Defining and Targeting BRAF Mutations in Solid Tumors

Concurrent Coprimary KIT Exon 17 and BRAF Mutations in a Small Intestinal GI Stromal Tumor-A Case Report

PURPOSE

Gastrointestinal stromal tumors (GISTs) are rare neoplasms driven by mutations in KIT, PDGFRA, or BRAF. Concomitant KIT/BRAF mutations are exceptionally rare and have historically been regarded as mutually exclusive. We report the first documented instance of a GIST with concurrent KIT exon 17 (D816H) and BRAF exon 15 (V600E) mutations, exploring the implications of these mutations for treatment and prognosis. KIT exon 17 mutations are rare and associated with imatinib resistance, and the literature on concurrent KIT/PDGFRA and BRAF mutations is limited, highlighting the potential of this case to provide valuable insights into the management of similar tumors.

METHODS

A 70-year-old woman presented with abdominal pain and a 20-year history of intermittent melena. Imaging and histopathological examination confirmed a duodenal GIST. The patient underwent en bloc tumor resection, and next-generation sequencing (NGS) identified co-occurring KIT exon 17 (D816H) and BRAF exon 15 (V600E) mutations. Postoperatively, the patient received adjuvant imatinib therapy for a planned duration of 3 years.

RESULTS

The patient tolerated adjuvant imatinib therapy well, experiencing only mild nausea and diarrhea. After 2 years of follow-up, no recurrence of the tumor was detected, and the patient remained in radiological remission with no signs of metastasis or tumor progression.

CONCLUSION

This case demonstrates a favorable outcome in a patient with localized GIST with concomitant KIT exon 17 and BRAF mutations following surgical resection with no evidence of recurrence. These findings underscore the significance of early comprehensive genotyping in GISTs to guide therapy and predict imatinib resistance.

Pancreatitis associated with BRAF inhibitors: a disproportionality analysis based on the Food and Drug Administration Adverse Event Reporting System

BACKGROUND

The relationship between the development of pancreatitis and the use of BRAF (B-Raf proto-oncogene, serine/threonine kinase) inhibitors remains incompletely understood, primarily due to the infrequency of such cases.

AIM

This study aimed to investigate the association between BRAF inhibitors and pancreatitis, and to describe the clinical characteristics of pancreatitis related to these agents.

METHOD

A disproportionality analysis was conducted using data from the Food and Drug Administration Adverse Event Reporting System between July 2011 and June 2024. The reporting odds ratio (ROR) and information component (IC) were employed to assess the association between BRAF inhibitors and pancreatitis. Additionally, subgroup analysis and time-to-onset analysis were further performed.

RESULTS

A total of 169 cases of pancreatitis were identified in association with BRAF inhibitors: 71 cases with vemurafenib, 63 with dabrafenib, and 35 with encorafenib. The median age of patients was 62 years. Vemurafenib, dabrafenib, and encorafenib all showed a positive signal for pancreatitis, with respective RORs and ICs as follows: vemurafenib (ROR 2.46, 95% CI 1.95-3.10; IC = 1.27, 95% CI 0.88-1.56), dabrafenib (ROR 1.56, 95% CI 1.22-2.00; IC = 0.63, 95% CI 0.21-0.93), and encorafenib (ROR 2.59, 95% CI 1.86-3.62; IC = 1.34, 95% CI 0.77-1.74). The shortest median time-to-onset for pancreatitis was observed with vemurafenib (6.5 days), followed by encorafenib (14.0 days) and dabrafenib (129.5 days).

CONCLUSION

This study reveals a significant reporting association between BRAF inhibitors and the development of pancreatitis, with a higher risk observed in the early stage of treatment.

Advances in Targeted and Systemic Therapy for Salivary Gland Carcinomas: Current Options and Future Directions

Salivary gland carcinomas (SGCs) represent a rare and heterogeneous group of malignancies accounting for 3-6% of all head and neck cancers. While surgical resection and radiotherapy remain the standard for locoregional control, systemic treatment is indicated for recurrent or metastatic disease. Advances in molecular profiling have identified actionable targets such as NTRK gene fusions, HER2, immune checkpoint regulators, androgen receptors, and RET receptors. These have facilitated the development of targeted therapies, including TRK inhibitors, HER2-directed agents, and androgen receptor modulators, as well as emerging combinations of immunotherapy and chemotherapy. Despite these advancements, challenges such as resistance mechanisms and limited therapeutic efficacy persist. Overall response rates remain relatively low across most systemic therapies, reflecting a persistent unmet clinical need. This review discusses the current landscape of treatment options and explores promising clinical trials and future directions to enhance outcomes for patients with SGCs.

