Integration of Multi-omic Data in a Molecular Tumor Board Reveals EGFR-Associated ALK-Inhibitor Resistance in a Patient With Inflammatory Myofibroblastic Cancer

Abstract

Inflammatory myofibroblastic tumors (IMTs) are intermediate-grade mesenchymal neoplasms commonly characterized by chromosomal rearrangements causing constitutive activation of anaplastic lymphoma kinase (ALK) and/or ALK mutations causing reduced sensitivity to ALK tyrosine kinase inhibitors (TKI). We present a patient with an IMT who initially responded to first-line alectinib, but who later suffered disease relapse and presently survives with moderate residual disease after receiving second-line lorlatinib. Biopsy specimens were analyzed using next generation sequencing (DNA-seq and RNA-seq) and reverse phase protein microarray (RPPA) as part of an institutional Molecular Tumor Board (MTB) study. An EML4-ALK rearrangement and EGFR activation (pEGFRY1068) were present in both the primary and recurrent tumors, while a secondary ALK I1171N mutation was exclusive to the latter. EGFR signaling in the background of a secondary ALK mutation is correlated with reduced ALK TKI sensitivity in vitro, implicating an important mechanism of drug resistance development in this patient. The RPPA results also critically demonstrate that ALK signaling (ALKY1604) was not activated in the recurrent tumor, thereby indicating that standard-of-care use of third- or fourth-line ALK TKI would not likely be efficacious or durable. These results underscore the importance of real-time clinical integration of functional protein drug target activation data with NGS in the MTB setting for improving selection of patient-tailored therapy.

Keywords: DNA sequencing; inflammatory myofibroblastic tumor; proteogenomics; proteomics; reverse phase protein microarray.

Figure 1.

Timeline of patient’s clinical history. Timeline depicts relevant clinical events during the patient’s disease history, beginning at day 0 when the patient presented in the clinic with symptomatic complaint and ending at day 351 as the time of last follow-up with the patient surviving with moderate residual disease. VATS = video-assisted thoracoscopic. CT = computed tomography. TKI = tyrosine kinase inhibitor. CLIA testing (NGS) = next generation DNA-sequencing (DNA-seq) and RNA-sequencing (RNA-seq) with validated fusion analysis performed on solid tissue and/or liquid biopsy specimens by Tempus Labs, Inc. RPPA = reverse phase protein microarray analysis.

Figure 2.

Representative computed tomography (CT) scans obtained throughout the patient’s clinical history. CT scan images depict the tumor size at baseline assessment 6 days prior to initiation of alectinib (day 54), near-complete response to alectinib (day 146), tumor size at disease recurrence while receiving alectinib (day 229), tumor size at recurrent biopsy surgery occurring 6 days after initiation of lorlatinib (day 257), and tumor size at the time of last follow-up (day 351).

Figure 3.

Proteogenomic clinical and research testing performed on biopsy tissue specimens. Biopsy tissue specimens were obtained from a left pleural mass from the patient’s primary (day 27; ALK TKI-naïve) and recurrent (day 257; post-alectinib, 6 days on-lorlatinib) tumors. Representative immunohistochemistry (IHC), next generation DNA- and RNA-sequencing, and reverse phase protein microarray (RPPA) results are shown for each biopsy specimen. IHC images (micrographs, top row) show the representative hematoxylin and eosin (H&E) stained tissue and tissue which was immunohistochemically stained for ALK (200× magnification). NGS results (summary tables, middle row) from DNA-sequencing using the Tempus xT 648-gene panel highlight biologically relevant gene variants, variants of unknown significance (VUS), and chromosomal rearrangements identified by RNA-sequencing with validated fusion detection. RPPA results (summary tables, bottom row) using the Theralink RPPA assay represent the total protein and phosphoprotein abundances of several known cancer-related targets.