BRAF Mutation Rate Research Articles

Real world characteristics and outcomes of patients with BRAFV600E-mutant metastatic colorectal cancer in Australia: The COALA project.

70 Background: BRAFV600E-mutant metastatic colorectal cancer (mCRC) represents a unique molecular subset with poor prognosis and less responsiveness to chemotherapy. The BEACON CRC study demonstrated that encorafenib plus cetuximab (EC) significantly improved overall survival (OS) compared to FOLFIRI plus cetuximab in BRAF-mutant mCRC as 2 nd or 3 rd line therapy. This combination was reimbursed in Australia from January 2022. Methods: We analysed data from the Australian TRACC mCRC clinical registry, encompassing patients (pts) with BRAF-mutant mCRC diagnosed in Australia from 2009 to 2024 at 31 hospitals. We assessed baseline demographics, uptake of EC following reimbursement and efficacy analysis of progression-free survival (PFS) and OS for pts that received EC and those who did not. Pts receiving EC on a clinical trial were excluded. Results: Among 2,800 pts with known BRAF mutation status, 365 (13%) were BRAF mutated. The BRAF mutant cohort had a median age of 63 years, with a significantly higher mutation rate in the 20-39 age group than other age groups (age 20-39, 25.5%; age 40-59, 10%; age 60+, 13.2%; P<0.001); 54.5% were female, 58% right-sided tumours, 64% with synchronous metastatic disease and 21.7% deficient mismatch repair (dMMR). Overall, 314 (86%) pts with BRAF mutant tumours and 2,079 (85%) BRAF wild-type (WT) tumours received 1 st line treatment, and 156 (43%) BRAF mutant and 1,144 (47%) BRAF WT pts received 2 nd line therapy. The median OS from diagnosis was 17.3 months for BRAF mutant pts versus 34.7 months for BRAF WT pts (p < 0.0001). All dMMR BRAF mutant pts received 1 st line pembrolizumab since its reimbursement in August 2021. Among 41 BRAF mutant pts progressing on 1 st line therapy since January 2022,(32 pMMR, 9 dMMR), 33 (80%) were subsequently treated with EC, and 4 (10%) did not receive further treatment. OS from the start of 2 nd line therapy was 9.6 months (95% CI: 7.2-12.5) for pts who received EC and 7.1 months (95% CI: 6.4-8.6) for those who received other systemic treatment. Median PFS for pts receiving EC was 4.6 months (95% CI: 3.4-5.8) and 3.3 months (95% CI: 2.5-5.3) for other 2 nd line treatments. Conclusions: mCRC pts younger than 40 have a high rate of BRAF mutation, where 1 in 4 tumours harbour the mutation. BRAF mutant mCRC has a poorer outcome than BRAF WT despite a similar proportion receiving 1 st and 2 nd line treatment. The majority of eligible BRAF mutant mCRC pts received EC following reimbursement in Australia, with PFS and OS outcomes consistent with the BEACON CRC trial.

Isolated Langerhans cell histiocytosis of the stomach in adults: An analysis of clinicopathologic characteristics and molecular genetics.

