BRAF-mutant Cancer Research Articles

Discovery of novel diaryl urea-oxindole hybrids as BRAF kinase inhibitors targeting BRAF and KRAS mutant cancers

In the current study, a novel series of diaryl urea incorporating oxindole moiety was rationally designed as type II BRAF inhibitors targeting BRAF and KRAS mutant cancers. Molecular hybridization between the diaryl urea scaffold which binds to the inactive conformation of protein kinases on one side and the oxindole core which exhibit adenine mimic properties to be settled in the hinge region on the other side was performed. Studying the antiproliferative activity of the synthesized candidates 9a-t on NCI cancer cell lines showed that they exhibit potent and broad spectrum of antiproliferative activity on the tested cancer cell lines with compounds 9c, 9p, 9q, 9s, and 9t demonstrating potent GI50 reaching 0.01 µM. Noteworthy, compound 9s demonstrated a potent GI50 on cell lines expressing mutant KRAS and those express BRAFV600E with GI50 ranges of 1.79 and 7.94 µM and 1.68 to 2.0 µM, respectively. Further analysis on A375 and Mel501 cell lines expressing BRAFV600E revealed that compound 9s has a potent growth inhibitory activity with IC50 of 0.7 and 1.5 µM, respectively, in reference to sorafenib (IC50 = 8.7 and 0.3 µM, respectively). Additionally, nearly all the target candidates did not show any cytotoxic effect on the normal fibroblast cell line BJ-1 with compound 9s showing IC50 of 20.2 µM in reference to sorafenib (IC50 = 6.1 µM). Further cellular assays on A375 cell line, revealed the ability of compound 9s to halt the cell cycle progression at the G2 phase besides its ability to induce apoptosis. In parallel, all the synthesized candidates 9a-t were biochemically evaluated for their inhibitory activity on BRAFWT and compounds 9b, 9c, and 9n revealed a sub-micromolar IC50 of 0.11, 0.84 and 0.80 µM, respectively. Further investigation of selected compounds on BRAFV600E showed that compounds 9c, 9n, 9s, and 9t exhibit a sub-micromolar IC50 range of 0.17 to 0.89 µM. Noteworthy, the examined candidates demonstrated a higher selectively towards BRAFV600E over BRAFWT highlighting their promising optimization for treating BRAFV600E expressing cancers. Molecular docking and molecular dynamics simulations in the inactive DFG-out kinase domain of BRAFWT/V600E protein kinases confirmed the planned design strategy.

Alantolactone enhances the sensitivity of melanoma to MAPK pathway inhibitors by targeting inhibition of STAT3 activation and down-regulating stem cell markers

Mitogen-activated protein kinase inhibitors (MAPKi) were the first line drugs for advanced melanoma patients with BRAF mutation. Targeted therapies have significant therapeutic effects; however, drug resistance hinders their long-term efficacy. Therefore, the development of new therapeutic strategies against MAPKi resistance is critical. Our previous results showed that MAPKi promote feedback activation of STAT3 signaling in BRAF-mutated cancer cells. Studies have shown that alantolactone inhibited the activation of STAT3 in a variety of tumor cells. Our results confirmed that alantolactone suppressed cell proliferation and promoted apoptosis by inhibiting STAT3 feedback activation induced by MAPKi and downregulating the expression of downstream Oct4 and Sox2. The inhibitory effect of alantolactone combined with a MAPKi on melanoma cells was significantly stronger than that on normal cells. In vivo and in vitro experiments showed that combination treatment was effective against drug-resistant melanomas. Our research indicates a potential novel combination therapy (alantolactone and MAPKi) for patients with BRAF-mutated melanoma.

Protein phosphatase 6 activates NF-κB to confer sensitivity to MAPK pathway inhibitors in KRAS- and BRAF-mutant cancer cells.

The Ras-mitogen-activated protein kinase (MAPK) pathway is a major target for cancer treatment. To better understand the genetic pathways that modulate cancer cell sensitivity to MAPK pathway inhibitors, we performed a CRISPR knockout screen with MAPK pathway inhibitors on a colorectal cancer (CRC) cell line carrying mutant KRAS. Genetic deletion of the catalytic subunit of protein phosphatase 6 (PP6), encoded by PPP6C, rendered KRAS- and BRAF-mutant CRC and BRAF-mutant melanoma cells more resistant to these inhibitors. In the absence of MAPK pathway inhibition, PPP6C deletion in CRC cells decreased cell proliferation in two-dimensional (2D) adherent cultures but accelerated the growth of tumor spheroids in 3D culture and tumor xenografts in vivo. PPP6C deletion enhanced the activation of nuclear factor κB (NF-κB) signaling in CRC and melanoma cells and circumvented the cell cycle arrest and decreased cyclin D1 abundance induced by MAPK pathway blockade in CRC cells. Inhibiting NF-κB activity by genetic and pharmacological means restored the sensitivity of PPP6C-deficient cells to MAPK pathway inhibition in CRC and melanoma cells in vitro and in CRC cells in vivo. Furthermore, a R264 point mutation in PPP6C conferred loss of function in CRC cells, phenocopying the enhanced NF-κB activation and resistance to MAPK pathway inhibition observed for PPP6C deletion. These findings demonstrate that PP6 constrains the growth of KRAS- and BRAF-mutant cancer cells, implicates the PP6-NF-κB axis as a modulator of MAPK pathway output, and presents a rationale for cotargeting the NF-κB pathway in PPP6C-mutant cancer cells.

