Molecular Residual Disease Detection Via Cancer Personalized Profiling By Deep Sequencing in Patients with PTCL Undergoing Autologous Stem Cell Transplantation
Authors: Sanghera Chandan , Ford Josie , Gunaratne Ruwan , Chopra Kusha , Rider Anna B , Sohani Aliyah R. , McCabe Sean M , Nemec Ronald A , Chen Yi-Bin , McAfee Steven , Hochberg Ephraim , Barnes Jeffrey A. , MacVicar Caroline , Jacobsen Eric D. , Merrill Mwanasha H. , Khodadoust Michael S. , Kurtz David , Jain Salvia 
Published: December 2024

Introduction:
Improved biomarkers are essential to guide autologous stem cell transplantation (ASCT) in patients with peripheral T-cell lymphoma (PTCL). We hypothesized that molecular residual disease (MRD) detection in pre-ASCT apheresis T-cells and post-ASCT plasma cell-free DNA (cfDNA) samples via Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) could predict relapse post-ASCT.
Methods:
The study initially focused on angioimmunoblastic T-cell lymphoma (AITL) subtype. Eligible patients had available diagnostic formalin-fixed paraffin-embedded (FFPE) biopsy tissue and underwent ASCT from 2005-2023. Autologous stem cells (ASC) harvested at the end of induction chemotherapy were sorted into T-, myeloid, NK- and B-cell populations. Whole exome sequencing (WES) was performed on DNA isolated from FFPE and cell populations, with NK/B-cells as the germline control to identify patient-specific ‘personalized’ tumor single nucleotide variants (SNVs) and design hybrid-capture panels. A PTCL-focused canonical ‘backbone’ panel (400kB) was designed to capture emerging pathogenic mutations. The ASC fractions and cfDNA samples were interrogated with the combined panels (personalized and backbone) as a composite approach to quantify MRD via tumor allele fraction and monitor clonal evolution.
Results:
52 patients have enrolled. Herein, we report on the initial 21 cases: 19 AITL and 2 PTCL-NOS. At diagnosis, the median age was 61.5 y (IQR 57.1-67.7), median IPI was 3 (IQR 2-3), and median Prognostic Index for T-cell lymphoma (PIT) was 2 (IQR 1-3). In the frontline setting, 6 (28.6%) patients received CHOP, 2 (9.5%) CHOP-azacitidine, 9 (42.9%) CHOEP, 3 (14.3%) BV-CHP, and 2 (4.8%) azacitidine-romidepsin. 18 (85.7%) patients received BEAM conditioning regimen, while 3 (14.3%) received busulfan and fludarabine prior to stem cell rescue.
A median of 20.5 (IQR 19-27.5) SNVs were recovered per patient to enable MRD detection. 89.8% (517/576) of total SNVs were derived from the ‘personalized’ space (i.e. from the exome), and 10.2% (59/576) from the ‘backbone’ panel. RHOA was the most frequently mutated gene across all cases (85.7%), followed by IDH2 (57.1%) and PLCG1 (28.6%). Interestingly, we also identified many shared mutations between tumor samples and multiple cell compartments, likely reflecting clonal hematopoiesis (CH) and mutations acquired in precursor cells. Across FFPE, myeloid, T- and B-cell populations, mutations in TET2 (23.8%) and DNMT3A (19.0%) were the most frequently shared between compartments, with the remainder being non-canonical PTCL variants.
We next explored the prognostic performance of MRD detection prior to ASCT. Here, MRD+ was defined as the detection of tumor-specific somatic mutations in the ASC T-cell fraction (T-ASC) as previously described (Newman et al, Nat Biotechnol 2016). When considering all identified SNVs from the tumor FFPE, 9/14 (64.3%) of T-ASC MRD+ patients relapsed post-ASCT, while 4/7 (57.1%) T-ASC MRD- patients did not. However, as certain somatic mutations were shared between cell compartments (i.e. between T- and B-cells or myeloid cells), and to remove any effect of CH variants, SNVs present in the myeloid and B-cell populations were removed. This approach significantly improved the performance of MRD detection, with 9/10 (90%) T-ASC MRD+ patients relapsing post-ASCT, compared to 3/11 (27.3%) T-ASC MRD- patients (specificity 88.9%, sensitivity 75%, PPV 90%). The singular T-ASC MRD+ patient without relapse received frontline tandem auto-allo SCT, which potentially prevented relapse. In T-ASC MRD+ patients, median PFS was 5.7 m (95% CI 3.1-NA). With a median follow-up of 38.7 m (IQR 19.3-45.6), T-ASC MRD- was associated with superior PFS (p=0.007, HR 5.1, 95% CI 1.4-19.1). Higher levels of T-ASC MRD tumor burden were also associated with inferior PFS (p=0.006, HR 1.4, 95% CI 1.1-1.7). MRD analysis in pre- and post-ASCT cfDNA samples was performed in a subset of patients and closely correlated with clinical disease status.
Conclusion:
Our PTCL-CAPP-Seq approach enables highly sensitive MRD detection in T-ASC and cfDNA, with remarkable specificity and potentially broad applicability to all common subtypes of non-leukemic PTCL. Results indicate MRD detection in T-ASC predicts high relapse risk post-ASCT, with a PPV of 90%. Additionally, MRD monitoring in longitudinal cfDNA samples can help facilitate early treatment decisions.