Isolated gastric Langerhans cell histiocytosis (LCH) occurs extremely rarely in adults. We characterized the clinicopathological and molecular genetics of this rare entity. We retrospectively analyzed the clinicopathologic and prognostic features of 3 patients with isolated gastric LCH during the past 10 years, with a review of an additional 20 patients from the literature. A total of 23 patients with isolated gastric LCH were included in this study. There were 15 males and 8 females, with a mean age of 44.5 (median, 48; range, 21-68) years. Stomach discomfort and abdominal pain were the most common presenting symptoms. The lesions were mainly concentrated in the gastric body and antrum (21/23). Gastroscopy often revealed an elevated lesion/polyp. Molecular tests showed that BRAF-V600E gene mutations were found in 10/11 (42%) patients, while none of the patients (0/5) harbored KRAS gene mutations. None of the 23 patients received further treatment. Twenty patients had follow-up results (from 4 to 66 months). One patient with atypical morphological features died of unknown cause 2 months after removal of the tumor. One patient was found to have secondary lesions in the skull and axillary region. The other 18 patients survived without any evidence of disease progression during the follow-up period. In the daily diagnosis of gastroscopic biopsy, it is necessary to be aware of the possibility of LCH in patients with lesions in the gastric body or antrum if endoscopy reveals bulge/polypoid changes and heavy microscopic inflammation. In addition, we should be alert to the possibility of LCH with malignant transformation if the histological morphology exhibits tumor cell nucleoli and mitotic figures or necrosis. The immunohistochemical marker CD56 may help differentiate between LCH and Langerhans cell sarcoma when the morphology is difficult to determine. Molecular detection has shown that the mutation rate of BRAF in gastric LCH is up to 90.9%; more work is needed as the number of cases is small. Current data show a good prognosis for isolated gastric LCH in adults, but long-term follow-up for early detection of disease progression or systemic involvement is necessary.

A rare incidence of signet ring cell carcinoma of the rectosigmoid junction: a case report

Introduction and importance: Signet ring cell carcinoma (SRCC) is a rare type of adenocarcinoma. SRCC comprises 1.0% of all colon cancer and 0.7% of all rectal cancer. The SRCC spreads both hematologically and through lymph nodes making it highly invasive. The pathophysiology of the colorectal SRCC involves an alteration in the function of the RNF43, CDH-1, and SMAD4 genes as well as TGF-B signaling pathways, which are responsible for epithelial-mesenchymal transitions and stem cell properties. This also shows a higher rate of BRAF mutation, microsatellite instability-high (MSI-H) and CpG island methylator phenotype positivity Case presentation: A 17-year-old female patient with no known comorbidities presented with copious, bright red colored per rectal bleeding along with painful defecation. Colonoscopy revealed an eccentric growth that led to luminal narrowing. Multiple biopsies confirmed a 4 cm × 6 cm neoplastic lesion with locoregional lymphadenopathy, but no metastasis. The patient underwent anterior resection of the rectum, colostomy, and rectal stump closure. The sigmoid colon was resected up to the middle up to the third mesorectum followed by multiple re-explorations. Discussion: SRCC presents at an advanced stage with a poor prognosis because signet ring cells infiltrate the mucosa without forming a significant mass, hindering early diagnosis of this carcinoma. Among the previously published large-scale studies, SRCC involves the proximal colon, i.e., the cecum, ascending, and transverse colon. However, our case presents a less common left-sided presentation in a less-commonly presented demographic, a 17-year-old girl. The patient’s non-specific symptoms contributed to a delayed diagnosis. Despite this, the absence of metastasis in our late-diagnosed case is atypical of SRCC. Conclusion: SRCC should be considered as a differential diagnosis for young adults presenting with per-rectal bleeding and other common symptoms often seen in frequently diagnosed conditions. Therefore, early diagnosis along with appropriate surgical intervention combined with supportive treatment are important for better patient outcomes.