The ERK inhibitor GDC-0994 selectively inhibits growth of BRAF mutant cancer cells

BRAF or RAS mutation-induced aberrant activation of the mitogen-activated protein kinase (MAPK) pathway is frequently observed in human cancers. As the key downstream node of MAPK pathway, ERK1/2 is as an important therapeutic target. GDC-0994 (ravoxertinib), an orally bioavailable, highly selective small-molecule inhibitor of ERK1/2, showed acceptable safety and pharmacodynamic profile in a recent phase I clinical trial. In this study, we investigated dependence of the anti-tumor effect of ERK inhibitor GDC-0994 on genetic alterations in the MAPK pathway. The results showed that GDC-0994 sharply inhibited cell proliferation and colony formation and induced remarkable G1 phase cell-cycle arrest in cancer cells harboring BRAF mutation but had little effect on cell behaviors in most RAS mutant or wild-type cell lines. The expression of a large number of genes, particularly the genes in the cell cycle pathway, were significantly changed after GDC-0994 treatment in BRAF mutant cells, while no remarkable expression change of such genes was observed in wild-type cells. Moreover, GDC-0994 selectively inhibited tumor growth in a BRAF mutant xenograft mice model. Our findings demonstrate a BRAF mutation-dependent anti-tumor effect of GDC-0994 and provide a rational strategy for patient selection for ERK1/2 inhibitor treatment.

A Next-Generation BRAF Inhibitor Overcomes Resistance to BRAF Inhibition in Patients with BRAF-Mutant Cancers Using Pharmacokinetics-Informed Dose Escalation.

RAF inhibitors have transformed treatment for patients with BRAFV600-mutant cancers, but clinical benefit is limited by adaptive induction of ERK signaling, genetic alterations that induce BRAFV600 dimerization, and poor brain penetration. Next-generation pan-RAF dimer inhibitors are limited by a narrow therapeutic index. PF-07799933 (ARRY-440) is a brain-penetrant, selective, pan-mutant BRAF inhibitor. PF-07799933 inhibited signaling in vitro, disrupted endogenous mutant-BRAF:wild-type-CRAF dimers, and spared wild-type ERK signaling. PF-07799933 ± binimetinib inhibited growth of mouse xenograft tumors driven by mutant BRAF that functions as dimers and by BRAFV600E with acquired resistance to current RAF inhibitors. We treated patients with treatment-refractory BRAF-mutant solid tumors in a first-in-human clinical trial (NCT05355701) that utilized a novel, flexible, pharmacokinetics-informed dose escalation design that allowed rapid achievement of PF-07799933 efficacious concentrations. PF-07799933 ± binimetinib was well-tolerated and resulted in multiple confirmed responses, systemically and in the brain, in patients with BRAF-mutant cancer who were refractory to approved RAF inhibitors. Significance: PF-07799933 treatment was associated with antitumor activity against BRAFV600- and non-V600-mutant cancers preclinically and in treatment-refractory patients, and PF-07799933 could be safely combined with a MEK inhibitor. The novel, rapid pharmacokinetics (PK)-informed dose escalation design provides a new paradigm for accelerating the testing of next-generation targeted therapies early in clinical development.

Abstract CT178: Phase 1 trial of PF-07799933 (ARRY-440), a next-generation BRAF inhibitor, for BRAF-mutant cancers

