BRAF Mutations Research Articles

Treatment resistance to melanoma therapeutics on a single cell level

Therapy targeting the BRAF-MEK cascade created a treatment revolution for patients with BRAF mutant advanced melanoma. Unfortunately, 80% patients treated will progress by 5 years follow-up. Thus, it is imperative we study mechanisms of melanoma progression and therapeutic resistance. We created a scRNA (single cell RNA) atlas of 128,230 cells from 18 tumors across the treatment spectrum, discovering melanoma cells clustered strongly by transcriptome profiles of patients of origins. Our cell-level investigation revealed gains of 1q and 7q as likely early clonal events in metastatic melanomas. By comparing patient tumors and their derivative cell lines, we observed that PD1 responsive tumor fraction disappears when cells are propagated in vitro. We further established three anti-BRAF-MEK treatment resistant cell lines using three BRAF mutant tumors. ALDOA and PGK1 were found to be highly expressed in treatment resistant cell populations and metformin was effective in targeting the resistant cells. Our study suggests that the investigation of patient tumors and their derivative lines is essential for understanding disease progression, treatment response and resistance.

Strongly ROS-Correlated, Time-Dependent, and Selective Antiproliferative Effects of Synthesized Nano Vesicles on BRAF Mutant Melanoma Cells and Their Hyaluronic Acid-Based Hydrogel Formulation.

Cutaneous metastatic melanoma (CMM) is the most aggressive form of skin cancer with a poor prognosis. Drug-induced secondary tumorigenesis and the emergency of drug resistance worsen an already worrying scenario, thus rendering urgent the development of new treatments not dealing with mutable cellular processes. Triphenyl phosphonium salts (TPPSs), in addiction to acting as cytoplasmic membrane disruptors, are reported to be mitochondria-targeting compounds, exerting anticancer effects mainly by damaging their membranes and causing depolarization, impairing mitochondria functions and their DNA, triggering oxidative stress (OS), and priming primarily apoptotic cell death. TPP-based bola amphiphiles are capable of self-forming nanoparticles (NPs) with enhanced biological properties, as commonly observed for nanomaterials. Already employed in several other biomedical applications, the per se selective potent antibacterial effects of a TPP bola amphiphile have only recently been demonstrated on 50 multidrug resistant (MDR) clinical superbugs, as well as its exceptional and selective anticancer properties on sensitive and MDR neuroblastoma cells. Here, aiming at finding new molecules possibly developable as new treatments for counteracting CMM, the effects of this TPP-based bola amphiphile (BPPB) have been investigated against two BRAF mutants CMM cell lines (MeOV and MeTRAV) with excellent results (even IC50 = 49 nM on MeOV after 72 h treatment). With these findings and considering the low cytotoxicity of BPPB against different mammalian non-tumoral cell lines and red blood cells (RBCs, selectivity indexes up to 299 on MeOV after 72 h treatment), the possible future development of BPPB as topical treatment for CMM lesions was presumed. With this aim, a biodegradable hyaluronic acid (HA)-based hydrogel formulation (HA-BPPB-HG) was prepared without using any potentially toxic crosslinking agents simply by dispersing suitable amounts of the two ingredients in water and sonicating under gentle heating. HA-BPPB-HA was completely characterized, with promising outcomes such as high swelling capability, high porosity, and viscous elastic rheological behavior.

The Raf/LIN-45 C-terminal distal tail segment negatively regulates signaling in Caenorhabditis elegans.

Raf protein kinases act as Ras-GTP sensing components of the ERK signal transduction pathway in animal cells, influencing cell proliferation, differentiation, and survival. In humans, somatic and germline mutations in the genes BRAF and RAF1 are associated with malignancies and developmental disorders. Recent studies shed light on the structure of activated Raf, a heterotetramer consisting of Raf and 14-3-3 dimers, and raised the possibility that a Raf C-terminal distal tail segment (DTS) regulates activation. We investigated the role of the DTS using the Caenorhabditis elegans Raf ortholog lin-45. Truncations removing the DTS strongly enhanced lin-45(S312A), a weak gain-of-function allele equivalent to RAF1 mutations found in patients with Noonan Syndrome. We genetically defined three elements of the LIN-45 DTS, which we termed the active site binding sequence (ASBS), the KTP motif, and the aromatic cluster. In the context of lin-45(S312A), mutation of each of these elements enhanced activity. We used AlphaFold to predict DTS protein interactions for LIN-45, fly Raf, and human BRAF, within the activated heterotetramer complex. We propose distinct functions for the LIN-45 DTS elements: i) the ASBS binds the kinase active site as an inhibitor, ii) phosphorylation of the KTP motif modulates DTS-kinase domain interaction, and iii) the aromatic cluster anchors the DTS in an inhibitory conformation. Human RASopathy-associated variants in BRAF affect residues of the DTS, consistent with these predictions. This work establishes that the Raf/LIN-45 DTS negatively regulates signaling in C. elegans and provides a model for its function in other Raf proteins.