Novel 5,6-dichlorobenzimidazole derivatives as dual BRAFWT and BRAFV600E inhibitors: design, synthesis, anti-cancer activity and molecular dynamics simulations

A new series of 1-substiuted-5,6-dichloro-2-(4-methoxyphenyl)-1H-benzo[d]imidazoles 10a-p was designed and synthesized to target both BRAFWT and BRAFV600E. The design strategy ensures that these derivatives would effectively occupy the ATP binding pocket of BRAFWT/V600E kinase domains and extend over the gate area interacting through hydrogen bonding with the surrounding key amino acids Glu500 and Asp593 and to finally occupy the allosteric hydrophobic back pocket. Some synthesized derivatives demonstrated impressive potency against BRAFWT with % inhibition approaching 91% at a concentration of 10 µM. The most potent candidate 10h demonstrated IC50 values of 1.72 and 2.76 µM on BRAFWT and BRAFV600E, respectively. At the same time, the synthesized benzimidazoles 10a-p were examined for their growth inhibitory activity on NCI-60 cancer cell lines. Again, compound 10h revealed a potent GI50 across a range of cancer cell lines. Moreover, it arrested cell cycle progression in HT29 colon cancer cell line at G2/M phase and induced apoptosis in the same cell line. Molecular dynamics simulations supported the validity of the design assumption, simultaneously, ADME prediction study displayed that the designed benzimidazoles exhibit promising physiochemical and drug-likeness properties as anticancer agents.

A Comprehensive Review of Advances in Molecular Mechanisms and Targeted Therapies for the Specific Type of Cystic Lung Cancer

BACKGROUND AND OBJECTIVE

Cystic lung cancer (CLC) presents diagnostic and treatment challenges due to its complex imaging features and unclear molecular mechanisms. Although surgery and standard chemotherapy are frequently used, there is limited information on targeted therapy and other precision treatments. It is crucial to comprehensively understand the molecular mechanisms and explore precision treatments based on targeted therapy.

METHODS

Topic keywords including "CLC", "cystic lung cancer", "cavitary lung cancer", "Lung cancer associated with cystic airspaces", and "lung cancer" with ("sac cavity" OR "cystic degeneration" OR "thin-walled cavity" OR "adenocystic carcinoma" OR "cystic airspaces" OR "pulmonary cysts" OR "adenoid cystic carcinoma") searched in the relevant databases, such as PubMed, Google Scholar, and CNKI (China National Knowledge Infrastructure). Then, we reviewed and analyzed the molecular mechanism and its precision therapeutics of CLC.

KEY CONTENT AND FINDINGS

Various subtypes of CLC can be identified through histopathological examination, such as cystic adenocarcinoma, and squamous cell carcinoma. However, we still have much to learn about the molecular mechanisms behind CLC. Gene mutation, the abnormal tumor microenvironment, and immune dysfunction are the main mechanisms, along with potential factors like epigenetic modifications and gene susceptibility related to COPD. Recent advancements in treatment include targeted therapies, such as targeted inhibitors for EGFR, ALK, ROS1, BRAF, and MET. Surgical treatment, standardized chemotherapy, immunotherapy, and combination therapy remain important. Future research should focus on genomic and molecular profiling, and the development of precision medicine based on insights into the heterogeneity of CLC. Additionally, investigating resistance mechanisms and developing predictive biomarkers are important for future CLC research.

CONCLUSION

The key molecular mechanisms of CLC involve gene mutations and TME immune dysfunction. CLC still requires standard comprehensive treatment based on lung cancer staging, and targeted therapy has shown significant advantages and development prospects.

Histone deacetylases in the regulation of cell death and survival mechanisms in resistant BRAF-mutant cancers

Small-molecule BRAF inhibitors (e.g., vemurafenib and dabrafenib) and MEK (MAPK/ERK) kinases inhibitors (e.g., trametinib) have distinctly improved the survival of patients suffering from BRAF-mutant cancers such as melanomas. However, the emergence of resistance to BRAF and MEK inhibitor-based melanoma therapy, as well as the reduced sensitivity of other BRAF-mutant cancers such as CRC, poses a considerable clinical problem. For instance, the reactivation of MAPK/ERK signaling hampering cell death induction mechanisms was responsible for BRAF inhibitor resistance, which can be correlated with distinct post-translational and epigenetic processes. Histone deacetylases (HDACs) are prominent epigenetic drug targets and some HDAC inhibitors have already been clinically approved for the therapy of various blood cancers. In addition, several HDACs were identified, which also play a crucial role in the drug resistance of BRAF-mutant cancers. Consequently, inhibition of HDACs was described as a promising approach to overcome resistance. This review summarizes the influence of HDACs (Zn2+-dependent HDACs and NAD+-dependent sirtuins) on BRAF-mutant cancers and BRAF inhibitor resistance based on upregulated survival mechanisms and the prevention of tumor cell death. Moreover, it outlines reasonable HDAC-based strategies to circumvent BRAF-associated resistance mechanisms based on downregulated cell death mechanisms.