Uncovering factors predicting BRAF mutation in cutaneous melanoma

Abstract Introduction/Objective BRAF mutations are considered to be the most common genetic alteration in cutaneous melanoma (CM). Patient management relies on assessing molecular biomarkers enabling the personalization of patients’ treatment. The goal of this study was to develop the tools for predicting BRAF mutation using routine clinical and histological features. Methods/Case Report A total of 2041 CM cases were enrolled in the study to identify factors associated with BRAF mutation. Variables included sex, age, primary location, stage, histological type, ulceration, mitosis, Clark level, Breslow thickness, lymphocytes, lymphovascular invasion (LVI), perineural invasion (PNI), regression, microsatellite, association with nevus. Results (if a Case Study enter NA) The Ukrainian population demonstrated a high rate of BRAF mutation in CM, associated with the younger age and location at non-sun-expose skin. This study also revealed gender-specific differences in CM anatomic distribution and BRAF mutation subtype prevalence. By using the genetic selection method, the minimal set of variables related to BRAF mutations was defined and included age, primary tumor location, histological type, ulceration, LVI, and association with nevus. To encounter non- linear links, the non-linear neural network modeling was applied. For this aim multilayer perceptron (MLP) with one hidden layer was used. The hidden layer architecture included 4 neurons with a logistic activating function. The AUROCMLP6 of the model was 0.79 (0.74 – 0.84). When applying the optimal threshold, the following characteristics of the model were reached: sensitivity - 89.4% (84.5 – 93.1%); specificity - 50.7% (42.2% – 59.1%); positive predictive value (PPV) - 73.1% (69.6% – 76.3%) and NPV - 76.0% (67.6% – 82.8%) respectively. The developed MLP model allows the prediction of BRAF status in CM, facilitating decisions concerning further patient management. Conclusion The developed MLP model, relying on 6 variables analysis allows the prediction of BRAF status in melanoma, facilitating decisions concerning further patient management.

Serum Uric Acid Level May Be a Predictive Factor for BRAF V600E Mutation in Older Patients with Metastatic Colorectal Cancer: An Exploratory Analysis

Introduction: This study aimed to show the relationship between the serum uric acid level measured at diagnosis and the BRAF mutation status in the primary tumor tissue in patients with metastatic colorectal cancer. Methods: In this retrospective cross-sectional study, 264 patients (64% male) whose serum uric acid level was measured at the time of diagnosis and whose BRAF mutation status in the primary tumor was determined were included. Results: The BRAF mutation rate was 14% (n = 37). The median serum uric acid levels of all patients were 6.9 mg/dL (25%, 75% percentile range 3.7, 8.2). The serum uric acid level cut-off value was 6.6 mg/dL. Sensitivity and specificity for BRAF mutated patients were 84% and 27%, respectively. These rates were calculated as 85% and 70% in BRAF-mutated patients aged 65 and over. There was a significant correlation between BRAF mutation and high serum uric acid level, female gender, tumor located in the ascending colon, and multiple metastatic sites. The independent factors affecting BRAF mutation were age 65 and over, tumor in the ascending colon, and high serum uric acid level. Conclusion: As a result, we concluded that high serum uric acid level measured during diagnosis in metastatic colorectal cancer is an accessible and economical biomarker that can predict BRAF mutation in patients aged 65 and over.

Clonal expansion of shared T cell receptors reveals the existence of immune commonality among different lesions of synchronous multiple primary lung cancer

The increase in the detection rate of synchronous multiple primary lung cancer (MPLC) has posed remarkable clinical challenges due to the limited understanding of its pathogenesis and molecular features. Here, comprehensive comparisons of genomic and immunologic features between MPLC and solitary lung cancer nodule (SN), as well as different lesions of the same patient, were performed. Compared with SN, MPLC displayed a lower rate of EGFR mutation but higher rates of BRAF, MAP2K1, and MTOR mutation, which function exactly in the upstream and downstream of the same signaling pathway. Considerable heterogeneity in T cell receptor (TCR) repertoire exists among not only different patients but also among different lesions of the same patient. Invasive lesions of MPLC exhibited significantly higher TCR diversity and lower TCR expansion than those of SN. Intriguingly, different lesions of the same patient always shared a certain proportion of TCR clonotypes. Significant clonal expansion could be observed in shared TCR clonotypes, particularly in those existing in all lesions of the same patient. In conclusion, this study provided evidences of the distinctive mutational landscape, activation of oncogenic signaling pathways, and TCR repertoire in MPLC as compared with SN. The significant clonal expansion of shared TCR clonotypes demonstrated the existence of immune commonality among different lesions of the same patient and shed new light on the individually tailored precision therapy for MPLC.

A novel exosome-related prognostic risk model for thyroid cancer.