Abstract C015: Selective and pairwise epistatic effects of somatic mutations in KRAS wild-type pancreatic cancer

Abstract About 8 to 10% of all pancreatic adenocarcinomas (PAAD) do not possess canonical mutations in KRAS. A sizable proportion of these KRAS wild-type (WT) pancreatic cancers harbor mutations in alternative MAPK-pathway driver genes. These alternative MAPK-pathway genes represent a set of therapeutic targets that might be exploited to treat individuals in this PAAD subset. Previous studies have prioritized the mutational- target landscape of KRAS WT PAAD by ranking genes determined by significance thresholds to be drivers by the prevalence of their somatic mutations in tumors. These prevalences usefully inform the size of the patient population that would be candidates for targeted therapeutics. However, prevalence is markedly influenced by underlying mutation rate. It is not a metric of cancer effect; it does not directly quantify the degree to which a driver mutation increases cancer cell survival and proliferation, nor do observations of co-occurrence or mutual exclusivity quantify epistasis. Therefore, to better guide the development of targeted therapeutics, we assembled a rich dataset of 6,391 PAAD tumor sequences from TCGA, UTSW, ICGC, QCMG, Yale-Gilead, and the AACR Project GENIE.We analyzed the cancer effect sizes of somatic variants in PAADs. Furthermore, we determined the selective epistatic interactions between KRAS and other PAAD driver genes. Nine of the 20 highest-effect variants were nonsynonymous substitutions in KRAS, with the prevalence of these mutations ranging from 18 to 2390 (median 93). This high frequency of highly oncogenic KRAS mutants supports the longstanding conception that KRAS mutations dominate the oncogenic landscape of PAAD. However, of the 6,391 cases analyzed, 627 (9.8%) were KRAS WT. To further investigate the oncogenic landscape of these samples, we employed a pairwise epistasis model of selection. We discovered that not only are alternative MAPK drivers (BRAF and NRAS) present in KRAS WT PAAD, but that they show antagonistic epistasis with KRAS mutation. Moreover, we found that non-MAPK drivers CTNNB1 and IDH1 also exhibit substantial antagonistic epistasis with KRAS. Also, in a KRAS-substituted background, selection for mutations in tumor suppressor genes TP53, CDKN2A, and SMAD4 was increased. Furthermore, mutations in BRAF, NRAS, CTNNB1, TP53, CDKN2A, and SMAD4, genes commonly considered to be drivers of PAAD, in addition to a previously unrecognized driver IDH1, suppressed selection for KRAS mutations. Not only MAPK drivers, but also other oncogenic drivers of PAAD at both high and low prevalence exhibit antagonistic somatic selective epistasis. Treatments targeting these variants that are antagonistically epistatic with KRAS may rescue the full strength of selection on KRAS variants, warranting continued monitoring for KRAS variants in resurgent cancer. Moreover, as resistance to KRAS inhibitors is likely caused by gained alterations in alternative MAPK drivers, exploration of treatments targeting these mutations may additionally provide an avenue to overcome therapeutic resistance in PAADs. Citation Format: Rishi M Shah, Can M Ersahin, Jeffrey D Mandell, Vincent L Cannataro, Jeffrey P Townsend. Selective and pairwise epistatic effects of somatic mutations in KRAS wild-type pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr C015.