Abstract BACKGROUND Approved BRAF inhibitors (BRAFi) have transformed the treatment of BRAF V600-mutant cancers. However, clinical benefit is limited by BRAF dimer-promoting resistance mutations, toxicity from paradoxical activation of signaling in BRAF wild-type cells, and poor brain penetration. Further, current RAF inhibitors are ineffective against non-V600 BRAF mutants. Next-generation agents that cause pan-RAF inhibition may more broadly target BRAF mutants but are limited by a narrow therapeutic index. PF-07799933 (ARRY-440) is a brain-penetrant BRAF-selective monomer/dimer inhibitor that spares ARAF and CRAF. METHODS We characterized PF-07799933 in patient (pt)-derived BRAF-mutant cancer cells in vitro and in vivo. We investigated PF-07799933 in pts with refractory BRAF-mutant solid tumors using a novel first-in-patient phase 1 design that enabled flexible, rapid dose escalation based on safety and pharmacokinetics (PK) assessments. RESULTS PF-07799933 inhibited signaling in vitro, disrupted BRAF-containing homo- and heterodimers, and caused less paradoxical signaling than approved agents. PF-07799933 alone and in combination with binimetinib inhibited tumor growth systemically and in the brain in mouse xenografts harboring de novo and acquired BRAF dimer-forming mutations. As of August 24, 2023 data cutoff, 30 pts with BRAF-mutant cancers started PF-07799933 treatment at 50 mg QD-450 mg BID as monotherapy (60%) or combination with binimetinib (27%) or cetuximab (all colorectal cancer [CRC]) (13%). Tumor types were melanoma (mel) (43%), CRC (17%), primary brain (PBT) (13%), thyroid (10%), and other (n=1/3% each). BRAF mutations were class I (V600E) (73%), Class II (13%), and class III (13%). All BRAF V600E+ cancer pts were previously treated with ≥1 approved BRAFi and all BRAF V600E+ mel pts also were previously treated with ≥1 immune checkpoint inhibitor. PF-07799933 was well-tolerated as monotherapy or combination. There were no DLTs and the MTD was not reached. Treatment-emergent adverse events (TEAEs) in ≥3 pts for monotherapy were fatigue (any grade 44%/grade ≥3 0%), headache (28%/0%), vision blurred (22%/6%), and lipase increased (16%/0%). The most common TEAEs for combination were peripheral edema (33%/0%), acneiform rash, diarrhea, and fatigue (each 28%/0%). The AE profile was consistent with less paradoxical signaling activation. PK-guided dose escalation enabled PF-07799933 efficacious concentrations to be reached by dose level 3 (225 mg BID), together with multiple confirmed responses in BRAF V600E+ cancer pts (n=4/7 at 225 mg BID ± binimetinib, includes 1 complete response [CR] in a BRAF V600E+ PBT pt) systemically, in the brain, and all after failure of approved BRAF inhibitors. A 5th confirmed response (2nd BRAF V600E+ PBT pt) occurred after data cutoff. This includes, to our knowledge, the first evidence of efficacy in a BRAF V600E+ pt with a dimerizing BRAF splice variant. A BRAF G466E+ (class III) adenoid cystic carcinoma pt had a molecular CR in ctDNA. CONCLUSION PF-07799933 treatment was associated with anti-tumor activity against BRAF V600- and non-V600-mutant cancers preclinically and in treatment-refractory pts. The novel, rapid PK-informed dose escalation design provides a new paradigm for accelerating testing of next-generation targeted therapies early in clinical development. TRIAL REGISTRATION NUMBER NCT05355701 Citation Format: Rona Yaeger, Meredith McKean, Rizwan Haq, Joseph T. Beck, Matthew H. Taylor, Jonathan Cohen, Daniel Bowles, Shirish M. Gadgeel, Catalin Mihalcioiu, Kyriakos P. Papadopoulos, Eli L. Diamond, Keren B. Sturtz, Gang Feng, Stefanie K. Drescher, Micaela B. Reddy, Bhaswati Sengupta, Arnab K. Maity, Suzy A. Brown, Anurag Singh, Eric N. Brown, Brian R. Baer, Jim Wong, Tung-Chung Mou, Wen I. Wu, Dean Kahn, Sunyana Gadal, Neal Rosen, John J. Gaudino, Patrice A. Lee, Dylan P. Hartley, Stephen Michael Rothenberg. Phase 1 trial of PF-07799933 (ARRY-440), a next-generation BRAF inhibitor, for BRAF-mutant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT178.

Abstract 4972: Bioinformatic analysis of an annotated genomic database is clinically useful in a private cancer center

Abstract Background: Sequencing of patient solid tumor tissue is not a common service provided by community cancer centers. Our community cancer center has collected and sequenced over 5,000 tumor tissue samples from patients with various types of cancer. Since April 2019, we have conducted whole-exome and whole-transcriptome sequencing and stored this data in an internal genomics database. To analyze large patient cohorts, we must first optimize bioinformatic workflows on a smaller scale, which can then be applied to studies of larger populations. Previous studies have shown BRAF mutations are associated with an increased activation of the mitogen-activated protein kinase (MAPK) pathway. We analyzed transcriptomes of a cohort of 30 patients with thyroid cancer, 15 with V600E BRAF mutations and 15 wild-type for BRAF, for MAPK Pathway Activation Scores (MPAS). MPAS serves as a transcriptomic measure of the activation state of the MAPK pathway and has been shown to be a reliable prognostic biomarker of MAPK activity. Method: We conducted a retrospective analysis of data from FFPE tumor samples sent to a commercial CLIA-certified laboratory from April 2019 to October 2023. Samples were profiled by whole exome, whole transcriptome sequencing and immunohistochemistry (IHC). Whole transcriptome sequencing (WTS) was executed using Illumina NovaSeq along with the Agilent SureSelect Human All Exon V7 bait panel. Resulting data were reported in transcripts per million (TPM) using the Salmon expression pipeline. MPAS was calculated using the expression profile of 10 MAPK-associated genes. Results: There was no significant difference in BRAF expression levels or MAPK activation between patients with BRAF mutant and BRAF wild-type thyroid cancer (median MPAS scores: -0.09 vs. 0.11, p=0.9). This analysis workflow will be repeated with a larger patient population of patients with melanoma in the future; however, the consistency of expression between the groups, the rank-order, and the low variability per group suggest that expression changes related to this BRAF mutation may occur upstream or via differential regulation of an indirect pathway. Rank-order statistics and percentiles become more precise as data per tumor type grows. Conclusions: Our community cancer center began building an internal genomics database including whole-exome and whole-transcriptome sequencing since 2019. This resource facilitates analysis of patient samples for tumor mutational burden, gene fusions, transcriptomic data, and other important characteristics which could reveal patterns or trends that inform cancer diagnosis and prognosis of other patients. Analysis of expression data for patients with advanced solid tumors who have mutations in genes of interest could inform on potential targeted treatments in the future. This study represents a single example of the potential of our internal clinically annotated genomics database. Citation Format: Carlos E. Zuazo, Sourat Darabi, David R. Braxton, Phillip Stafford, Michael J. Demeure. Bioinformatic analysis of an annotated genomic database is clinically useful in a private cancer center [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4972.