The aim was to build an exosome-related gene (ERG) risk model for thyroid cancer (TC) patients. Note that, 510 TC samples from The Cancer Genome Atlas database and 121 ERGs from the ExoBCD database were obtained. Differential gene expression analysis was performed to get ERGs in TC (TERGs). Functional enrichment analyses including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted on the TERGs. Then we constructed a model based on LASSO Cox regression analysis. Kaplan-Meier survival analysis was applied and a Nomogram model was also built. The immune landscape was evaluated by CIBERSORT. Thirty-eight TERGs were identified and their functions were enriched on 591 GO terms and 30 KEGG pathways. We built a Risk Score model based on FGFR3, ADRA1B, and POSTN. Risk Scores were significantly higher in T4 than in other stages, meanwhile, it didn't significantly differ in genders and TNM N or M classifications. The nomogram model could reliably predict the overall survival of TC patients. The mutation rate of BRAF and expression of cytotoxic T-lymphocyte-associated protein 4 were significantly higher in the high-risk group than in the low-risk group. The risk score was significantly correlated to the immune landscape. We built a Risk Score model using FGFR3, ADRA1B, and POSTN which could reliably predict the prognosis of TC patients.

Epidemiological and clinicopathological features of KRAS, NRAS, BRAF mutations and MSI in Chinese patients with stage I-III colorectal cancer.

The selection of appropriate treatment modalities based on the presence or absence of mutations in KRAS, NRAS, BRAF, and the microsatellite instability (MSI) status has become a crucial consensus in colorectal cancer (CRC) therapy. However, the distribution pattern of these genetic mutations and the prevalence of MSI status in Chinese stage I-III CRCs remain unclear. We retrospectively analyzed clinicopathological features, mutations in the KRAS, NRAS, and BRAF genes, as well as MSI status of 411 patients with stage I-III CRC who underwent surgery from June 2020 to December 2022 in the First Affiliated Hospital of Nanjing Medical University. The mutation rates of KRAS, NRAS, and BRAF were 48.9%, 2.2%, and 3.2%, respectively, and the microsatellite instability-high rate was 9.5%. KRAS mutation was independently associated with mucinous adenocarcinoma. Multivariate analysis suggested that tumor location and mucinous adenocarcinoma were independently associated with BRAF mutation. Only T stage was associated with NRAS mutations in the univariate analysis. Multivariate analysis revealed that factors such as larger tumor size, tumor location, younger age, and poor differentiation were independently associated with microsatellite instability-high status. The results illustrate the mutation frequencies of KRAS, NRAS, BRAF genes and MSI status in stage I-III CRC from the eastern region of China. These findings further validate the associations between these genes status and various clinicopathological characteristics.

Correlation between genetic alterations and clinicopathological features of papillary thyroid carcinomas.

To investigate the correlations between multigene alterations and clinicopathological features in papillary thyroid carcinoma (PTC) samples. In this retrospective study, 111 cytological specimens of thyroid nodules, including 74 PTC samples and 37 benign samples, were analyzed using a 22-gene mutation assay employing next-generation sequencing. Clinicopathological information was retrospectively collected and analyzed. Gene alterations were associated with a higher rate of lymph node metastasis (LNM) and thyroid capsular invasion, a lower rate of coexisting Hashimoto's thyroiditis, the classical PTC subtype, and younger age (<45 years). Among the 22 genes tested, the BRAF mutation rates showed a significant difference between the PTC and benign groups. In the subgroup analysis, younger age (odds ratio = 12.512, 95% confidence interval: 3.126-50.087) was an independent risk factor for LNM. In further analyses, BRAF mutation was significantly associated with LNM in the older subgroup (age ≥ 45 years), suggesting that the BRAF mutation test has greater value for determining PTC prognosis in the older age group. Our findings will provide a more comprehensive understanding of the relationship between gene mutations and PTC and may contribute to improved PTC management.