Prognostic determinants in cancer survival: a multidimensional evaluation of clinical and genetic factors across 10 cancer types in the participants of Genomics England’s 100,000 Genomes Project

BackgroundCancer is a complex disease, caused and impacted by a combination of genetic, demographic, clinical, environmental and lifestyle factors. Analysis of cancer characteristics, risk factors, treatment options and the heterogeneity across cancer types has been the focus of medical research for years. The aim of this study is to describe and summarise genetic, clinicopathological, behavioural and demographic characteristics and their differences across ten common cancer types and evaluate their impact on overall survival outcomes.MethodsThis study included data from 9977 patients with bladder, breast, colorectal, endometrial, glioma, leukaemia, lung, ovarian, prostate, and renal cancers. Genetic data collected through the 100,000 Genomes Project was linked with clinical and demographic data provided by the National Cancer Registration and Analysis Service (NCRAS), Hospital Episode Statistics (HES) and Office for National Statistics (ONS). Descriptive and Kaplan Meier survival analyses were performed to visualise similarities and differences across cancer types. Cox proportional hazards regression models were applied to identify statistically significant prognostic factor associations with overall survival.Results161 clinical and 124 genetic factors were evaluated for prognostic association with overall survival. Of these, 116 unique factors were found to have significant prognostic effect for overall survival across ten cancer types when adjusted for age, sex and stage. The findings confirmed prognostic associations with overall survival identified in previous studies in factors such as multimorbidity, tumour mutational burden, and mutations in genes BRAF, CDH1, NF1, NRAS, PIK3CA, PTEN, TP53. The results also identified new prognostic associations with overall survival in factors such as mental health conditions, female health-related conditions, previous hospital encounters and mutations in genes FANCE, FBXW7, GATA3, MSH6, PTPN11, RB1, RNF43.ConclusionThis study provides a comprehensive view of clinicopathological and genetic prognostic factors across different cancer types and draws attention to less commonly known factors which might help produce more precise prognosis and survival estimates. The results from this study contribute to the understanding of cancer disease and could be used by researchers to develop complex prognostic models, which in turn could help predict cancer prognosis more accurately and improve patient outcomes.

Associations of SEMA7A, SEMA4D, ADAMTS10, and ADAM8 with KRAS, NRAS, BRAF, PIK3CA, and AKT Gene Mutations, Microsatellite Instability Status, and Cytokine Expression in Colorectal Cancer Tissue.

Semaphorins (SEMAs), ADAM, and ADAMTS family members are implicated in various cancer progression events within the tumor microenvironment across different cancers. In this study, we aimed to evaluate the expression of SEMA7A, SEMA4D, ADAM8, and ADAMTS10 in colorectal cancer (CRC) in relation to the mutational landscape of KRAS, NRAS, BRAF, PIK3CA, and AKT genes, microsatellite instability (MSI) status, and clinicopathological features. We also examined the associations between the expression of these proteins and selected cytokines, chemokines, and growth factors, assessed using a multiplex assay. Protein concentrations were quantified using ELISA in CRC tumors and tumor-free surgical margin tissue homogenates. Gene mutations were evaluated via RT-PCR, and MSI status was determined using immunohistochemistry (IHC). GSEA and statistical analyses were performed using R Studio. We observed a significantly elevated expression of SEMA7A in BRAF-mutant CRC tumors and an overexpression of ADAM8 in KRAS 12/13-mutant tumors. The expression of ADAMTS10 was decreased in PIK3CA-mutant CRC tumors. No significant differences in the expression of the examined proteins were observed based on MSI status. The SEMA7A and SEMA4D expressions were correlated with the expression of numerous cytokines associated with various immune processes. The potential immunomodulatory functions of these molecules and their suitability as therapeutic targets require further investigation.

Final, 10-Year Outcomes with Nivolumab plus Ipilimumab in Advanced Melanoma.