Abstract 7363: Clinical, genomic, transcriptomic and immunologic profile of BRAF mutant colorectal tumors

Abstract Background: Colorectal cancer (CRC) is the second leading cause of cancer-related death worldwide. BRAF, a protein kinase of the Mitogen-Activated Protein Kinase (MAPK) pathway, is mutated in 12% of colorectal cancers and is a poor prognostic factor for patients. BRAF mutations at the V600 codon are most studied but non-V600 BRAF mutations also exist and behave differently. BRAF V600 CRC treated with BRAF+MEK inhibitors show 12% response rates while we observe 65% response rates in BRAF V600 Melanoma. Additionally, no approved targeted therapies exist for non-V600 BRAF mutant cancers and retrospective studies show poorer PFS with BRAF+MEK inhibitors vs BRAF V600 cancers. We interrogated publicly available data of BRAF mutant CRC to uncover differences in the tumor microenvironment and signalling pathways of BRAF V600 and non-V600 tumors in hopes of uncovering better treatments. Methods: We analyzed the clinical and genomic profile of BRAF mutant CRC tumors from the GENIE v12 data. Gene Set Enrichment Analysis was performed on RNAseq from the TCGA data (discovery cohort) and the combined data from CPTAC and Sidra-LUMC data (validation cohort). We investigated the composition of tumor infiltrating immune cells using CIBERSORTx (deconvolution algorithm for bulk RNAseq). Results: Non-V600 mutations (n=219/1061) were most represented in patients of Asian or Black race compared to White patients (p<0.0001) and importantly, were found in younger patients (p<0.0001). We identified n=67 and n=74 BRAF mutant RNAseq samples in the discovery and validation cohorts, respectively. In the discovery cohort: BRAF V600 CRC were enriched for Interferon Gamma Signaling, Complement pathway, and IL6 JAK STAT3 Signaling (p<0.05) while the non-V600 BRAF mutant CRC showed an enrichment for Wnt-beta Catenin, Notch, and Hedgehog Signaling pathways (p<0.05). In the validation cohorts these same pathways were enriched in V600 and non-V600 BRAF mutant tumors. Interestingly, enrichment of genes co-mutated (GENIE data) in non-V600 BRAF mutant CRC also revealed the Wnt pathway. Non-V600 CRC tumors have a higher proportion of M0 macrophages (p=0.0035) and CD4 memory resting T cells (p<0.0001) while patients with V600 CRC have higher proportions of CD8 T cells (p=0.006) and activated mast cells (p=0.0341). Conclusion: No optimal therapeutic strategies have been defined for these potentially actionable non-V600 BRAF mutant CRCs. By exploring the multi-omic landscape of these tumors we have identified unique characteristics of non-V600 BRAF mutant CRC that could be therapeutically exploited. Citation Format: Emmanuelle Rousselle, Suzanne Kazandjian, April Rose. Clinical, genomic, transcriptomic and immunologic profile of BRAF mutant colorectal tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7363.

Abstract 5063: Exploring the mutational landscape of KRAS and NRAS in tumors with non-V600 BRAF mutations

