High peripheral T cell diversity is associated with lower risk of toxicity and superior response to dual immune checkpoint inhibitor therapy in patients with metastatic NSCLC

Abstract

Introduction: Despite significant successes, immune checkpoint blockade fails to achieve clinical responses in a significant proportion of patients, predictive markers for responses are imperfect and immune-related adverse events (irAEs) are unpredictable. We used T-cell receptor (TCR) sequencing to systematically analyze prospectively collected patient blood samples from a randomized clinical trial of dual immune checkpoint inhibitor therapy to evaluate changes in the T-cell repertoire and their association with response and irAEs.

Methods: Patients with immunotherapy-naïve metastatic non-small cell lung cancer (NSCLC) were treated with ipilimumab and nivolumab according to trial protocol (LONESTAR, NCT03391869). Blood samples were systematically obtained at baseline (n=107), after 12 weeks of ipilimumab and nivolumab (n=91), and at the time of grade ≥2 irAEs (n=77). For analysis of T-cell repertoire, we performed immunoSEQ to assess the complementary determining region 3β region of the TCR involved in antigen binding.

Results: A total of 250 samples from 119 patients were analyzed. Patients who had a response to therapy exhibited greater T-cell diversity at baseline. Interestingly, patients with irAEs demonstrated lower T-cell richness at the time of toxicity compared with those without irAEs.

Conclusion: Our study highlights the potential impact of peripheral blood T-cell repertoire on clinical response and toxicities from the combination of ipilimumab and nivolumab in patients with metastatic NSCLC. These findings suggest that analysis of peripheral blood T-cell repertoire may help to guide patient selection for treatment with ipilimumab and nivolumab.

Trial registration number: NCT03391869.

Keywords: Immune Checkpoint Inhibitor; Immune related adverse event - irAE; Lung Cancer; T cell Receptor - TCR.

Figure 1. Time points for blood collection. Time point A: Baseline (prior to ICI therapy, n=107). Time point B: After 12 weeks of ICI therapy 12-week samples (this time point also used as control for treated patients with no irAEs, n=91). Time point C: At the time of irAE (if applicable, n=77). 25 toxicity samples had an overlapping collection time point (eg, postinduction and toxicity, as described in methods). ICI, immune checkpoint inhibitors; irAEs, immune-related adverse events; LCT, local consolidation therapy.

Figure 2. Overview of treatment response, clinicopathologic features and T cell indices. (A) T cell indices from the baseline peripheral blood represented in a heatmap with clinicopathologic features and treatment responses. (B) T cell indices from the post 12-week therapy peripheral blood represented in a heatmap with clinicopathological features and treatment responses. Cell.type: Histopathology of the NSCLC (Adeno, adenocarcinoma; NOS, NSCLC otherwise non-specified; SCC, squamous cell carcinoma). Radiological responses further defined as CR, complete response; PD, progressive disease; PR, partial response; SD, stable disease. NSCLC, non-small cell lung cancer.

Figure 3. T cell receptor repertoire (T-cell richness, T cell clonality, T cell max frequency) comparisons in baseline (prior to ipilimumab and nivolumab therapy) for responders (complete response (CR)+partial response (PR)+stable disease (SD)) versus progressive disease measured by RECIST V.1.1 (A, B and C). Comparisons of baseline T cell repertoire parameters among radiologic response groups CR+PR versus SD versus PD (D, E and F). Total of 69 responders (complete response: 1 patient; partial response: 28 patients; stable disease: 40 patients), 24 non-responder (progressive disease). PD, progressive disease; RECIST, Response Evaluation Criteria in Solid Tumors.

Figure 4. T cell receptor repertoire comparisons at the time of toxicity (grade ≥2 immune related adverse events) versus postinduction (after 12-week treatment with ipilimumab and nivolumab therapy) in patients with no toxicity. Total of 77 toxicity samples and 36 end of induction/no toxicity samples are included in the analysis.

Figure 5. T cell richness and density at the time of toxicity (A) Longitudinal changes of T cell richness in patients’ samples with toxicity, baseline (prior to ipilimumab and nivolumab therapy) and end of induction (after 12-week treatment with ipilimumab and nivolumab therapy). Toxicity: grade ≥2 immune related adverse events. (B) Box plots for T cell density when end of induction (after 12-week treatment with ipilimumab and nivolumab therapy) samples in no toxicity group compared with toxicity samples in patients with toxicity. Toxicity: grade ≥2 immune related adverse events.

Figure 6. Comparison of TCR repertoire related with the timing of irAE, Early grade ≥2 immune related adverse events (within 12 weeks of therapy; 30 samples) versus delayed grade ≥2 immune related adverse events (>12 weeks of therapy; 38 samples.).

Figure 7. UB enrichment analysis using TCR database and assessment of overlaps with irAE pneumonitis and diarrhea. Enrichment analysis using VDJdb and assessment of overlaps with samples from at the time of grade ≥2 irAE for pneumonitis (A), diarrhea/colitis (B). Significantly expressed sequences among patients with pneumonitis and diarrhea/colitis were extracted and then tested for enriched antigen species referring to VDJdb. A higher value of “−log10(FDR)” shows more significance. CMV, Cytomegalovirus; DENV, Dengue virus type 1; EBV, Epstein-Barr virus; FDR, false discovery rate; HCV, hepatitis C virus; irAE, immune-related adverse event; LCMV, lymphocytic choriomeningitis virus; MCMV, murine Cytomegalovirus; RSV, respiratory syncytial virus; SIV, simian immunodeficiency virus; sTCR, T-cell receptor; VDJdb, variable, diversity, joining database; YFV, yellow fever virus.