Previous results from this trial showed longer overall survival after treatment with nivolumab plus ipilimumab or with nivolumab monotherapy than with ipilimumab monotherapy in patients with advanced melanoma. Given that patients with advanced melanoma are living longer than 7.5 years, longer-term data were needed to address new clinically relevant questions. We randomly assigned patients with previously untreated advanced melanoma, in a 1:1:1 ratio, to one of the following regimens: nivolumab (1 mg per kilogram of body weight) plus ipilimumab (3 mg per kilogram) every 3 weeks for four doses, followed by nivolumab (3 mg per kilogram) every 2 weeks; nivolumab (3 mg per kilogram) every 2 weeks plus placebo; or ipilimumab (3 mg per kilogram) every 3 weeks for four doses plus placebo. Treatment was continued until the occurrence of disease progression, unacceptable toxic effects, or withdrawal of consent. Randomization was stratified according to BRAF mutation status, metastasis stage, and programmed death ligand 1 expression. Here, we report the final, 10-year results of this trial, including results for overall survival and melanoma-specific survival, as well as durability of response. With a minimum follow-up of 10 years, median overall survival was 71.9 months with nivolumab plus ipilimumab, 36.9 months with nivolumab, and 19.9 months with ipilimumab. The hazard ratio for death was 0.53 (95% confidence interval [CI], 0.44 to 0.65) for nivolumab plus ipilimumab as compared with ipilimumab and was 0.63 (95% CI, 0.52 to 0.76) for nivolumab as compared with ipilimumab. Median melanoma-specific survival was more than 120 months with nivolumab plus ipilimumab (not reached, with 37% of the patients alive at the end of the trial), 49.4 months with nivolumab, and 21.9 months with ipilimumab. Among patients who had been alive and progression-free at 3 years, 10-year melanoma-specific survival was 96% with nivolumab plus ipilimumab, 97% with nivolumab, and 88% with ipilimumab. The final trial results showed a continued, ongoing survival benefit with nivolumab plus ipilimumab and with nivolumab monotherapy, as compared with ipilimumab monotherapy, in patients with advanced melanoma. (Funded by Bristol Myers Squibb and others; CheckMate 067 ClinicalTrials.gov number, NCT01844505.).

Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer Under-Represented by Clinical Trials.

Since the initial US FDA approval of an immune checkpoint inhibitor (ICI) for the treatment of non-oncogene-driven non-small-cell lung cancer (NSCLC) nine years ago, this therapeutic strategy has been cemented as a crucial component of treatment for most of these patients. However, there is a clear efficacy-effectiveness gap whereby patients in the 'real world' seem to have more modest clinical outcomes compared to those enrolled in landmark clinical trials. This gap may be driven by the under-representation of important patient populations, including populations defined by clinical or molecular characteristics. In this review, we summarize the data outlining the evidence of ICIs in patients with poor Eastern Cooperative Oncology Group performance status (ECOG PS), underlying autoimmune disease (AID), older age, active brain metastases (BMs), and molecular aberrations such as EGFR mutations, ALK fusions, BRAF mutations and ROS1 fusions.

The prognostic significance of growth pattern, tumor budding, poorly differentiated clusters, desmoplastic reaction pattern and tumor-stroma ratio in colorectal cancer and an evaluation of their relationship with KRAS, NRAS, BRAF mutations

Growth pattern (GP), tumor budding (TB), poorly differentiated clusters (PDC), desmoplastic reaction pattern (DRP) and tumor-stroma ratio (TSR) are prognostic histomorphological parameters in colorectal cancer (CRC). Correlations between these parameters, their individual prognostic values, and their relationship with KRAS/NRAS/BRAF mutations have not been comprehensively examined. We aimed to investigate these associations, which have not been previously explored in this combination. 126 CRC cases were included. GP, TB, PDC, DRP and TSR were evaluated by two experienced pathologists. KRAS/NRAS/BRAF mutation profile were determined using qPCR. Demographic, clinicopathological and survival data were recorded. Interrelations were investigated by statistical analysis. Infiltrative GP was more frequent in high-score TB, PDC-G3, and stroma-high tumors (p < 0.05). High-score TB was more common in PDC-G3 and stroma-high tumors (p < 0.05). Immature DRP was more frequent in stroma-high tumors (p = 0.014). Among histomorphological parameters, a significant relationship was found only between infiltrative GP and the presence of KRAS mutation (p = 0.023). Moreover, GP was significantly associated with pT, lymphatic invasion, perineural invasion (p < 0.05). Effects on survival were assessed using Kaplan-Meier method and Cox proportional hazards model. TB and PDC were identified as independent predictors of overall survival. Higher TB score (p = 0.008) and higher PDC grade (p = 0.013) lead to worse survival. Interestingly, GP, DRP, TSR or KRAS/NRAS/BRAF mutations were not associated with overall survival. Our results highlight the prognostic significance of TB and PDC. We suggest incorporating TB and PDC into routine CRC reports. The association of KRAS mutation with infiltrative GP supports its role in the acquisition of invasive behavior.