Abstract Background: BRAF, a key modulator of the Mitogen-Activated Protein Kinase (MAPK) pathway, is observed in 7% of all cancers. Therapeutic response to MAPK inhibition (MAPKi) often relies on molecular distinctions between members of varying classes: Class 1 (V600), Class 2 and 3 (non-V600) BRAF mutants. Preliminary data indicates that co-occurring RAS mutations in non-V600 BRAF mutant cancers are less responsive to MAPKi treatment. This emphasizes the need to investigate the characteristics of RAS co-mutations in non-V600 BRAF mutant tumors. Methods: Genomic data was obtained from a cohort of 183,292 patients provided by the AACR GENIE database (v14.1). Patient samples were clustered according to their BRAF mutation status and co-occurring K/NRAS mutations: WT BRAF (n=60,845) vs. non-V600 BRAF (n=1009). Samples were grouped based on cancer type: melanoma (n=3841), colorectal (n=15,434), and non-small cell lung cancer (n=14640) and were further categorized according to key biochemical features of RAS GTPase function and overall GTPase activity. Results: This dataset revealed a diverse array of allelic variants of K/NRAS between cancer types and their underlying BRAF mutation status (Table 1). Non-V600 BRAF mutant cancers showed an enrichment for KRAS mutations linked to amplified nucleotide exchange (37.9% vs. 13.4%; p<0.0001) and hydrolysis-impairing NRAS mutations (41.9% vs. 23%; p<0.0001), compared to WT BRAF cancers. Rare allelic variants including KRAS L19F, KRAS A146T, and NRAS G60E were seen in Class 2/3 BRAF mutants. Conclusion: This data suggests that non-V600 BRAF mutant tumors are characterized by a unique distribution of RAS mutations. More research into the difference in downstream effectors of RAS mutants overrepresented in non-V600 BRAF mutant tumors could provide important insights into how these tumors develop and resist targeted therapies. Table 1. Classification of KRAS and NRAS mutations in WT BRAF vs. non-V600 BRAF mutant tumors GTPase Function Cancer Type All cancers NSCLC Colorectal Melanoma BRAF mutation WT non-V600 p-value WT non-V600 p-value WT non-V600 p-value WT non-V600 p-value KRASmutation class Impaired hydrolysis n=20731 (79.8%) n=167 (51.9%) <0.0001 n=6068 (86.1%) n=60 (56.6%) <0.0001 n=4799 (68.2%) n=16 (29.1%) <0.0001 n=38 (48.1%) n=13 (50.0%) 0.4047 Nucleotide Exchange n=3475 (13.4%) n=122 (37.9%) n=530 (7.5%) n=36 (34.0%) n=1842 (26.2%) n=36 (65.5%) n=30 (38.0%) n=12 (46.2%) Hybrid n=1765 (6.8%) n=33 (10.2%) n=446 (6.3%) n=10 (9.4%) n=395 (5.6%) n=3 (5.5%) n=11 (13.9%) n=1 (3.8%) NRAS mutation class Impaired hydrolysis n = 974 (23.0%) n=78 (41.9%) <0.0001 n=29 (18.7%) n=9 (39.1%) 0.0196 n=188 (32.6%) n=17 (68.0%) <0.0001 n=86 (5.5%) n=22 (27.8%) <0.0001 Nucleotide Exchange n=459 (10.8%) n=22 (11.8%) n=5 (3.2%) n=2 (8.7%) n=48 (8.3%) n=4 (16.0%) n=93 (5.9%) n=10 (12.7%) Hybrid n=2811 (66.2%) n=86 (46.2%) n=121 (78.1%) n=12 (52.2%) n=341 (59.1%) n=4 (16.0%) n=1385 (88.6%) n=47 (59.5%) GTPase Activity BRAF mutation WT non-V600 p-value WT non-V600 p-value WT non-V600 p-value WT non-V600 p-value KRASmutation class Intermediate activity n=14408 (55.3%) n=142 (44.4%) 0.0001 n=5082 (72.3%) n=54 (50.5%) <0.0001 n=3540 (49.9%) n=17 (31.5%) 0.0089 n=46 (56.8%) n=13 (50.0%) 0.6516 High activity n=11630 (44.7%) n=178 (55.6%) n=1947 (27.7%) n=53 (49.5%) n=3552 (50.1%) n=37 (68.5%) n=35 (43.2%) n=13 (50.0%) NRAS mutation class Intermediate activity n=1364 (32.2%) n=101 (55.8%) <0.0001 n=36 (23.4%) n=12 (54.5%) 0.0041 n=239 (41.8%) n=20 (87.0%) <0.0001 n=190 (12.3%) n=34 (43.0%) <0.0001 High activity n=2868 (67.8%) n=80 (44.2%) n=118 (76.6%) n=10 (45.5%) n=333 (58.2%) n=3 (13.0%) n=1357 (87.7%) n=45 (57.0%) Citation Format: Chantel L. Mukonoweshuro, Emmanuelle Rousselle, April A. Rose. Exploring the mutational landscape of KRAS and NRAS in tumors with non-V600 BRAF mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5063.

Abstract 4100: AMP-peptide vaccination against mutant BRAF epitopes promotes lymph node delivery to generate potent, functional T cell immunity

Abstract Background Mutations in BRAF cause ~8% of human cancers[1]. Nonetheless, therapies designed to promote immune responses against mutated BRAF (mBRAF) have led to limited clinical success[2], despite evidence confirming T cell recognition of these mutations[3,4]. The Amphiphile (AMP) platform improves the potency of vaccine immunotherapy by programming the delivery of vaccine components to the lymph nodes where efficient uptake by resident immune cells initiates tumor-targeted immune responses. AMP-modification of vaccine components including peptide antigens and molecular adjuvants results in covalent conjugation to albumin-binding lipids. Upon injection, AMP-vaccines associate with tissue resident albumin which efficiently distributes to draining lymph nodes. This approach was shown to promote activation of polyfunctional, cytotoxic T cells with promising safety, and improved clinical outcomes in a Phase 1 trial of ELI-002, an mKRAS AMP therapeutic vaccine (AMPLIFY-201 NCT04853017). Application of this strategy to prevalent BRAF mutations with ELI-007 offers the potential for improved therapeutic activity in a setting of significant unmet need, as BRAF inhibitors benefit only a fraction of patients, with near universal progression. Methods Following multi-dose immunization of C57BL/6J mice with AMP-modified or soluble comparator vaccines consisting of mBRAF V600E/K peptides and CpG adjuvant, immunological readouts were performed 7 days after dosing. Antigen-specific T cell responses were assessed after ex vivo re-stimulation of cells with mBRAF overlapping peptides. Assays included analysis of antigen-specific T cell frequencies, multiplexed proteomics determining polyfunctionality, and effector function and cytotoxic potential evaluation. Responses were determined in secondary lymphoid tissues (spleen), as well as lung, to which many BRAF driven cancers metastasize. Results AMP-immunization generated robust in vivo immune responses yielding strong T cell activation against mBRAF epitopes. Non-lymph node targeted vaccination using soluble comparators were inactive with no response above mock treated mice. Responses to AMP-vaccination were characterized by the generation of significantly increased frequency of Th1-skewed, polyfunctional T cells (IFNγ, TNFα, IL2) specific to mBRAF V600E and V600K. Induced T cells further exhibited mBRAF-specific cytotoxic function. Conclusions AMP-conjugation enhances efficient delivery directly to the lymph nodes and thus improves the immunogenicity of peptide vaccination. These enhanced immune responses provide an encouraging therapeutic opportunity to treat >90% of BRAF-mutated cancers[5] with the AMP-mBRAF vaccine, ELI-007. Moreover, the AMP-platform technology is simple, rapidly executable, and scalable, promising broad clinical off-the-shelf application for BRAF. Citation Format: Martin P. Steinbuck, Xavier Cabana-Puig, Erica Palmer, Mimi M. Jung, Thomas Williams, Kristen Osaer, Jeff Zhang, Christopher M. Haqq, Peter C. DeMuth. AMP-peptide vaccination against mutant BRAF epitopes promotes lymph node delivery to generate potent, functional T cell immunity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4100.

