Autoantibodies as predictors for immune-related adverse events in checkpoint inhibition therapy of metastatic melanoma

Abstract

Background: Immune checkpoint inhibitors have transformed melanoma therapy but frequently cause immune-related adverse events (irAEs), including colitis, that limit treatment. Reliable biomarkers predicting toxicity remain lacking.

Methods: In this retrospective, multicenter study, we analyzed pretreatment serum samples from 331 patients with metastatic melanoma treated with anti-CTLA-4 (ipilimumab), anti-PD-1 (pembrolizumab or nivolumab), or combination ipilimumab/nivolumab. IgG autoantibody reactivity against 832 human protein antigens, including autoimmune targets, cytokines, tumor-associated antigens, and cancer pathway proteins, was profiled using multiplex bead-based arrays. Statistical analysis (Significance Analysis of Microarrays and Cox regression) identified autoantibody signatures associated with subsequent irAEs and immune-related colitis (ir-colitis).

Results: We detected 47 autoantibodies predictive of irAEs, with KRT7, RPLP2, UBE2Z, and GPHN emerging as the strongest markers. Anti-KRT7 and anti-GPHN were specifically predictive in patients receiving PD-1 monotherapy, whereas anti-RPLP2 was associated with irAEs in ipilimumab/nivolumab combination therapy. For ir-colitis, 38 autoantibodies were identified, with five (PIAS3, RPLP0, UBE2Z, KRT7, and SDCBP) showing consistent predictive value across treatment groups. Anti-PIAS3 and anti-RPLP0 increased ir-colitis risk, while anti-SDCBP conferred protection. Notably, predictive profiles differed between PD-1-based and CTLA-4-based regimens, underscoring divergent mechanisms of toxicity. Several autoantibodies predictive of irAEs or ir-colitis also correlated with clinical outcome. ATG4D, MAGEB4, and IL4R were associated with prolonged progression-free and overall survival, whereas FGFR1 predicted both reduced irAE risk and inferior survival, consistent with the link between heightened immune activation, toxicity, and therapeutic benefit.

Conclusions: This study, to our knowledge, is the largest pretreatment autoantibody screen in melanoma immunotherapy, demonstrates that serum autoantibody profiles can stratify patients at risk for irAEs and ir-colitis. The identified signatures connect tumor-related and immunity-related antigens, stress-response pathways, and autoimmune mechanisms. Pretreatment autoantibody profiling offers a promising biomarker-driven approach for individualizing risk assessment, improving patient selection, and guiding early intervention strategies to enhance the safety of immune checkpoint blockade in melanoma. Beyond toxicity prediction, our findings also suggest that specific autoantibodies may reflect underlying immune activation states linked to therapeutic response.

Keywords: Antibody; Autoimmune; Biomarker; Immune Checkpoint Inhibitor; Immune related adverse event - irAE.

Figure 1. Summary of all 47 baseline autoantibodies associated with irAE, ir-colitis, PFS, or OS across all treatment groups. (A) Summary of baseline autoantibodies predictive for irAE and ir-colitis across all treatment groups. Autoantibodies associated with increased risk for irAE and ir-colitis are shown with red dots and those with reduced risk with a green dot. Only significant findings (unadjusted p<0.05) are shown. (B) The same autoantibodies identified for irAE and ir-colitis were analyzed for their association with OS and PFS. Autoantibodies associated with longer OS and PFS are shown with a green dot and those with shorter OS or PFS with a red dot. irAE, immune-related adverse event; OS, overall survival; PFS, progression-free survival.

Figure 2. Autoantibodies positively and negatively associated with risk of irAE. Log2 HRs (indicated by squares), 95% CIs (indicated by horizontal lines), and p values were from a Cox proportional hazards model. ∗Unadjusted p<0.05. Autoantibodies associated with an increased risk are shown with a red box and those with lower risk of irAE with green boxes. (A) Patients from all treatment groups, (B) patients receiving ipi/nivo, and (C) patients receiving pembro without prior ipi treatment. irAE, immune-related adverse event.

Figure 3. Kaplan-Meier curves of immune-related adverse events (irAEs) in immune checkpoint inhibitor (ICI)-treated patients stratified by baseline autoantibody levels. Kaplan-Meier showing associations between baseline serum autoantibody reactivity and the occurrence of irAEs, including ir-colitis. Autoantibody levels were dichotomized using the log₂ mean reactivity across all patients plus one SD. Red lines indicate patients with high baseline autoantibody levels; black lines indicate patients with low levels. In the overall treatment group, higher baseline autoantibodies to RPLP2 and UBE2Z were associated with increased risk of irAEs. In the ipilimumab/nivolumab combination group, higher baseline autoantibodies to RPLP2 and PIAS3 predicted higher risk, while in patients receiving pembrolizumab without prior ipilimumab, elevated autoantibodies to KRT7 and GPHN were associated with increased risk. Ipi/Nivo, ipilimumab/nivolumab.

Figure 4. Autoantibodies positively and negatively associated with risk of ir-colitis. Log2 HRs (indicated by squares), 95% CIs (indicated by horizontal lines), and p values were from a Cox proportional hazards model. ∗Unadjusted p<0.05. Autoantibodies associated with an increased risk are shown with a red box and those with lower risk of ir-colitis with green boxes. (A) Patients from all treatment groups, (B) patients receiving ipi/nivo, and (C) patients receiving pembro without prior ipi treatment. ipi/nivo, ipilimumab/nivolumab.

Figure 5. Kaplan-Meier curves of ir-colitis in immune checkpoint inhibitor-treated patients stratified by baseline autoantibody levels. Kaplan-Meier survival showing associations between baseline serum autoantibody reactivity and the occurrence of ir-colitis. Autoantibody levels were dichotomized using the log₂ mean reactivity across all patients plus one SD. Red lines indicate patients with high baseline autoantibody levels; black lines indicate patients with low levels. In the overall treatment group, higher baseline autoantibodies to UBE2Z were associated with increased risk, and SDCBP was associated with lower risk of ir-colitis. In the ipilimumab/nivolumab combination group, higher baseline autoantibodies to PIAS3 predicted higher risk and to SDCBP lower risk of ir-colitis, while in patients receiving pembrolizumab without prior ipilimumab, elevated autoantibodies to RPLP2 and KRT7 were associated with increased risk. Ipi/Nivo, ipilimumab/nivolumab.

Figure 6. Overlap of autoantibodies predicting irAE (left panel) and ir-colitis (right panel) identified in patients treated with ipi-mono compared with pembro never ipi. irAE, immune-related adverse event.