Detection of the BRAFV600E Mutation in Circulating Free Nucleic Acids as a Biomarker of Thyroid Cancer: A Review.

Background: Liquid biopsy is a method that could potentially improve the management of thyroid cancer (TC) by enabling the detection of circulating tumor DNA and RNA (ctDNA, ctRNA). The BRAFV600E mutation appears to be the most representative example of a biomarker in liquid biopsy, as it is the most specific mutation for TC and a target for molecular therapeutics. The aim of this review is to summarize the available data on the detection of the BRAFV600E mutation in liquid biopsy in patients with TC. Methods: A comprehensive analysis of the available literature on the detection of the BRAFV600E mutation in liquid biopsy in TC was performed. Thirty-three papers meeting the inclusion criteria were selected after full-text evaluation. Results: Eleven papers discussed correlations between BRAF mutation and clinicopathological characteristics. Nine studies tested the utility of BRAFV600E detection in the assessment of residual or recurrent disease. Seven studies investigated BRAF-mutated circulating tumor nucleic acids (ctNA) as a marker of response to targeted therapy. In seven studies the method did not detect the BRAFV600E mutation. Conclusions: This review shows the potential of BRAFV600E-mutated ctNA detection in monitoring disease progression, particularly in advanced TC. The diagnostic value of BRAFV600E-mutated ctNA detection appears to be limited to advanced TC. The choice of the molecular method (quantitative PCR [qPCR], droplet digital polymerase chain reaction [ddPCR], and next-generation sequencing [NGS]) should be made based on the turnaround time, sensitivity of the test, and the clinical indications. Despite the promising outcomes of some studies, there is a need to verify these results on larger cohorts and to unify the molecular methods.

Analysis of BRAF Gene Mutation in Hashimoto’s Thyroiditis With Multifocal Papillary Thyroid Carcinoma

Background Thyroid cancer (TC) is a highly prevalent malignant tumor of the head and neck. Papillary thyroid carcinoma (PTC) is the primary pathological type of TC, accounting for more than 80% of all TCs. BRAF mutations are closely associated with PTC. However, the relationship among HT, PTC, and BRAF mutations has not yet been clarified. We aimed to investigate the BRAF mutation in Hashimoto’s thyroiditis (HT) with PTC. Methods A total of 72 patients with multifocal PTC were included and grouped based on surgical pathology examination. Group A (n = 32) had pure multifocal PTC and Group B (n = 40) had HT with multifocal PTC. Various features were compared: BRAF mutation, multifactorial analysis of BRAF mutations, pathological features in patients with HT and multifocal PTC, and multifactorial analysis of factors affecting HT with multifocal PTC. Results Significant differences were seen in thyroid peroxidase antibody levels, central lymph node metastasis, extra-thyroidal invasion, main and non-main lesion diameters, and BRAF mutation positivity ( P &lt; 0.05). Patients with the BRAF mutation had significantly higher rates of extra-thyroidal invasion and lymph node metastasis than those without the BRAF mutation ( P &lt; 0.05). Logistic regression analysis showed that BRAF mutation and main lesion nodule diameter were independent risk factors affecting extra-thyroidal invasion and central lymph node metastasis in patients with HT and multifocal PTC ( P &lt; 0.05). Discussion BRAF mutations were more prevalent and closely associated with extra-thyroidal invasion and central lymph node metastasis in patients with HT and multifocal PTC.

The Relationship Between DNA Mismatch Repair Status and Clinicopathologic Characteristics in Colon Cancer.