A comprehensive review of targeting RAF kinase in cancer

RAF kinases, particularly the BRAF isoform, play a crucial role in the MAPK/ERK signaling pathway, regulating key cellular processes such as proliferation, differentiation, and survival. Dysregulation of this pathway often caused by mutations in the BRAF gene or alterations in upstream regulators like Ras and receptor tyrosine kinases contributes significantly to cancer development. Mutations, such as BRAF-V600E, are present in a variety of malignancies, with the highest prevalence in melanoma. Targeted therapies against RAF kinases have achieved substantial success, especially in BRAF-V600E-mutant melanomas, where inhibitors like vemurafenib and dabrafenib have demonstrated remarkable efficacy, leading to improved patient outcomes. These inhibitors have also shown clinical benefits in cancers such as thyroid and colorectal carcinoma, although to a lesser extent. Despite these successes, therapeutic resistance remains a major hurdle. Resistance mechanisms, including RAF dimerization, feedback reactivation of the MAPK pathway, and paradoxical activation of ERK signaling, often lead to diminished efficacy over time, resulting in disease progression or even secondary malignancies. In response, current research is focusing on novel therapeutic strategies, including combination therapies that target multiple components of the pathway simultaneously, such as MEK inhibitors used in tandem with RAF inhibitors. Additionally, next-generation RAF inhibitors are being developed to address resistance and enhance therapeutic specificity. This review discusses the clinical advancements in RAF-targeted therapies, with a focus on ongoing efforts to overcome therapeutic resistance and enhance outcomes for cancer patients. It also underscores the persistent challenges in effectively targeting RAF kinase in oncology.

Assessing Novel Antibody-Based Therapies in Reconstructive 3D Cell Models of the Tumor Microenvironment

Targeted, combinatorial, and immunomodulatory therapies, such as antibody-drug conjugates (ADCs) and immunomodulatory antibodies (Abs), are powerful weapons against tumor cells and immune cells within the tumor microenvironment (TME). Therefore, the evaluation of such therapies should be conducted in pre-clinical models able to recapitulate the complex cellular and molecular crosstalk of the TME. To build-in critical hallmarks of the TME, a breast cancer heterotypic 3D cell model (3D-3) is devised using a microencapsulation strategy with an inert biomaterial (alginate) and agitation-based cultures. Both stromal and immune components are added to multicellular tumor spheroids, therefore fostering cancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs) immunomodulatory interactions. The potential of the methodology to assess Ab-based therapies is then addressed by employing a series of anti-HER2-based ADCs. ADCs induced tumor-cell specific cytotoxicity toward HER2+ breast cancer spheroids while sparing HER2-negative CAFs. In addition, an immunomodulatory blocking Ab against colony-stimulating factor 1 receptor (CSF1R) decreases the expression of immunosuppressive and anti-inflammatory markers in TAMs, like what is previously observed upon in vivo α-CSF1R administration. Collectively, the human TME-based 3D-3 cell model is a suitable tool to evaluate the anti-tumor and immunomodulatory potential of novel antibody-based therapies directed against TME targets, such as cancer cells and macrophages.

Erdheim-Chester Disease With Eyelid and Orbital Involvement: A Review of Treatment Modalities at One Institution From 2014 to 2022

PURPOSE

To review all cases of Erdheim-Chester disease (ECD) with orbital involvement treated at Bascom Palmer Eye Institute in Miami, Florida from 2014 to 2022 and compare presentations, treatment modalities, and outcomes.

METHODS

A retrospective chart review of all patients diagnosed with ECD who presented to Bascom Palmer Eye Institute from 2014 to 2022 was performed. Data collected included demographics, pretreatment history and ophthalmic examination, pathology report, treatment, subsequent examination, and relevant laboratory results. Histopathology, treatments, and outcomes were reviewed and compared between patients.

RESULTS

Four cases were included. Primary treatments included vemurafenib (n = 2), cobimetinib (n = 1), and prednisone (n = 1). All patients demonstrated improvement of ophthalmic symptoms. Vemurafenib was the only medical treatment that was tolerated well and resulted in significant improvement in proptosis despite some reported dry eye; all other medications were discontinued due to intolerable side effects.

CONCLUSIONS

BRAF inhibitors such as vemurafenib have been used as novel therapy in the treatment of ECD. Vemurafenib demonstrated its utility in reducing proptosis in ECD patients at one ophthalmic institution. Vemurafenib may be a favorable treatment option for BRAF -positive ECD patients presenting with orbital disease.

Efficacy of trametinib in a metastatic urothelial carcinoma patient with a BRAF mutation

Introduction

BRAF mutations in bladder cancer are rare. MEK inhibitors have excellent clinical benefits in the treatment of melanoma.

