CHOP therapy and one patient (4%) did not receive treatment. In total 92 plasma samples were analyzed. At diagnosis, a total of 285 SNVs were detected in cfDNA sampl