Mutations in the Serine/Threonine Kinase BRAF: Oncogenic Drivers in Solid Tumors.

Since their discovery in 2002, BRAF mutations have been identified as clear drivers of oncogenesis in several cancer types. Currently, their incidence rate is nearly 7% of all solid tumors with BRAF V600E constituting approximately 90% of these diagnoses. In melanoma, thyroid cancer, and histiocytic neoplasms, BRAF hotspot mutations are found at a rate of about 50%, while in lung and colorectal cancers they range from 3% to 10% of reported cases. Though present in other malignancies such as breast and ovarian cancers, they constitute a small portion of diagnoses (<1%). Given their frequency along with advancements in screening technologies, various methods are used for the detection of BRAF-mutant cancers. Among these are targeted next-generation sequencing (NGS) on tumor tissue or circulating tumor DNA (ctDNA) and immunohistochemistry (IHC)-based assays. With advancements in detection technologies, several approaches to the treatment of BRAF-mutant cancers have been taken. In this review, we retrace the milestones that led to the clinical development of targeted therapies currently available for these tumors.

Case reports of BRAF V600E-mutated tumors effectively treated using the agnostic approach

A tumor-agnostic approach to cancer treatment that implies the selection of agents targeting specific genetic aberrations and signaling pathways regardless of the tumor site of origin represents a new direction in personalized oncology. Pembrolizumab is the first therapy approved for unresectable microsatellite instability-high (MSI-H) tumors of any location. In 2022, the combination of dabrafenib and trametinib was approved by the US Food and Drug Administration (FDA) for the treatment of patients with solid tumors harboring BRAF V600E mutations. Melanomas, colorectal cancers, and non-small cell lung cancers are BRAF-mutated in 60 %, 15 %, and 5–8 % of cases, respectively. BRAF-mutated glioblastoma (3 %), cholangiocarcinoma (5–7 %), pancreatic cancer (1–16 %), and Langerhans cell histiocytosis (57 %) have also been reported.We present two case reports of BRAF-mutated salivary gland and pancreatic cancers in patients with progressive disease despite standard-of-care therapy who were treated with a combination of dabrafenib and trametinib according to the agnostic approach.The presented case reports have demonstrated that the agnostic approach and treatment with BRAF / MEK inhibitors stabilize the disease in patients with BRAF-positive cancers, including those with multiple metastases, and represent an additional therapeutic option for patients with rare BRAF-mutated cancers for which very few pharmacologic options are available.

Role and Function of Receptor Tyrosine Kinases in BRAF Mutant Cancers

Role and Function of Receptor Tyrosine Kinases in BRAF Mutant Cancers

BRAF - a tumour-agnostic drug target with lineage-specific dependencies.

In June 2022, the FDA granted Accelerated Approval to the BRAF inhibitor dabrafenib in combination with the MEK inhibitor trametinib for the treatment of adult and paediatric patients (≥6 years of age) with unresectable or metastatic BRAFV600E-mutant solid tumours, except for BRAFV600E-mutant colorectal cancers. The histology-agnostic approval of dabrafenib plus trametinib marks the culmination of two decades of research into the landscape of BRAF mutations in human cancers, the biochemical mechanisms underlying BRAF-mediated tumorigenesis, and the clinical development of selective RAF and MEK inhibitors. Although the majority of patients with BRAFV600E-mutant tumours derive clinical benefit from BRAF inhibitor-based combinations, resistance to treatment develops in most. In this Review, we describe the biochemical basis for oncogenic BRAF-induced activation of MAPK signalling and pan-cancer and lineage-specific mechanisms of intrinsic, adaptive and acquired resistance to BRAF inhibitors. We also discuss novel RAF inhibitors and drug combinations designed to delay the emergence of treatment resistance and/or expand the population of patients with BRAF-mutant cancers who benefit from molecularly targeted therapies.

A phase 1 study of triple-targeted therapy with BRAF, MEK, and AKT inhibitors for patients with BRAF-mutated cancers.

