cfDNA Sequencing Uncovers Resistance Mechanisms in Colorectal Cancer
See article, p. 164
cfDNA sequencing has high concordance with direct tumor sequencing in patients with colorectal cancer.
EGFR ECD domain mutations that disrupt anti-EGFR antibody binding may promote drug resistance.
cfDNA profiling can characterize the tumor genomic landscape and discover resistance mutations.
Liquid biopsy approaches can be used to analyze cell-free DNA (cfDNA) in patients with cancer when there is insufficient tissue for direct tumor sequencing or metastatic lesions cannot be directly biopsied. However, it is not clear if cfDNA sequencing can accurately describe the tumor genomic landscape, prompting Strickler and colleagues to compare 1,772 cfDNA profiles from 1,397 patients with advanced colorectal cancer to tissue-sequencing databases. Genomic alterations were detected in 85% of cfDNA samples, and the mutational frequency was largely concordant with the tumor tissue cohorts. However, EGFR mutations were largely subclonal and detected at a higher frequency in cfDNA compared with tumor tissue. Many of these mutations occurred in the EGFR extracellular domain (ECD) and have previously been linked to acquired resistance to anti-EGFR antibodies. Overall, 58 patients had a recurrent EGFR ECD mutation, and 42 patients harbored mutations in EGFR domain III where the anti-EGFR antibodies cetuximab and panitumumab bind. These mutations included the previously undescribed recurrent EGFR mutations V441D and V441G, which were also found to reduce binding to cetuximab and panitumumab, suggesting potential resistance mechanisms. The large majority of patients with EGFR ECD mutations also had at least one additional co-occurring resistance alteration, and there was profound heterogeneity in the number of acquired resistance mutations. Collectively, these findings reveal strong concordance between cfDNA and tumor sequencing, and suggest that cfDNA profiling can provide insights into the tumor genomic landscape and uncover potential resistance mechanisms.
Hotspot Mutation Analysis Uncovers Potential Therapeutic Targets
See article, p. 174
Analysis of hotspot mutations in 24,592 patients with cancer revealed 1,165 hotspots in 247 genes.
Seven patients with identified hotspot mutations benefited from enrollment in matched clinical trials.
Hotspot analysis may facilitate precision medicine by accelerating discovery of rare driver mutations.
Only a fraction of tumor mutations are used to guide treatment selection in patients with cancer, whereas the large majority of mutations are rare and lack biological and clinical validation. Thus, approaches are needed to characterize mutations of unknown significance and identify those that may be druggable driver mutations. To this end, Chang and colleagues analyzed somatic mutational data from 24,592 patients (including 14,256 retrospectively sequenced patients with untreated cancer and 10,336 prospectively sequenced active patients with recurrent and metastatic disease) across 322 cancer types and 32 organ sites to identify hotspot mutations that may be clinically actionable. In total, 1,165 mutational hotspots were identified in 247 genes, and 840 of these hotspots were previously unidentified. The majority of these hotspots were rare, with 82% occurring in no more than 0.1% of patients. Although substitution mutations were most common, 55 recurrent in-frame indel hotspots were discovered in 36 genes. Based on these findings, seven patients who had previously undescribed rare hotspot mutations in known oncogenes were enrolled in matched clinical trials. All seven patients derived clinical benefit, including two patients with an ERBB2V697 hotspot treated with the HER inhibitor neratinib, four patients with various PIK3CA hotspot mutations treated with PIK3CA or mTORC1/2 inhibitors, and one patient with a BRAFL485W mutation treated with an ERK inhibitor. Collectively, these findings indicate that hotspot mutation analysis can accelerate the discovery of rare driver mutations in cancer to facilitate selection of targeted therapies.
The ERK Inhibitor Ulixertinib Is Safe and Has Antitumor Activity
See article, p. 184
ERK inhibition with ulixertinib achieves responses in patients with MAPK-mutant advanced solid tumors.