Case presentation

A 60-year-old male was diagnosed with muscle-invasive bladder cancer and underwent total cystectomy and ileal conduit diversion. Despite 4 cycles of gemcitabine and cisplatin chemotherapy and 3 courses of pembrolizumab, the left obturator lymph node enlarged. Cancer multi-gene panel testing confirmed the BRAF G469A mutation and trametinib was recommended. Three months after the initiation of trametinib (2 mg, qd), the left obturator lymph node shrank by more than 50%. The disease has remained stable for more than 18 months.

Conclusion

The present case indicates the potential of trametinib to treat mBUC patients with the BRAF G469A mutation in this setting.

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.

Extracellular vesicles promote migration despite BRAF inhibitor treatment in malignant melanoma cells

Extracellular vesicles (EVs) constitute a vital component of intercellular communication, exerting significant influence on metastasis formation and drug resistance mechanisms. Malignant melanoma (MM) is one of the deadliest forms of skin cancers, because of its high metastatic potential and often acquired resistance to oncotherapies. The prevalence of BRAF mutations in MM underscores the importance of BRAF-targeted therapies, such as vemurafenib and dabrafenib, alone or in combination with the MEK inhibitor, trametinib. This study aimed to elucidate the involvement of EVs in MM progression and ascertain whether EV-mediated metastasis promotion persists during single agent BRAF (vemurafenib, dabrafenib), or MEK (trametinib) and combined BRAF/MEK (dabrafenib/trametinib) inhibition.Using five pairs of syngeneic melanoma cell lines, we assessed the impact of EVs - isolated from their respective supernatants - on melanoma cell proliferation and migration. Cell viability and spheroid growth assays were employed to evaluate proliferation, while migration was analyzed through mean squared displacement (MSD) and total traveled distance (TTD) measurements derived from video microscopy and single-cell tracking.Our results indicate that while EV treatments had remarkable promoting effect on cell migration, they exerted only a modest effect on cell proliferation and spheroid growth. Notably, EVs demonstrated the ability to mitigate the inhibitory effects of BRAF inhibitors, albeit they were ineffective against a MEK inhibitor and the combination of BRAF/MEK inhibitors. In summary, our findings contribute to the understanding of the intricate role played by EVs in tumor progression, metastasis, and drug resistance in MM.

Conformation selection by ATP-competitive inhibitors and allosteric communication in ERK2

Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named 'L' and 'R,' where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.

Importance of targeting various cell signaling pathways in solid cancers

Most adult human cancers are solid tumors prevailing in vital organs and lead to mortality all over the globe. Genetic and epigenetic alterations in cancer genes or genes of associated signaling pathways impart the most common characteristic of malignancy, that is, uncontrolled proliferation. Unless the mechanism of action of these cells signaling pathways (involved in cell proliferation, apoptosis, metastasis, and the maintenance of the stemness of cancer stem cells and cancer microenvironment) and their physiologic alteration are extensively studied, it is challenging to understand tumorigenesis as well as develop new treatments and precision medicines. Targeted therapy is one of the most promising strategies for treating various cancers. However, cancer is an evolving disease, and most patients develop resistance to these drugs by acquired mutations or mediation of microenvironmental factors or due to tumor heterogeneity. Researchers are striving to develop novel therapeutic options like combinatorial approaches targeting multiple responsible pathways effectively. Thus, in-depth knowledge of cell signaling and its components remains a critical topic of cancer research. This chapter summarized various extensively studied pathways in solid cancer and how they are targeted for therapeutic strategies.

Antitumor activity of the new tyrphostin briva against BRAFV600E-mutant colorectal carcinoma cells

Because of a reduced sensitivity of BRAF-mutant colorectal cancers to BRAF inhibitor treatment when compared with BRAF-mutant melanoma, it is essential to develop efficient drugs to cope with this disease. The new 2-(4-bromophenyl)-3-arylacrylonitrile compound Briva was prepared in one step from commercially available starting compounds. Briva and two known thiophene analogs (Thio-Iva and Thio-Dam) were tested for their cytotoxic activity against various tumor cell lines including colorectal and breast cancer cells. The antitumor activities of the test compounds were assessed in vitro via the MTT assay, DAPI staining of nuclei, RT-PCR and immunoblotting, wound healing, clonogenic assay, collagen I adhesion assay, and kinase inhibition assays. A selective activity of Briva was observed against BRAFV600E-mutant HT-29 and COLO-201 colorectal carcinoma (CRC) cells. Briva caused inhibition of HT-29 clonogenic tumor growth and was found to induce cytotoxicity by activating the intrinsic apoptosis pathway. In addition, Briva reduced HT-29 cell adhesion and migration. Kinase inhibition experiments revealed that Briva inhibits VEGFR2. Thus, Briva can be considered as a promising antitumor compound against BRAFV600E-mutant colon carcinoma by targeting VEGFR2 tyrosine kinase and consequently reducing cell adhesion and metastasis formation.

Conformation Selection by ATP-competitive Inhibitors and Allosteric Communication in ERK2

Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named "L" and "R", where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.