Tumor location matters, next generation sequencing mutation profiling of left-sided, rectal, and right-sided colorectal tumors in 552 patients

Despite the introduction of new molecular classifications, advanced colorectal cancer (CRC) is treated with chemotherapy supplemented with anti-EGFR and anti-VEGF targeted therapy. In this study, 552 CRC cases with different primary tumor locations (250 left side, 190 rectum, and 112 right side) were retrospectively analyzed by next generation sequencing for mutations in 50 genes. The most frequently mutated genes were TP53 in left-sided tumors compared to right-sided tumors and BRAF in right-sided tumors compared to left-sided tumors. Mutations in KRAS, NRAS, and BRAF were not detected in 45% of patients with left-sided tumors and in 28.6% of patients with right-sided tumors. Liver metastases were more common in patients with left-sided tumors. Tumors on the right side were larger at diagnosis and had a higher grade (G3) than tumors on the left. Rectal tumors exhibit distinctive biological characteristics when compared to left-sided tumors, including a higher absence rate of KRAS, NRAS, and BRAF mutations (47.4% in rectal versus 42.8% in left-sided tumors). These rectal tumors are also unique in their primary metastasis site, which is predominantly the lungs, and they have varying mutation rates, particularly in genes such as BRAF, FBXW7, and TP53, that distinguish them from tumors found in other locations. Primary tumor location has implications for the potential treatment of CRC with anti-EGFR therapy.

Prevalence, risk factors, and BRAF mutation of colorectal sessile serrated lesions among Vietnamese patients.

Sessile serrated lesions (SSLs) are considered precancerous colorectal lesions that should be detected and removed to prevent colorectal cancer. Previous studies in Vietnam mainly investigated the adenoma pathway, with limited data on the serrated pathway. To evaluate the prevalence, risk factors, and BRAF mutations of SSLs in the Vietnamese population. This is a cross-sectional study conducted on patients with lower gastrointestinal symptoms who underwent colonoscopy at a tertiary hospital in Vietnam. SSLs were diagnosed on histopathology according to the 2019 World Health Organization classification. BRAF mutation analysis was performed using the Sanger DNA sequencing method. The multivariate logistic regression model was used to determine SSL-associated factors. There were 2489 patients, with a mean age of 52.1 ± 13.1 and a female-to-male ratio of 1:1.1. The prevalence of SSLs was 4.2% [95% confidence interval (CI): 3.5-5.1]. In the multivariate analysis, factors significantly associated with SSLs were age ≥ 40 [odds ratio (OR): 3.303; 95%CI: 1.607-6.790], male sex (OR: 2.032; 95%CI: 1.204-3.429), diabetes mellitus (OR: 2.721; 95%CI: 1.551-4.772), and hypertension (OR: 1.650, 95%CI: 1.045-2.605). The rate of BRAF mutations in SSLs was 35.5%. The prevalence of SSLs was 4.2%. BRAF mutations were present in one-third of SSLs. Significant risk factors for SSLs included age ≥ 40, male sex, diabetes mellitus, and hypertension.

Predicting BRAF Mutations in Cutaneous Melanoma Patients Using Neural Network Analysis.