Aberrant PI3K/AKT signaling in BRAF-mutant cancers contributes to resistance to BRAF inhibitors. The authors examined dual MAPK and PI3K pathway inhibition in patients who had BRAF-mutated solid tumors (ClinicalTrials.gov identifier NCT01902173). Patients with BRAF V600E/V600K-mutant solid tumors received oral dabrafenib at 150mg twice daily with dose escalation of oral uprosertib starting at 50mg daily, or, in the triplet cohorts, with dose escalation of both oral trametinib starting at 1.5mg daily and oral uprosertib starting at 25mg daily. Dose-limiting toxicities (DLTs) were assessed within the first 56days of treatment. Radiographic responses were assessed at 8-week intervals. Twenty-seven patients (22 evaluable) were enrolled in parallel doublet and triplet cohorts. No DLTs were observed in the doublet cohorts (N=7). One patient had a DLT at the maximum administered dose of triplet therapy (dabrafenib 150mg twice daily and trametinib 2mg daily plus uprosertib 75mg daily). Three patients in the doublet cohorts had partial responses (including one who had BRAF inhibitor-resistant melanoma). Two patients in the triplet cohorts had a partial response, and one patient had an unconfirmed partial response. Pharmacokinetic data suggested reduced dabrafenib and dabrafenib metabolite exposure in patients who were also exposed to both trametinib and uprosertib, but not in whose who were exposed to uprosertib without trametinib. Concomitant inhibition of both the MAPK and PI3K-AKT pathways for the treatment of BRAF-mutated cancers was well tolerated, leading to objective responses, but higher level drug-drug interactions affected exposure to dabrafenib and its metabolites.

The Clinical, Genomic, and Transcriptomic Landscape of BRAF Mutant Cancers.

BRAF mutations are classified into four molecularly distinct groups, and Class 1 (V600) mutant tumors are treated with targeted therapies. Effective treatment has not been established for Class 2/3 or BRAF Fusions. We investigated whether BRAF mutation class differed according to clinical, genomic, and transcriptomic variables in cancer patients. Using the AACR GENIE (v.12) cancer database, the distribution of BRAF mutation class in adult cancer patients was analyzed according to sex, age, primary race, and tumor type. Genomic alteration data and transcriptomic analysis was performed using The Cancer Genome Atlas. BRAF mutations were identified in 9515 (6.2%) samples among 153,834, with melanoma (31%), CRC (20.7%), and NSCLC (13.9%) being the most frequent cancer types. Class 1 harbored co-mutations outside of the MAPK pathway (TERT, RFN43) vs. Class 2/3 mutations (RAS, NF1). Across all tumor types, Class 2/3 were enriched for alterations in genes involved in UV response and WNT/β-catenin. Pathway analysis revealed enrichment of WNT/β-catenin and Hedgehog signaling in non-V600 mutated CRC. Males had a higher proportion of Class 3 mutations vs. females (17.4% vs. 12.3% q = 0.003). Non-V600 mutations were generally more common in older patients (aged 60+) vs. younger (38% vs. 15% p < 0.0001), except in CRC (15% vs. 30% q = 0.0001). Black race was associated with non-V600 BRAF alterations (OR: 1.58; p < 0.0001). Class 2/3 BRAFs are more present in Black male patients with co-mutations outside of the MAPK pathway, likely requiring additional oncogenic input for tumorigenesis. Improving access to NGS and trial enrollment will help the development of targeted therapies for non-V600 BRAF mutations.

Enhanced SREBP2-driven cholesterol biosynthesis by PKCλ/ι deficiency in intestinal epithelial cells promotes aggressive serrated tumorigenesis

The metabolic and signaling pathways regulating aggressive mesenchymal colorectal cancer (CRC) initiation and progression through the serrated route are largely unknown. Although relatively well characterized as BRAF mutant cancers, their poor response to current targeted therapy, difficult preneoplastic detection, and challenging endoscopic resection make the identification of their metabolic requirements a priority. Here, we demonstrate that the phosphorylation of SCAP by the atypical PKC (aPKC), PKCλ/ι promotes its degradation and inhibits the processing and activation of SREBP2, the master regulator of cholesterol biosynthesis. We show that the upregulation of SREBP2 and cholesterol by reduced aPKC levels is essential for controlling metaplasia and generating the most aggressive cell subpopulation in serrated tumors in mice and humans. Since these alterations are also detected prior to neoplastic transformation, together with the sensitivity of these tumors to cholesterol metabolism inhibitors, our data indicate that targeting cholesterol biosynthesis is a potential mechanism for serrated chemoprevention.

Oncogenic BRAF noncanonically promotes tumor metastasis by mediating VASP phosphorylation and filopodia formation.

BRAF is frequently mutated in various cancer types and contributes to tumorigenesis and metastasis. As an important switch in RAS signaling pathway, BRAF typically enables the activation of MEK and ERK, and its mutation significantly promotes metastasis. However, whether BRAF could stimulate metastasis via a distinct manner is still unknown. Herein, we found that a portion of the BRAF protein localized at the plasma membrane and that the BRAFV600E mutation led to abundant formation of filopodia, which is a hallmark of invasive cancer cells. Mechanistically, BRAF physically interacts with the pseudopod formation-related protein Vasodilator-stimulated phosphoprotein (VASP), and BRAF specifically catalyzes VASP phosphorylation at Ser157. VASP depletion or disruption of Ser157 phosphorylation preferentially reduced the motility, invasion and metastasis of tumor cells harboring oncogenic BRAF or KRAS. Moreover, in clinical cancer tissues, BRAFV600E was positively correlated with the extent of invasion, and tissues with BRAFV600E expression exhibited elevated levels of VASP Ser157 phosphorylation. Our study therefor reveals a noncanonical mechanism by which oncogenic BRAF or KRAS promotes metastasis, suggests that VASP Ser157 phosphorylation might serve as a valuable therapeutic target in BRAF or KRAS mutant cancers.

