AACR-Bayer Innovation and Discovery Grantee Identifies Expression Signatures Associated with Immune Checkpoint Inhibitor Resistance in Bladder Cancer

Bladder cancer is the tenth most common cancer worldwide, and more than 80,000 people are diagnosed with the disease each year in the US (1). The approval of checkpoint immunotherapy (CPI) has led to improved survival in first- and second-line treatment of metastatic bladder cancer (2). However, only 25% of patients are responsive, and unfortunately no accurate biomarkers exist to identify patients who will benefit from CPI treatment. A recent study published in Nature Communications uncovered signatures associated with response to CPI that can be used to molecularly stratify patients and identified potential therapeutic alternatives for those with poor response to neoadjuvant immunotherapy.

The study was led by Joshua Meeks, MD, PhD, an associate professor at Northwestern University Feinberg School of Medicine. A recipient of an AACR-Bayer Innovation and Discovery Grant in 2019, he sought to define CPI resistance mechanisms in bladder cancer. He elaborated, “The goal of our AACR-Bayer Innovation and Discovery Grant was to assess FGFR3 alterations in tumors treated with checkpoint inhibitors. We found that FGFR3 alterations were associated with resistance to checkpoint immunotherapy. However, we found that increased gene expression of FGFR3 was a more significant predictor for resistance than FGFR3 mutation. This has significant implications for targeted therapies that may be used for patients with overexpression rather than just mutation.”

In the study, Dr. Meeks and his colleagues assessed tumor samples from 82 patients enrolled in the PURE01 clinical trial, a Phase II prospective study of neoadjuvant pembrolizumab. By performing bulk RNA-seq transcriptional profiling of pre-treatment samples, followed by unsupervised consensus clustering, they identified five transcriptomic subtypes (S1 – S5) associated with response to pembrolizumab.

The researchers characterized the subtypes further by investigating the biology, mutations and copy number variations associated with each subtype. They found that tumors with the worse pathological response to pembrolizumab, classified as S1, had repressed inflammatory, immune checkpoint, and antigen presentation pathways. Also, whilst 35% of S1 tumors had mutations in FGFR3, FGFR3 expression was enhanced in the S1 tumors. Whereas tumors within the most pathologically responsive subtypes, S2 and S3, had upregulation of genes involved in IFN-α and IFN-γ pathways, antigen presentation machinery, and frequent mutations in ATR and TP53.

Dr. Meeks and his colleagues then assessed and compared paired pre- and post-treatment tumors taken from the same anatomical site and identified two new subtypes (S6 and S7) which the majority of post-treatment tumors clustered within. Notably, they found that 50% of the pembrolizumab-resistant post-treatment tumors in S6 and S7 originated from S1 tumors.

The investigators then explored the transcriptional factors regulating the repressed inflammatory gene network in the S1 tumors. They identified S1 tumors had the highest activity of KDM5B, a histone H3K4 demethylase with multiple negatively regulated immune target genes. This led the researchers to assess the KDM5 inhibitor C70, in an S1-like bladder cancer cell line with oncogenic FGFR3-TACC3 fusion. As S1 tumors also had frequent mutations in FGFR3 and enhanced FGFR3 expression, the research team also assessed the FDA-approved FGFR3 inhibitor erdafitinib in the bladder cancer cell line. They found that both inhibitors upregulated an inflammatory phenotype associated with expression of genes from IFN-α, IFN-γ and IL-6 JAK-STAT3 gene sets, suggesting that subtype specific targeting of KDM5B or FGFR3 can enhance immunogenicity, and potentially sensitize S1 tumors to CPI. 

Reflecting on receiving the AACR-Bayer Discovery and Innovation grant, Dr. Meeks highlighted the benefit of attending the AACR Annual Meeting to receive his award, saying, “At the AACR Annual meeting, I was able to meet so many inspiring scientists who were incredibly supportive of our work. As this happened right before the pandemic, I carried these interactions over the last three years as the science matured into our publication.”

References:

1. Siegel RL, Miller KD, Jemal A. Cancer statistics, 2020. Ca. Cancer J. Clin 2020; 70: 7–30.
2. Bidnur S, Savdie R, Black PC. Inhibiting immune checkpoints for the treatment of bladder cancer. Bladder Cancer 2016; 2: 15–25.