Point mutations at codon 600 of the BRAF oncogene are the most common alterations in cutaneous melanoma (CM). Assessment of BRAF status allows to personalize patient management, though the affordability of molecular testing is limited in some countries. This study aimed to develop a model for predicting alteration in BRAF based on routinely available clinical and histological data. Methods: For identifying the key factors associated with point mutations in BRAF, 2041 patients with CM were recruited in the study. The presence of BRAF mutations was an endpoint. The variables included demographic data (gender and age), anatomic location, stage, histological subtype, number of mitosis, and also such features as ulceration, Clark level, Breslow thickness, infiltration by lymphocytes, invasiveness, regression, microsatellites, and association with nevi. Results: A relatively high rate of BRAF mutation was revealed in the Ukrainian cohort of patients with CM. BRAF-mutant melanoma was associated with younger age and location of nonsun-exposed skin. Besides, sex-specific differences were found between CM of various anatomic distributions and the frequency of distinct BRAF mutation subtypes. A minimal set of variables linked to BRAF mutations, defined by the genetic input selection algorithm, included patient age, primary tumor location, histological type, lymphovascular invasion, ulceration, and association with nevi. To encounter nonlinear links, neural network modeling was applied resulting in a multilayer perceptron (MLP) with one hidden layer. Its architecture included four neurons with a logistic activation function. The AUROCMLP6 of the MLP model comprised 0.79 (95% CІ: 0.74-0.84). Under the optimal threshold, the model demonstrated the following parameters: sensitivity: 89.4% (95% CІ: 84.5%-93.1%), specificity: 50.7% (95% CІ: 42.2%-59.1%), positive predictive value: 73.1% (95% CІ: 69.6%-76.3%), and negative predictive value: 76.0% (95% CІ: 67.6%-82.8%). The developed MLP model enables the prediction of the mutation in BRAF oncogene in CM, alleviating decisions on personalized management of patients with CM. In conclusion, the developed MLP model, which relies on the assessment of 6 variables, can predict the BRAF mutation status in patients with CM, supporting decisions on patient management.

KRAS and BRAF Mutation Rates and Survival Outcomes in Colorectal Cancer in an Ethnically Diverse Patient Cohort.

KRAS and BRAF mutation rates in colorectal cancer (CRC) reported from various mono-ethnic studies vary amongst different ethnic groups. However, these differences in mutation rates may not be statistically significant or may be due to differences in environmental and/or laboratory factors across countries rather than racial genetic differences. Here, we compare the KRAS/BRAF mutation rates and survival outcomes in CRC between ethnic groups at a single institution. We also investigate the contributions of genetic, environmental, and laboratory factors to the variations in KRAS/BRAF mutation rates reported from different countries. Clinicopathological data from 453 ethnically diverse patients with CRC were retrospectively analyzed at Liverpool Hospital, NSW Australia (2014-2016). KRAS/BRAF mutations were detected using real-time PCR (Therascreen kits from Qiagen). Mismatch repair (MMR) status was determined using immunohistochemical staining. Four ethnic groups were analyzed: Caucasian, Middle Eastern, Asian, and South American. Overall survival data were available for 406 patients. There was no significant difference in KRAS mutation rates between Caucasians (41.1%), Middle Easterners (47.9%), Asians (44.8%), and South Americans (25%) (p = 0.34). BRAF mutation rates differed significantly between races (p = 0.025), with Caucasians having the highest rates (13.5%) and Middle Easterners the lowest (0%). A secondary analysis in which Caucasians were divided into three subgroups showed that ethnic grouping correlated significantly with KRAS mutation rate (p = 0.009), with central and eastern Europeans having the highest rates (58.3%). There were no significant differences in overall survival (OS) or disease-free survival (DFS) between the four races. The similarity in KRAS mutation rates across races raises the possibility that the differences in KRAS mutation rates reported from various countries may either not be statistically significant or may be due to environmental and/or laboratory factors rather than underlying racial genetic differences. In contrast, we verified that BRAF mutation rates differ significantly between races, suggesting racial genetic differences may be responsible for the discrepant BRAF mutation rates reported from different countries.

Effect and Interactions of BRAF on Lymph Node Metastasis in Papillary Thyroid Carcinoma With Hashimoto Thyroiditis.