DNA mismatch repair (MMR) proteins are essential for repairing genetic mutations that occur during DNA replication. Deficiency of MMR proteins results in a phenotype called microsatellite instability (MSI), which occurs in Lynch syndrome as well as sporadic colorectal cancers (CRC), and it is associated with several clinicopathological features. We aimed to investigate the association of the loss of MMR proteins with clinicopathologic considerations in our CRC series. In this retrospective study, DNA MMR protein status in CRC is evaluated in a total of 200 colorectal resection specimens by immunohistochemistry (IHC) for MLH1, MSH2, MSH6 and PMS2 protein expression. The BRAF mutation was investigated by the real-time PCR in cases with loss of MLH1 protein expression. The relationship between MMR status and clinicopathological parameters was investigated statistically. Loss of MMR protein expression was detected in 26 of 200 CRC cases. The BRAFV600E mutation was detected in 2 of the cases with MLH1 loss and accepted as sporadic. The remaining 24 cases (12%) were identified as Lynch syndrome candidates. There were statistical differences observed regarding the presence of tumor-infiltrating lymphocytes (P < .001), Crohn's-like reaction (P = .001), expansile growth (P < .001), tumor heterogeneity (P < .001), mucinous differentiation (P < .001), and presence of metastatic lymph nodes (P = .045) between sporadic cases with preserved MMR and Lynch candidates. However, difference in the survival rates between sporadic cases and Lynch candidates was not significant. Immunohistochemical staining for MMR is a practical method for predicting MSI phenotype as well as Lynch candidates. MMR expression status was found to be associated with certain clinicopathological features some of which also have prognostic significance.

RAS, BRAF, and MMR system mutations in metastatic colorectal cancers: an observational study

Introduction: Colorectal cancers (CRCs) are the second cause of malignancy-related deaths and over half of CRCs become metastatic. Genetics plays a critical role in understanding metastatic colorectal cancers (MCRCs), as various genetic mutations influence progression and treatment responses. While there exists plenty of research on genetic mutations in CRCs, few studies have focused on mutations in MCRC patients. The present study aims to provide an overview of the prevalence of KRAS, NRAS, BRAF, and MMR mutations in Iranian MCRC patients. Methods: The present study is a descriptive cross-sectional study on patients with MCRCs referred to a tertiary medical center in Iran from March 2015 to March 2022. Ethics approval was obtained from the ethics committee of the University of Medical Sciences. The patient’s MCRC was confirmed by pathology and Genotyping Assessments of tissue for KRAS, NRAS, BRAF, and MMR mutations. Results: A total of 136 MCRC patients were included in this study; 44 patients (40.7%) had KRAS mutations in their lesions. KRAS mutation status was not significantly related to age or gender (P &gt; 0.05). Only one NRAS mutation was found in one patient. There were no cases of BRAF mutation identified. Among 48 patients assessed for MMRs deficiency, 8 cases (16.7%) were positive, 7 cases (14.6%) were MSI-H, and 1 case (2.1%) was MSI-L. Conclusion: Although no significant relation was found between the KRAS mutation pattern and gender, age, or tumor primary location, the MSI-H mutation-positive tumors were significantly more prevalent in younger patients.

Identifying Genetic Mutations in Vascular Anomalies Using a Sequencing Panel for Childhood Cancers: A Pilot Study

Introduction: Genetic mutations have been identified in the pathogenesis of vascular anomalies. Due to overlaps in genetic variants causing vascular anomalies and cancer, we used a next-generation sequencing panel for genomic profiling of childhood cancers to detect somatic mutations in children with vascular anomalies. We aim to review the utility of an oncology panel for the molecular diagnosis of vascular anomalies. Methods: Nine patients with histologically confirmed vascular anomalies were included. DNA was extracted from formalin-fixed paraffin-embedded tissue specimens obtained from affected tissue following diagnostic punch biopsies of the skin and core biopsies of the vascular malformation or tumor during sclerotherapy or surgical excision. Molecular analysis of the tissue samples was performed using AmpliSeq for Childhood Cancer DNA Assay Panel. Results: Two patients had antenatally detected vascular anomalies. The median age at diagnosis for the remaining patients was 7.0 years (IQR, 0.6–10.0 years). Seven were diagnosed with vascular malformations, while 2 had vascular tumors. Pathological somatic mutations were identified in 4 patients, leading to a diagnostic yield of 44.4%. Two different PIK3CA mutations were identified in 3 cases: 1 in a case of macrocystic lymphatic malformation, the other in a case of Congenital Lipomatous Overgrowth, Vascular malformations, Epidermal nevus, Spinal/Skeletal anomalies syndrome and Klippel–Trenaunay syndrome. BRAF mutation was identified in a patient with a veno-lymphatic malformation. Conclusion: An oncology next-generation sequencing panel can be used for genetic profiling of vascular anomalies. However, a more customized and sensitive panel may be of better diagnostic yield, as detection of somatic mutations in vascular anomalies is challenging due to tissue mosaicism, low-abundant genetic variants, and specimen limitations.

