In the paper published in the New England Journal of Medicine, researchers used Mission Bio's Tapestri platform to characterize cancer sample genomes at the single-cell level, thereby identifying mutational patterns in the B cell receptor pathway that could shape future treatment paradigms.

Covalent BTK inhibitors like ibrutinib have been used as a first-line long-term treatment for B cell malignancies like chronic lymphocytic leukemia (CLL). The majority of patients will develop treatment resistance through a mutation at cysteine residue 481 (C481), where covalent inhibitors bind BTK. To avoid this, a new generation of noncovalent BTK inhibitors is in clinical development with different binding sites. One of them, pirtobrutinib, is currently in late-stage clinical trials for patients with CLL who have failed covalent BTK inhibitors.

The authors confirmed some patients developed resistance to pirtobrutinib, with disease progression seen in 9 of 55 patients with CLL. They performed bulk genomic sequencing on samples from pirtobrutinib-resistant patients to identify resistance-associated mutations. To investigate the evolution of subclones harboring these resistance mutations, the team performed single-cell DNA sequencing on samples taken from two patients before treatment and at relapse.

These studies revealed that both primary (pre-existing) and secondary (acquired) resistance mechanisms were present. The Tapestri Platform allowed the investigators to identify the co-occurring mutations within each subclone, providing a picture of how new subclones evolved from pre-existing ones.

If patients can be screened at the single-cell level to identify mutational patterns like these, it could predict whether they are likely to respond to a BTK inhibitor and hence guide personalized treatment, according to the company.