Ulixertinib has antitumor activity in patients with NRAS-, BRAFV600-, and non-V600 BRAF-mutant tumors.
Ulixertinib warrants further investigation to treat patient with MAPK activating alterations.
Mutations affecting MAPK signaling occur frequently in patients with cancer, and combined inhibition of BRAF and MEK is the standard of care in BRAFV600-mutant melanoma. However, a variety of resistance mechanisms can lead to reactivation of ERK signaling, leading most patients to develop acquired resistance. ERK inhibitors may overcome upstream mechanisms of resistance, and the ATP-competitive ERK1/2 inhibitor ulixertinib has antitumor activity in BRAF- and RAS-mutant xenografts. Sullivan, Infante, Janku, and colleagues evaluated the safety and activity of ulixertinib in patients with advanced solid tumors in an open-label, first-in-human, phase I study. A total of 135 patients were enrolled, including 91 patients with BRAF-mutant tumors, 24 with NRAS-mutant tumors, 9 with MEK-mutant tumors, 5 with KRAS-mutant tumors, 1 with a GNAS-mutant tumor, and 5 with no identified mutations. Ulixertinib achieved near-complete ERK inhibition at the determined recommended phase II dose and exhibited an acceptable safety profile. Treatment-related grade 3 adverse events occurred in 41% of patients. In the dose-escalation phase, 3/25 (12%) evaluable patients achieved partial responses, all of whom had BRAFV600E melanoma. In the dose expansion, 11/81 (14%) evaluable patients achieved partial responses, including 3/18 patients with NRAS-mutant melanoma, 3/12 patients with BRAF-mutant lung cancer, 1/15 patients with BRAF/MEK inhibitor refractory BRAFV600E melanoma, and 4 patients with other BRAF-mutant cancers including gallbladder cancer and glioblastoma. The finding that ulixertinib is well tolerated and exhibits antitumor activity in patients with a variety of solid tumors supports its further clinical investigation in patients with MAPK activating alterations.
Organotypic Tumor Spheroid Profiling Predicts Response to Anti–PD-1
See article, p. 196
Organotypic tumor spheroids recapitulate the tumor-immune microenvironment.
Tumor spheroids derived from mice (MDOTS) or patients (PDOTS) may predict drug response and resistance.
MDOTS/PDOTS may facilitate precision immunotherapy to enhance immune checkpoint blockade.
Immune checkpoint blockade (ICB) achieves clinical responses in a subset of patients with cancer, but biomarkers and precision medicine approaches to determine which patients will benefit from ICB are lacking. Jenkins and colleagues developed murine-derived organotypic tumor spheroids (MDOTS) and patient-derived organotypic tumor spheroids (PDOTS) to model the interactions between tumor and immune cells and predict responses and resistance to ICB. MDOTS derived from melanoma, glioma, and lung and colon tumors retained the immune cell components of the tumor microenvironment. Treating MDOTS with an anti–PD-1 antibody recapitulated the sensitivity or resistance observed in vivo in the corresponding mouse models. CT26-derived colon cancer MDOTS exhibited partial sensitivity to anti–PD-1 and were thus used to test possible combination therapies to overcome ICB resistance. A TBK1/IKKϵ inhibitor, Cmpd1, suppressed tumor cytokine signaling and enhanced T-cell activation, thereby enhancing the effects of PD-1 blockade. These findings were confirmed in vivo, with Cmpd1 potentiating anti–PD-1, increasing antitumor activity and extending survival, indicating that MDOTS profiling can predict responses in vivo. In PDOTS, profiles of secreted cytokines predicted response to and resistance to PD-1 blockade. Elevated expression of CCL19 and CXCL13 and reduced expression of immunosuppressive cytokines were associated with extended survival after ICB. Collectively, these findings suggest that ex vivo organotypic tumor spheroid cultures may recapitulate the tumor-immune microenvironment, allowing evaluation of combination therapies to enhance precision immune-oncology efforts.