Genetic Analysis of Cerebrovascular Diseases

With advances in genetic analysis technology, the genetic and molecular backgrounds of cerebrovascular diseases have become clearer. In moyamoya disease and intracranial artery stenosis, RNF213 p.Arg4810Lys has been identified as a disease susceptibility gene variant(germline variant), and various analyses have been conducted. PDGFRB mutations have been identified as characteristic somatic variants in cerebral aneurysms and are attracting attention. In addition, PIK3CA and MAP3K3 mutaions have been identified in cerebral cavernous malformations as somatic variants. Moreover, KRAS and BRAF mutations have been identified in arteriovenous malformations as somatic variants, respectively. Further studies are in progress. We reviewed the results of recent genetic analyses of cerebrovascular diseases, focusing particularly on genetic mutations.

CDK4 gene copy number increase and concurrent genetic changes in acral melanoma of a Chinese cohort

Acral melanoma (AM) is the most common subtype of melanoma in Asian population. Abnormalities in the p16-cyclin D1-CDK4 signalling pathway play a crucial role in the development and progression of AM. However, the alterations of CDK4 gene copy number in AM are underreported. In this study, we investigated CDK4 gene copy number and concurrent molecular changes in a Chinese cohort with AM, in aim of exploring CDK4 gene alterations and its significance in AM. We examined copy number alterations of CDK4 with fluorescence in situ hybridisation (FISH) in 31 patients with AM. Six patients with CDK4 high-level copy number increase were examined by next-generation sequencing to detect concurrent molecular changes. Using FISH, 12 (12/31, 38.7%) cases showed CDK4 copy number increase, with 6 (6/31, 19.4%) low-level copy number increase and 6 (6/31, 19.4%) high-level copy number increase. Five of six CDK4 low-level copy number increase cases were accompanied by polysomy of chromosome 12, while one case was not. Two of six CDK4 high-level copy number increase cases were accompanied by polysomy of chromosome 12, while four cases were not. CDK4 copy number increase was significantly correlated with younger patient age. In six CDK4 high-level copy number increase cases, one case was found to be accompanied by NRAS mutation, one case was accompanied by HER2 mutation, one case was accompanied by BCL2L11 mutation ​and one case was accompanied by BRAF, HER2 and BCL2L11 mutations. Our study confirmed the presence of CDK4 copy number increase in AM cases. Detecting CDK4 copy number increase by FISH can be reliable in the diagnosis of AM. Some CDK4 copy number increases are the results of polysomy of chromosome 12. CDK4 high-level copy number increase coexists with other pathogenic mutations in AM. CDK4 appears to be a promising target for AM treatment and is expected to be combined with other targeted therapies.

Cooperative genomic lesions in HRAS-mutant cancers predict resistance to farnesyltransferase inhibitors.

In the clinical development of farnesyltransferase inhibitors (FTIs) for HRAS-mutant tumors, responses varied by cancer type. Co-occurring mutations may affect responses. We aimed to uncover cooperative genetic events specific to HRAS-mutant tumors and to study their effect on sensitivity to FTIs. Using targeted sequencing data from the MSK-IMPACT and Dana-Farber Cancer Institute Genomic Evidence Neoplasia Information Exchange databases, we identified comutations that were observed predominantly in HRAS-mutant versus KRAS-mutant or NRAS-mutant cancers. HRAS-mutant cancers had a higher frequency of coaltered mutations (48.8%) in the MAPK, PI3K, or RTK pathway genes, compared with KRAS-mutant (41.4%) and NRAS-mutant (38.4%) cancers (p < 0.05). Class 3 BRAF, NF1, PTEN, and PIK3CA mutations were more prevalent in HRAS-mutant lineages. To study the effects of comutations on sensitivity to FTIs, HrasG13R was transfected into "RASless" (Kraslox/lox/Hras-/-/Nras-/-/RERTert/ert) mouse embryonic fibroblasts (MEFs), which sensitized nontransfected MEFs to tipifarnib. Comutation in the form of Pten or Nf1 deletion and Pik3caH1047R transduction led to resistance to tipifarnib in HrasG13R-transfected MEFs in the presence or absence of KrasWT, whereas BrafG466E transduction led to resistance to tipifarnib only in the presence of KrasWT. Combined treatment with tipifarnib and MEK inhibition sensitized cells to tipifarnib in all settings, including in MEFs with PI3K pathway comutations. HRAS-mutant tumors demonstrate lineage-dependent MAPK or PI3K pathway alterations, which confer resistance to tipifarnib. The combined use of FTIs and MEK inhibition is a promising strategy for HRAS-mutant tumors.