The role of B-Raf proto-oncogene (BRAF) in papillary thyroid carcinoma (PTC) with Hashimoto thyroiditis (HT) is unknown. We aimed to explore risk factors affecting lymph node (LN) metastasis and interaction effect of BRAF in PTC patients with HT. We retrospectively collected the data of 994 PTC patients with HT who underwent surgery at the West China Hospital. We analyzed the correlations between preoperative characteristics and LN metastasis in overall, and different BRAFV600E-mutation patients. Logistic regression was applied to analyze the risk factors for LN metastasis. Finally, we performed an interaction effect analysis to identify the interaction effect of BRAF. The overall LN metastasis rate was 52.71% (524/994); the overall BRAF mutation rate was 26.9% (268/994). BRAF mutation rates were significantly different in LN metastasis and nonmetastasis patients (31.7% vs 21.5%; P < .001). In all 994 patients, age, body mass index (BMI), hypertension, tumor maximum diameter, BRAF mutation, tumor location, aspect ratio, calcification, and extrathyroidal invasion were risk factors for LN metastasis (P < .05). In BRAF-mutant patients, smoking, hypertension, maximum diameter, calcification, and multifocality were risk factors for LN metastasis (P < .05). In BRAF wild-type patients, age, BMI, maximum diameter, tumor location, aspect ratio, tumor shape, calcification, and extrathyroidal invasion were risk factors (P < .05). Additionally, we found statistically significant interactions between BRAF and BMI, hypertension, maximum diameter, and calcification (P < .05), suggesting the potential interaction effect of BRAF. BRAF is a risk factor for LN metastasis in PTC with HT. Meanwhile, BRAF can interact with age, BMI, hypertension, and calcification, which together influence LN metastasis.

Association of KRAS, NRAS, BRAF and PIK3CA gene mutations with clinicopathological features, prognosis and ring finger protein 215 expression in patients with colorectal cancer.

The relationships of KRAS, NRAS, BRAF and PIK3CA gene mutations with the clinicopathological features and prognosis of colorectal cancer (CRC) in patient are lacking. Furthermore, the role of ring finger protein 215 (RNF215) in CRC patients with KRAS, NRAS, BRAF and PIK3CA mutations remains unclear. In the present study, 182 surgical resection specimens from patients with primary CRC for retrospective analysis, were collected. KRAS/NRAS/BRAF/PIK3CA gene mutations were confirmed by an amplification-refractory mutation system. Immunohistochemistry (IHC) was conducted to confirm KRAS, NRAS, BRAF and PIK3CA protein expression. RNF215 expression in patients with CRC was evaluated using TIMER 2.0 database and IHC. The individual mutation rates of KRAS, NRAS, BRAF and PIK3CA were 40.7% (74/182), 4.4% (8/182), 4.4% (8/182) and 3.3% (6/182), respectively. The KRAS exon 2 mutation rate was the highest (61.5%, 64/104), and these mutations mainly occurred at codons 12 and 13. KRAS/NRAS/BRAF/PIK3CA wild-type CRC patients had significantly longer overall survival and disease-free survival than mutated KRAS/NRAS/BRAF/PIK3CA CRC patients (P<0.05). Overall, 45.4% (5/11) of patients with PIK3CA mutations had concomitant KRAS mutations. The KRAS/NRAS/BRAF/PIK3CA gene mutation rate in patients with lymph node metastasis (76.1%, 35/46) was significantly higher than that in patients without lymph node metastasis (50.8%, 69/136) (P=0.0027). There were no significant differences in IHC expression between patients with and without KRAS, NRAS, BRAF and PIK3CA mutations (P>0.05). The TIMER 2.0 analysis showed that RNF215 expression was significantly higher in the mutated BRAF group than in the wild-type BRAF group in CRC (P<0.05). In conclusion, KRAS is the most commonly mutated gene, and KRAS mutations may be a poor prognostic factor for patients with CRC. KRAS wild-type patient resistance may be related to PIK3CA gene mutations, although this needs further verification in larger cohorts. BRAF mutations may be associated with RNF215 expression in patients with CRC.