Development and clinical validation of a microfluidic-based platform for CTC enrichment and downstream molecular analysis

Background

Although many CTC isolation and detection methods can provide information on cancer cell counts, downstream gene and protein analysis remain incomplete. Therefore, it is crucial to develop a technology that can provide comprehensive information on both the number and profile of CTC.

Methods

In this study, we developed a novel microfluidics-based CTC separation and enrichment platform that provided detailed information about CTC.

Results

This platform exhibits exceptional functionality, achieving high rates of CTC recovery (87.1%) and purification (∼4 log depletion of WBCs), as well as accurate detection (95.10%), providing intact and viable CTCs for downstream analysis. This platform enables successful separation and enrichment of CTCs from a 4 mL whole-blood sample within 15 minutes. Additionally, CTC subtypes, selected protein expression levels on the CTC surface, and target mutations in selected genes can be directly analyzed for clinical utility using immunofluorescence and real-time polymerase chain reaction, and the detected PD-L1 expression in CTCs is consistent with immunohistochemical assay results.

Conclusion

The microfluidic-based CTC enrichment platform and downstream molecular analysis together provide a possible alternative to tissue biopsy for precision cancer management, especially for patients whose tissue biopsies are unavailable.

The Cytoprotective Role of Autophagy in Response to BRAF-Targeted Therapies

BRAF-targeted therapies are widely used for the treatment of melanoma patients with BRAF V600 mutations. Vemurafenib, dabrafenib as well as encorafenib have demonstrated substantial therapeutic activity; however, as is the case with other chemotherapeutic agents, the frequent development of resistance limits their efficacy. Autophagy is one tumor survival mechanism that could contribute to BRAF inhibitor resistance, and multiple studies support an association between vemurafenib-induced and dabrafenib-induced autophagy and tumor cell survival. Clinical trials have also demonstrated a potential benefit from the inclusion of autophagy inhibition as an adjuvant therapy. This review of the scientific literature relating to the role of autophagy that is induced in response to BRAF-inhibitors supports the premise that autophagy targeting or modulation could be an effective adjuvant therapy.

Mutational landscape of cancer-driver genes across human cancers

The genetic mutations that contribute to the transformation of healthy cells into cancerous cells have been the subject of extensive research. The molecular aberrations that lead to cancer development are often characterised by gain-of-function or loss-of-function mutations in a variety of oncogenes and tumour suppressor genes. In this study, we investigate the genomic sequences of 20,331 primary tumours representing 41 distinct human cancer types to identify and catalogue the driver mutations present in 727 known cancer genes. Our findings reveal significant variations in the frequency of cancer gene mutations across different cancer types and highlight the frequent involvement of tumour suppressor genes (94%), oncogenes (93%), transcription factors (72%), kinases (64%), cell surface receptors (63%), and phosphatases (22%), in cancer. Additionally, our analysis reveals that cancer gene mutations are predominantly co-occurring rather than exclusive in all types of cancer. Notably, we discover that patients with tumours displaying different combinations of gene mutation patterns tend to exhibit variable survival outcomes. These findings provide new insights into the genetic landscape of cancer and bring us closer to a comprehensive understanding of the underlying mechanisms driving the development of various forms of cancer.

BRAF v600E-mutant cancers treated with vemurafenib alone or in combination with everolimus, sorafenib, or crizotinib or with paclitaxel and carboplatin (VEM-PLUS) study

Combined BRAF + MEK inhibition is FDA approved for BRAF V600E-mutant solid tumors except for colorectal cancer. However, beyond MAPK mediated resistance several other mechanisms of resistance such as activation of CRAF, ARAF, MET, P13K/AKT/mTOR pathway exist among other complex pathways. In the VEM-PLUS study, we performed a pooled analysis of four phase one studies evaluating the safety and efficacy of vemurafenib monotherapy and vemurafenib combined with targeted therapies (sorafenib, crizotinib, or everolimus) or carboplatin plus paclitaxel in advanced solid tumors harboring BRAF V600 mutations. When vemurafenib monotherapy was compared with the combination regimens, no significant differences in OS or PFS durations were noted, except for inferior OS in the vemurafenib and paclitaxel and carboplatin trial (P = 0.011; HR, 2.4; 95% CI, 1.22-4.7) and in crossover patients (P = 0.0025; HR, 2.089; 95% CI, 1.2-3.4). Patients naïve to prior BRAF inhibitors had statistically significantly improved OS at 12.6 months compared to 10.4 months in the BRAF therapy refractory group (P = 0.024; HR, 1.69; 95% CI 1.07-2.68). The median PFS was statistically significant between both groups, with 7 months in the BRAF therapy naïve group compared to 4.7 months in the BRAF therapy refractory group (P = 0.016; HR, 1.80; 95% CI 1.11-2.91). The confirmed ORR in the vemurafenib monotherapy trial (28%) was higher than that in the combination trials. Our findings suggest that, compared with vemurafenib monotherapy, combinations of vemurafenib with cytotoxic chemotherapy or with RAF- or mTOR-targeting agents do not significantly extend the OS or PFS of patients who have solid tumors with BRAF V600E mutations. Gaining a better understanding of the molecular mechanisms of BRAF inhibitor resistance, balancing toxicity and efficacy with novel trial designs are warranted.

