Identification of prognostic and predictive biomarkers in lymphoma patients treated with anti-CD19 CAR T-cell therapy

Chimeric Antigen Receptor T-cell (CAR T-cell) therapy has emerged as a promising treatment for patients with relapsed or refractory B-cell non-Hodgkin lymphoma (r/r B-NHL) who have failed standard therapies. The overall response rate is 50–60%, but severe toxicities such as cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS) can occur in about 30% of patients. In addition, CAR T-cell activity may be hampered by T-cell exhaustion or senescence. My PhD project aimed to study the post-infusion CAR T-cell biology and to identify biomarkers of therapy-related toxicity and clinical outcome. We collected whole blood, peripheral blood mononuclear cells (PBMCs), and plasma samples from 88 r/r B-NHL patients treated with Axi-cel or Tisa-cel before and after treatment, to investigate patients immunophenotype, CAR T-cell fitness and expansion kinetic, and circulating nucleic acids as therapy biomarkers. The molecular tracking of CAR T-cell DNA, obtained with droplet digital PCR, showed expansion kinetics comparable to those measured using flow cytometry, but an improved capability to detect the CAR T-cell DNA at 1 year after therapy. To what concern toxicity, patients with high levels of circulating monocytic myeloid-derived suppressor cells (M-MDSCs) and a distinct miRNA profile before lymphodepletion were more prone to developing CRS or ICANS. As for outcome prediction, we reported that elevated pre-lymphodepletion levels of M-MDSCs and circulating cell-free DNA (ccfDNA) were associated with significantly worse overall survival (OS), progression-free survival (PFS), and time to progression (TTP), when compared to patients with low levels. Moreover, using multivariate logistic regression we identified a 4-variable model including 3 miRNAs (miR-542-5p, miR-21-5p, miR-26b-3p), able to predict a 3-month outcome with an accuracy of 82%. In conclusion, our analysis demonstrated the potential of liquid biopsy testing before anti-CD19 CAR T-cell therapy to assist the clinician in prognostic assessment and treatment decisions.