CDK4/6 Inhibition Potentiates Immune Checkpoint Blockade
See article, p. 216
CDK4/6 inhibitors promote T-cell activation and tumor infiltration to enhance antitumor immunity.
CDK4/6 inhibition derepresses NFAT to increase T-cell activity and sensitivity to anti–PD-1 therapy.
CDK4/6 inhibitors may improve the efficacy of immune checkpoint blockade in patients with cancer.
Immune checkpoint blockade including inhibitors of PD-1 are successful in a subset of patients in a variety of tumor types. However, some tumor types are less responsive, and acquired resistance can develop in responding patients. Deng, Wang, Jenkins, and colleagues sought to identify small-molecule inhibitors that would enhance the efficacy of immune checkpoint blockade to overcome these challenges. A compound screen found that cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors enhanced the activity of PD-1 overexpressing T cells, promoting IL2 secretion even when suppressed by PD-1 signaling. The NFAT transcription factors regulate IL2 expression and T-cell activation, and CDK6 phosphorylated NFAT proteins, blocking their nuclear localization and activity. Thus, CDK4/6 inhibition relieved NFAT suppression, promoting NFAT signaling, IL2 secretion, and T-cell activity. In vivo, in a mouse model of non–small cell lung cancer, CDK4/6 inhibition enhanced T-cell tumor infiltration despite reducing T-cell proliferation. Further, antigen-experienced T cells were more sensitive to CDK4/6 inhibitors than naïve T cells. CDK4/6 inhibitors cooperated with anti–PD-1 therapy to induce T-cell mediated antitumor immunity and synergized with anti–PD-1 antibodies in multiple syngeneic tumor models. Taken together, these findings elucidate a mechanism by which CDK4/6 inhibitors may promote T-cell activity and enhance the efficacy of anti–PD-1 therapy, suggesting that combined treatment with CDK4/6 inhibitors and immune checkpoint blockade may be beneficial in patients with cancer.
FOXF1 Is Required for the Growth of Gastrointestinal Stromal Tumors
See article, p. 234
FOXF1 acts as a pioneer factor, remodeling chromatin to promote lineage-specific GIST gene expression.
FOXF1 recruits ETV1 to enhancers and promotes expression of target genes including ETV1 and KIT.
The transcriptional addiction to FOXF1 may make it a candidate biomarker or target in patients with GIST.
Gastrointestinal stromal tumors (GIST) are a common type of soft-tissue sarcoma that arise from interstitial cells of Cajal (ICC) and frequently harbor activation mutations in KIT, which encodes a receptor tyrosine kinase. KIT mutations activate downstream MAPK signaling to stabilize the transcription factor ETV1, and ETV1 also promotes mutant KIT expression, establishing a positive feedback loop by which mutant KIT and ETV1 enhance GIST tumorigenesis. Ran, Chen, and colleagues sought to determine the mechanism by which KIT and ETV1 are regulated in GIST. The transcription factor FOXF1 was highly expressed in GIST but rarely expressed in other types of sarcoma. Chromatin immunoprecipitation sequencing showed that FOXF1 was enriched at GIST/ICC-specific enhancers, including KIT and ETV1 enhancers, and promoted their expression. FOXF1 acted as a pioneer factor, modulating chromatin accessibility and recruiting ETV1 to lineage-specific GIST enhancers. Consistent with these findings, FOXF1 was required for GIST cell growth in vitro. FOXF1 depletion downregulated ETV1 and KIT, reduced downstream MAPK and AKT signaling, and inhibited cell-cycle progression. In vivo, deletion of FOXF1 in KIT-mutant GIST suppressed tumor growth, indicating that FOXF1 is required for GIST maintenance. In addition to identifying FOXF1 as a pioneer factor responsible for defining the core transcriptional regulatory circuitry in GIST, these findings suggest that FOXF1 may be a potential biomarker or therapeutic target in patients with GIST.
Note: In This Issue is written by Cancer Discovery editorial staff. Readers are encouraged to consult the original articles for full details.