Cyanidin as potential anticancer agent targeting various proliferative pathways

A natural compound cyanidin, which is a type of anthocyanin present in pigmented leaves, fruits, and flowers; distributed widely in berries, apples, and oranges possess anticancer activities, thus curing various types of cancer such as breast, liver, lung, prostate, and thyroid cancer. The article provides an insight into the potential of using a single phytochemical, cyanidin to treat various cancer types including breast, liver, lung, prostate, and thyroid cancer. Information about cyanidin and its pharmacological impact on cancer was collected from books, scientific journals, and reports through electronic data search (Web of Science, Scifinder, PubMed, Scopus, Google Scholar, Elsevier, Springer, Wiley, ACS, Science Direct, CNKI as well as Kew Plants of the Word Online) and library. Cyanidin produces its effects against cancer probably by inhibiting (RAS, MAPK) and activating (caspases-3 and P-38) innovative molecular pathways. It may cause cell cycle arrest, cell differentiation processes and changes in redox status which trigger the cytotoxic chemotherapeutic effects. However, it also optimizes the chemotherapeutic targets which are cancer cells less responsive to chemotherapy. Cancer is considered the most widely spread disease and cyanidin from natural origin provides an essential role in treatment of cancer by approaching various mechanistic pathways.

Assessment of Two Commercial Comprehensive Gene Panels for Personalized Cancer Treatment

(1) Background: Analysis of tumor DNA by next-generation sequencing (NGS) plays various roles in the classification and management of cancer. This study aimed to assess the performance of two similar and large, comprehensive gene panels with a focus on clinically relevant variant detection and tumor mutation burden (TMB) assessment; (2) Methods: DNA from 19 diagnostic small cell lung cancer biopsies and an AcroMetrix™ assessment sample with >500 mutations were sequenced using Oncomine™ Comprehensive Assay Plus (OCAP) on the Ion Torrent platform and TruSight Oncology 500 Assay (TSO500) on the Illumina platform; (3) Results: OCAP and TSO500 achieved comparable NGS quality, such as mean read coverage and mean coverage uniformity. A total of 100% of the variants in the diagnostic samples and 80% of the variants in the AcroMetrix™ assessment sample were detected by both panels, and the panels reported highly similar variant allele frequency. A proportion of 14/19 (74%) samples were classified in the same TMB category; (4) Conclusions: Comparable results were obtained using OCAP and TSO500, suggesting that both panels could be applied to screen patients for enrolment in personalized cancer treatment trials.

The role of angiogenesis in melanoma: Clinical treatments and future expectations

The incidence of melanoma has increased rapidly over the past few decades, with mortality accounting for more than 75% of all skin cancers. The high metastatic potential of Melanoma is an essential factor in its high mortality. Vascular angiogenic system has been proved to be crucial for the metastasis of melanoma. An in-depth understanding of angiogenesis will be of great benefit to melanoma treatment and may promote the development of melanoma therapies. This review summarizes the recent advances and challenges of anti-angiogenic agents, including monoclonal antibodies, tyrosine kinase inhibitors, human recombinant Endostatin, and traditional Chinese herbal medicine. We hope to provide a better understanding of the mechanisms, clinical research progress, and future research directions of melanoma.

The Evolution of BRAF Activation in Non-Small-Cell Lung Cancer

Non-small-cell lung cancer (NSCLC) is the most common subtype of lung cancer, of which approximate 4% had BRAF activation, with an option for targeted therapy. BRAF activation comprises of V600 and non-V600 mutations, fusion, rearrangement, in-frame deletions, insertions, and co-mutations. In addition, BRAF primary activation and secondary activation presents with different biological phenotypes, medical senses and subsequent treatments. BRAF primary activation plays a critical role in proliferation and metastasis as a driver gene of NSCLC, while secondary activation mediates acquired resistance to other targeted therapy, especially for epidermal growth factor tyrosine kinase inhibitor (EGFR-TKI). Treatment options for different activation of BRAF are diverse. Targeted therapy, especially two-drug combination therapy, is an important option. Besides, immune checkpoint inhibitors (ICIs) would be another option since BRAF activation would be a positive biomarker of tumor response of ICIs therapy. To date, no high level evidences support targeted therapy or immunotherapy as prioritized recommendation. After targeted therapy, the evolution of BRAF includes the activation of the upstream, downstream and bypass pathways of BRAF. In this review, therapeutic modalities and post-therapeutic evolutionary pathways of BRAF are discussed, and future research directions are also provided.

