Multi-Omic Profiling Reveals Genetic and Epigenetic Pirtobrutinib Resistance Pathways in MCL

Pirtobrutinib resistance in MCL is driven by heterogeneous genetic and epigenetic mechanisms, the identification of which has offered insights into potential strategies to extend the therapeutic benefit of this noncovalent BTK inhibitor, according to Fangfang Yan, PhD. 

On January 27, 2023, the FDA approved the noncovalent BTK inhibitor pirtobrutinib for the treatment of adult patients with relapsed/refractory MCL who had received 2 or more prior lines of systemic therapy, including a BTK inhibitor.¹ However, although pirtobrutinib has demonstrated activity in the relapsed/refractory population, including generating an ORR of 50% (95% CI, 41%-59%) in the pivotal phase 1/2 BRUIN trial (NCT03740529), patients may develop resistance to this agent.^1,2

Yan and colleagues conducted a study to investigate the molecular dynamics that drive pirtobrutinib resistance, using single-cell multi-omic profiling on samples from patients with MCL taken before pirtobrutinib treatment, as well as after pirtobrutinib relapse.² The study found that pirtobrutinib resistance developed across both genetic and non-genetic routes, including stepwise copy number gains, as well as epigenetic and transcriptional reprogramming. Furthermore, a stem-like malignant B-cell population was found to be enriched in the resistant samples. Additionally, RAD21 was shown to be a potential driver of resistance, and may be a therapeutic target for overcoming resistance.

“If we can show [this strategy] works, it means patients will have more [treatment] options, even after relapse or resistance,” Yan said in an interview with OncLive®.

In the interview, Yan discussed the need for identifying strategies to optimize pirtobrutinib use in patients with MCL, the ins and outs of this multi-omic analysis, and what the future may hold.

Yan is a postdoctoral fellow at The University of Texas MD Anderson Cancer Center in Houston.

OncLive: What is the current role of pirtobrutinib in MCL management?

Yan: Pirtobrutinib is a next-generation BTK inhibitor. [In 2023] it was approved by the FDA for patients with relapsed MCL. It's different from [previously developed] BTK inhibitors, which are covalent. Pirtobrutinib is noncovalent, so its mechanism of action is slightly different, and it has meaningful clinical efficacy and a favorable safety profile. It's an important treatment option for heavily pretreated patients with MCL.

What are some mechanisms of pirtobrutinib resistance that may arise in MCL?

In patients who develop resistance to pirtobrutinib, potential mechanisms [of resistance] include the activation of alternative signaling pathways to support tumor growth. [Patients] may also have copy number changes in DNA and RNA.

What was the design of the multi-omic study of pirtobrutinib resistance mechanisms in MCL?

We know the patients were heterogeneous; even for patients with the same response [to pirtobrutinib] can be different [from each other]. How do we control this patient heterogeneity? In this study, we collected paired patient samples. For each patient, we collected samples before treatment, at which point they were still sensitive [to pirtobrutinib], as well as after treatment. At that point, the patients were resistant to the therapy. In this way, we could conduct a more controlled comparison to understand what was going on. For the sequencing technology, we used single-cell RNA sequencing, which measures gene expression, and we performed single-cell assay for transposase accessible chromatin using sequencing. In this way, we [aimed to] understand which genes [drive] pirtobrutinib resistance, as well as why these genes [drive this resistance], to understand what controls this gene expression from upstream regulation.

What were the key findings from the analysis of pirtobrutinib resistance mechanisms in MCL samples?

These patients were different [from each other]. The patients had 2 different routes [to resistance]. One was the genetic route. These patients had stepwise copy number gains, so that means they had changes in DNA, and then at follow-up, changes in RNA expression. The other patients didn't have such changes in DNA. They only had nongenetic transcriptomic changes. Our main conclusion was that the patients had 2 different routes, both genetic and nongenetic.

What are the next steps for this research?

The next step is to still conduct experiments in the Michael Wang Laboratory [at The University of Texas MD Anderson Cancer Center] to validate whether targeting [RAD21] will reverse pirtobrutinib resistance.

Disclosures: Yan had no financial disclosures to report.

References

1. US FDA approves Jaypirca (pirtobrutinib), the first and only non-covalent (reversible) BTK inhibitor, for adult patients with relapsed or refractory mantle cell lymphoma after at least two lines of systemic therapy, including a BTK inhibitor. News release. Loxo@Lilly. January 27, 2023. Accessed January 30, 2026. https://investor.lilly.com/news-releases/news-release-details/us-fda-approves-jaypircatm-pirtobrutinib-first-and-only-non
2. Yan F, Liu Y, Lee H, et al. Dissecting pirtobrutinib resistance in mantle cell lymphoma through single-cell multi-omics. Blood. 2025;146(suppl 1):1765. doi:10.1182/blood-2025-1765