A powerful drug combination strategy targeting BRAF-mutant melanoma.

3152 Background: BRAF inhibitors, such as vemurafenib and dabrafenib, are effective in treating patients with melanoma harboring (V600E) BRAF mutations. These drugs block the activity of the mutated BRAF protein, which impacts the development and progression of melanoma. Despite initial efficacy, drug resistance reliably occurs leading to disease relapse. Here we show how BRAF inhibitors cause metabolic reprogramming in melanoma cells to achieve drug resistance and promote cell survival. Previously we demonstrated that wild-type isocitrate dehydrogenase 1 (wtIDH1) supports mitochondrial function and maintains redox homeostasis in melanoma, and that an FDA-approved mutant IDH1 inhibitor, ivosidenib (AG-120), is actually a potent wtIDH1 inhibitor. Thus, we hypothesized that wtIDH1 inhibition would synergize with BRAF inhibition. Methods: Metabolomic profiling using LC-MS determined the impact of BRAF inhibition on cellular metabolism. Cell viability was assessed by PicoGreen in drug combination assays. Synergism was calculated using the Bliss-Independence dose-response model for drug interaction. In vivo modeling of AG-120 in combination with BRAF inhibition used melanoma cell xenografts in athymic nude mice for tumor volume analyses, and survival studies were performed in both immunocompetent C57BL/6J mice (murine YUMM1.7 cells) and immunocompromised athymic nude mice (human A375 cells). Results: Metabolomics data suggest that BRAF-mutated melanoma cells treated with BRAF inhibitors increased oxidative metabolism and mitochondrial dependence (i.e., survival adaptations). These alterations suggest an opportunity for mitochondrial inhibitors to improve drug efficacy. Targeting wtIDH1 with AG-120 in combination with dabrafenib significantly reduced melanoma cell viability. A positive synergy score and Bliss score greater than 1 indicate that the combined treatment was more effective in reducing cell viability than either treatment alone. Further, the combination of AG-120 and dabrafenib was the most effective in vivo, reducing tumor growth in the BRAF-mutated melanoma xenograft model, and improving mouse survival compared to monotherapy controls. Mice tolerated combination therapy with no reduction in body weight observed. Conclusions: Our findings indicate that dual inhibition of mutated BRAF and wild-type IDH1 represents a novel treatment strategy for BRAF-mutated melanomas, with potential for application to other BRAF-mutated cancers (e.g., colon, hepatobiliary, thyroid, etc.).

BRAF Inhibitors in Non-Small Cell Lung Cancer.

Simple SummaryThe identification of BRAF mutations in 1.5–3.5% of NSCLC patients represents a step forward towards new targeted agents for tackling NSCLC. The positive results and favourable safety profile observed with the combination of dabrafenib and trametinib for the treatment of BRAF V600E metastatic NSCLC patients, led to the approval of these two agents in this setting. In this review, we will discuss the clinical, prognostic and therapeutic implications of BRAF mutations in NSCLC patients. Moreover, we will review MEKs’ functions and their role as a potential targeted treatment, both alone and combined with anti-BRAF therapies. Finally, we will discuss ongoing studies and future perspectives in this field. The clinical research on BRAF inhibitors in NSCLC is just beginning, and a number of relevant questions remain to be addressed regarding the role of other BRAF inhibitors in NSCLC, the possibility of facing resistance mechanisms to BRAF inhibitors, and the efficacy of other therapeutic strategies for BRAF-mutated NSCLC.RAF family proteins are serine–threonine kinases that play a central role in the MAPK pathway which is involved in embryogenesis, cell differentiation, cell proliferation and death. Deregulation of this pathway is found in up to 30% of all human cancers and BRAF mutations can be identified in 1.5–3.5% of NSCLC patients. Following the positive results obtained through the combination of BRAF and MEK inhibitors in BRAF-mutant melanoma, the same combination was prospectively assessed in BRAF-mutant NSCLC. In cohort B of the BRF113928 trial, 57 pretreated NSCLC patients were treated with dabrafenib plus trametinib: an ORR of 68.4%, a disease control rate of 80.7%, a median PFS of 10.2 months and a median OS of 18.2 months were observed. Similar results were reported in the first-line setting (cohort C), with an ORR of 63.9%, a DCR of 75% and a median PFS and OS of 10.2 and 17.3 months, respectively. The combination was well tolerated: the main adverse events were pyrexia (64%), nausea (56%), diarrhoea (56%), fatigue (36%), oedema (36%) and vomiting (33%). These positive results led to the approval of the combination of dabrafenib and trametinib for the treatment of BRAF V600E metastatic NSCLC patients regardless of previous therapy. Ongoing research should better define the role of new generation RAF inhibitors for patients with acquired resistance, the activity of chemo-immunotherapy or the combination of TKIs with chemotherapy or with immunotherapy in patients with BRAF-mutated cancers.