Targeted therapies in the medical management of craniopharyngioma

Craniopharyngioma (CP) is an intracranial benign tumor that behaves aggressively due to its location, infiltration of the surrounding nervous tissue and high capacity for recurrence. Treatment of choice is surgery followed or not by radiotherapy. Recent advances in molecular biology techniques and the better understanding of the genetic alterations of the two histological types of CP have open new therapeutic perspectives with targeted drugs. Adamantinomatous CP (ACP) is associated with activating mutations of the CTNNB1 gene. Such mutations are accompanied by intracellular accumulation of β-catenin, an oncogenic protein that activates the intracellular Wnt/ β-catenin signaling pathway, which regulates the transcription of genes involved in cell proliferation. Therefore, the use of molecular therapies directed against the activation of the Wnt/ β-catenin pathway could be an attractive and promising therapeutic option in the management of ACPs. On the other hand, papillary CP (PCP) is associated with activating mutations in the BRAF gene. This gene encodes a BRAF protein that plays an important role in the intracellular mitogen-activated protein kinase (MAPK) signaling pathway, which also regulates cell proliferation. The use of BRAF inhibitors either in monotherapy or in combination with mitogen-activated protein kinase (MEK) inhibitors has demonstrated therapeutic efficacy in isolated clinical cases of relapsed PCPs. A preliminary report of a recent phase II clinical trial has shown a therapeutic response in 93.7% of patients with BRAF ^V600E -mutated PCP, with an 85% reduction in tumor size. In the present review we comment on the efficacy and safety of the different drugs being used in patients with PCP.

Managing stage 4 ameloblastoma with dual BRAF/MEK inhibition: A case report with 8-year clinical follow-up

We present 8-year follow-up on the first patient with stage 4 ameloblastoma carrying a BRAF V600E mutation treated with dual BRAF/MEK inhibition (BRAF/MEKi). He experienced a durable clinical response while on dabrafenib (BRAFi) and trametinib (MEKi) without toxicity nor evidence for drug-resistant tumor progression. He was asymptomatic when he self-discontinued therapy after 4 years of sustained clinical response. He did not return for follow-up until 2.5 years later with onset of painful mandibular tumor recurrence associated with recurrent bilateral lung metastases. He was rechallenged with dabrafenib/trametinib and experienced another prompt tumor response and remains in a second durable clinical remission (currently > 16 months) on continuous dual targeted therapy. We discuss the implications of this case study for future treatment strategies.

Intermittent treatment of BRAFV600E melanoma cells delays resistance by adaptive resensitization to drug rechallenge

Preclinical studies of metastatic melanoma treated with targeted therapeutics have suggested that alternating periods of treatment and withdrawal might delay the onset of resistance. This has been attributed to drug addiction, where cells lose fitness upon drug removal due to the resulting hyperactivation of mitogen-activated protein (MAP) kinase signaling. This study presents evidence that the intermittent treatment response can also be explained by the resensitization of cells following drug removal and enhanced cell loss upon drug rechallenge. Resensitization is accompanied by adaptive transcriptomic switching and occurs despite the sustained expression of resistance genes throughout the intermittent treatment.

Patients with melanoma receiving drugs targeting BRAF^V600E and mitogen-activated protein (MAP) kinase kinases 1 and 2 (MEK1/2) invariably develop resistance and face continued progression. Based on preclinical studies, intermittent treatment involving alternating periods of drug withdrawal and rechallenge has been proposed as a method to delay the onset of resistance. The beneficial effect of intermittent treatment has been attributed to drug addiction, where drug withdrawal reduces the viability of resistant cells due to MAP kinase pathway hyperactivation. However, the mechanistic basis of the intermittent effect is incompletely understood. We show that intermittent treatment with the BRAF^V600E inhibitor, LGX818/encorafenib, suppresses growth compared with continuous treatment in human melanoma cells engineered to express BRAF^V600E, p61-BRAF^V600E, or MEK2^C125 oncogenes. Analysis of the BRAF^V600E-overexpressing cells shows that, while drug addiction clearly occurs, it fails to account for the advantageous effect of intermittent treatment. Instead, growth suppression is best explained by resensitization during periods of drug removal, followed by cell death after drug readdition. Continuous treatment leads to transcriptional responses prominently associated with chemoresistance in melanoma. By contrast, cells treated intermittently reveal a subset of transcripts that reverse expression between successive cycles of drug removal and rechallenge and include mediators of cell invasiveness and the epithelial-to-mesenchymal transition. These transcripts change during periods of drug removal by adaptive switching, rather than selection pressure. Resensitization occurs against a background of sustained expression of melanoma resistance genes, producing a transcriptome distinct from that of the initial drug-naive cell state. We conclude that phenotypic plasticity leading to drug resensitization can underlie the beneficial effect of intermittent treatment.