Investigating EGFR, BRAF, and RAS Mutations in Oral and Cutaneous Squamous Cell Neoplasms: A Preliminary Report on Romanian Patients

Background: Head and neck cancers, and particularly, oral cancers have a complex pathogenesis that includes genetic mutations and epigenetic alterations which interfere with cellular signaling and can trigger tumor development. The purpose of this study was to reveal whether low-frequency hotspot mutations may be detected in a study lot with histopathological evidence of squamous cell carcinoma (SCC) of the oral mucosa and skin of the head and neck. Methods: Tumor biopsies from treatment naïve patients were tested for BRAF V600, NRAS G12/G13, NRAS Q61, KRAS Q61 mutations, and EGFR exon 19 deletions (Ex19Del) using droplet digital PCR (ddPCR). The tumors were also analyzed for EGFR T790M mutations by RT-PCR, using a CE-IVD validated kit, with a limit of detection of 0.05%. Results: None of the examined cases exhibited NRAS G12/G13, NRAS Q61, KRAS Q61, BRAF V600, or EGFR T790M mutations, indicating that these alterations are rare events in SCC pathogenesis. Interestingly, among the 12 specimens tested by ddPCR for EGFR Ex19Del, an HPV-negative cSCC tumor occurring in the parotid region tested positive for this drug-sensitizing mutation, offering unexplored therapeutic perspectives to the patient from whom it was collected. Conclusions: Our study highlights the important clinical implications of detecting low-frequency hotspot mutations in tumor biopsies by ddPCR. We believe that the ddPCR-assisted analysis of these mutations in larger SCC cohorts may provide us with mechanistic insights regarding their role in SCC pathogenesis and guide the development of novel therapeutic strategies for this problematic disease.

Unveiling the role of KRAS in Chinese colorectal cancer patients: a positive influence on tumor mutational burden.

One of the main challenges associated with the development of therapeutic and diagnostic strategies for patients with colorectal cancer (CRC) is the establishment of minimally invasive and efficient biomarkers. Pertinent genes in CRC have been identified through their functions in systematic mutagenesis screens. KRAS is considered a dominant mutated oncogene that contributes to pathogenesis of CRC. This study aimed to explore the genomic alternations of KRAS in a CRC population. Sequencing data of 94 Chinese patients with CRC were prospectively collected and analyzed using next-generation sequencing (NGS). The influence of KRAS and its associated subtype co-mutations on the expression level of the tumor mutational burden (TMB) was investigated. The objective of our study was to assess the potential prognostic significance of KRAS and other driving oncogenes in determining the clinical efficacy of immunotherapy. The gene mutation rates of TP53, APC, and KRAS were 81.91%, 71.28%, and 43.62%, respectively. Additionally, KRAS G12D displayed a relatively higher mutation rate than other KRAS-mutant subtypes. Increased TMB was observed in cases of KRAS and BRAF mutation combined with APC single mutation; furthermore, the expression of TMB in G12V was the highest, and G12D presented the lowest TMB in single KRAS-mutant subtypes or the combination with APC mutations. The TMB driven by KRAS co-mutations may have the potential to be used as a key biomarker for prediction of treatment outcomes of immune checkpoint inhibitors (ICIs) in patients with CRC, especially with APC co-mutation.

612O Preliminary results from a phase I study of CFT1946, a novel BIDAC degrader in mutant BRAF V600 solid tumors

612O Preliminary results from a phase I study of CFT1946, a novel BIDAC degrader in mutant BRAF V600 solid tumors