Vemurafenib Combined With Trametinib Significantly Benefits the Survival of a Patient With Stage IV Pancreatic Ductal Adenocarcinoma With BRAF V600E Mutation: A Case Report

Vemurafenib and trametinib have a lot of successful experiences in the treatment of unresectable or metastatic melanoma with BRAF V600E mutation. However, they have not been reported in the treatment of advanced pancreatic ductal adenocarcinoma (PDAC). We report here a 66-year-old male who was diagnosed as PDAC with multiple metastases of the abdominal cavity and liver according to pathological examination. After three cycles of gemcitabine plus nab-paclitaxel (GA) regimen chemotherapy, the liver metastasis of the patient progressed, and the patient could not continue to receive chemotherapy because of poor physical condition. BRAF V600E mutation was found by genetic detection in this patient, so targeted therapy with vemurafenib combined with trametinib was performed and the follow-up period was up to 24 months. To the best of our knowledge, this is a rare report that patients with stage IV PDAC with BRAF V600E mutation can receive significantly survival benefits from targeted therapy with vemurafenib combined with trametinib. This report provides experience for the use of these two drugs in patients with advanced PDAC.

An Insight into Cholangiocarcinoma and Recent Advances in its Treatment

BACKGROUND

Cholangiocarcinoma (CCA) is a malignant disease of the epithelial cells of the intrahepatic and extrahepatic bile ducts. This review focuses on various aspects of cholangiocarcinoma such as its associated causes, treatment criteria, and more.

METHODS

Although it remains a rare malignancy and is the second most common primary malignancy of the liver, the incidence is increasing, especially the incidence of intrahepatic CCA. Several studies suggested that surgery is not only solution; recently, reported targeted drugs may have the potential to become an alternative option.

RESULTS

This review provides an overview of the current scenario of targeted therapies for CCA, which were tabulated with their current status and it also included its associated causes and its treatment criteria.

CONCLUSION

Because of its rarity and complexity, surgery remains the preferred treatment in resectable patients. Howerver, the studies suggested that the recently reported drugs may have the potential to be an alternative option for the treatment of CCA and related complications. In addition, this review will certainly benefit the community and researcher for further investigation.

Diverse landscape of dermatologic toxicities from small-molecule inhibitor cancer therapy

BACKGROUND

Advances in molecular biology and genetics have contributed to breakthrough treatments directed at specific pathways associated with the development of cancer. Small-molecule inhibitors (Nibs) aimed at a variety of cellular pathways have been efficacious; however, they are associated with significant dermatologic toxicities.

METHODS

We conducted a comprehensive review of dermatologic toxicities associated with Nibs categorized into the following five groups: (a) mitogen-activated protein kinase; (b) growth factor/multi-tyrosine kinase; (c) cell division/DNA repair; (d) signaling associated with myeloproliferative neoplasms; and (e) other signaling pathways. Prospective phase I, II, or III clinical trials, retrospective literature reviews, systematic reviews/meta-analyses, and case reviews/reports were included for analysis.

RESULTS

Dermatologic toxicities reviewed were associated with every class of Nibs and ranged from mild to severe or life-threatening adverse skin reactions. Inflammatory reactions manifesting as maculopapular, papulopustular/acneiform, and eczematous lesions were frequent types of dermatologic toxicities seen with Nibs. Squamous cell carcinoma with keratoacanthoma-like features was associated with a subset of Nibs. Substantial overlap in dermatologic toxicities was found between Nibs.

CONCLUSIONS

Dermatologic toxicities from Nibs are diverse and may overlap between classes of Nibs. Recognition of the various types of toxicities from Nibs is critical for patient care in the era of "oncodermatology/dermatopathology."

Targeted Therapies in Rare Brain Tumours

Rare central nervous system (CNS) tumours represent a unique challenge. Given the difficulty of conducting dedicated clinical trials, there is a lack of therapies for these tumours supported by high quality evidence, and knowledge regarding the impact of standard treatments (i.e., surgery, radiotherapy or chemotherapy) is commonly based on retrospective studies. Recently, new molecular techniques have led to the discovery of actionable molecular alterations. The aim of this article is to review recent progress in the molecular understanding of and therapeutic options for rare brain tumours, both in children and adults. We will discuss options such as targeting the mechanistic target of rapamycin (mTOR) pathway in subependymal giant cells astrocytomas (SEGAs) of tuberous sclerosis and BRAF V600E mutation in rare glial (pleomorphic xanthoastrocytomas) or glioneuronal (gangliogliomas) tumours, which are a model of how specific molecular treatments can also favourably impact neurological symptoms (such as seizures) and quality of life. Moreover, we will discuss initial experiences in targeting new molecular alterations in gliomas, such as isocitrate dehydrogenase (IDH) mutations and neurotrophic tyrosine receptor kinase (NTRK) fusions, and in medulloblastomas such as the sonic hedgehog (SHH) pathway.