Clinicopathological relevance of BRAF and SMO mutations in Chinese patients with ameloblastoma

Ameloblastomas are benign tumors associated with recurrence and morbidity. Mutations in the V-Raf murine sarcoma viral oncogene homolog B1 (BRAF) and smoothened (SMO) genes have been identified in ameloblastomas. The mutation rate of BRAF in different regions and mutation sites of SMO remains controversial. This study assesses the relationship between these mutations and clinicopathological features of ameloblastoma in Chinese patients. Ameloblastomas were surgically removed from 30 patients and BRAF gene polymorphisms were detected using DNA sequencing analysis. We also examined the relationship between BRAF or SMO mutations and clinicopathological parameters. BRAF V600E mutation was detected in 18 of 30 ameloblastomas. No significant correlation was found between BRAF V600E mutation and age, sex, location, histologic type, capsular invasion, or tumor recurrence. Five cases carried an SMO T364N mutation in exon 5, whereas six carried an SMO S590 T mutation in exon 10. The SMO mutation rate in patients aged ≤ 20 years was significantly higher than that in patients aged > 20 years. SMO T364N and S590 T mutations were closely related to age and capsular invasion. These findings indicate that BRAF V600E, SMO T364N, and SMO S590 T mutations play important roles in the pathogenesis of ameloblastoma. Key highlights The BRAF V600E mutation was highly prevalent in Chinese patients with ameloblastoma. SMO T364N and S590 T mutations are closely related to age and capsular invasion. The BRAF V600E, SMO T364N, and SMO S590 T mutations play important roles in the pathogenesis of ameloblastoma.

Analysis Characteristics of Genetic Alterations in Colorectal Cancer

This study aims to evaluate the mutation status of KRAS, BRAF, NRAS, PIK3CA, and AKT and analyze the association of gene mutations with clinicopathological characteristics of colorectal cancer. 151 colorectal cancer patients were diagnosed at Pathology and Molecular Biology Center in National Cancer Hospital K. The research was conducted as a cross-sectional study using methods such as genomic DNA extraction; mutation analysis by Real-time PCR. Mutation rates of KRAS, BRAF, NRAS, PIK3CA, and AKT were 37.1%, 7.3%, 2.6%, 12.6%, and 1.3%, respectively. KRAS mutation was significantly associated with the size tumor. Additionally, KRAS mutation was mutually exclusive against that of BRAF mutation and tended to coexist with PIK3CA mutation (p&lt;0.05). In conclusion, the most popular mutation in colorectal cancer was KRAS. These were different in gene mutations with clinicopathological characteristics as well as each mutation with others.

Characterization of MCL-1 in patients with colorectal cancer (CRC): Expression, molecular profiles, and outcomes.

3085 Background: Myeloid cell leukemia 1 (MCL-1) is a member of the BCL-2 protein family and is anti-apoptotic/pro-survival in function. Dysregulation of MCL-1 expression has been reported in several solid tumors, including lung and breast cancer. In CRC, MCL-1 has been associated with resistance to chemotherapeutic drugs and multi-kinase inhibitor regorafenib. Our study aimed to characterize the molecular features associated with MCL-1 gene expression in CRC. Methods: 28,576 CRC samples were analyzed by Caris Life Sciences (Phoenix, AZ) with WTS (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES). MCL-1 expression was stratified by quartiles where top quartile transcripts per million (TPM) were considered high (Q4) and bottom quartile low (Q1). Cell infiltration (CI) in the tumor microenvironment (TME) was estimated by RNA deconvolution analysis using QuantiSEQ. Interferon-gamma and T-cell inflamed signatures were also calculated from RNA data. X2 and Fisher-Exact tests were used, and statistical significance was determined as a P-value adjusted for multiple comparisons ( q &lt; 0.05). Real world survival was obtained from insurance claims data and Kaplan-Meier estimates were calculated for molecularly defined patients. Results: MCL-1 expression was significantly increased in rectal tumors compared to other primary tumor sites (median TPM [mTPM] 20.8 vs 18.9 vs 18.7, in rectal vs left-sided vs right-sided, respectively, q &lt; 0.0001). MCL-1 high tumors were associated with increased rate of PD-L1 IHC levels (Q1 vs Q4: 4.2% vs 9.7% [all CRC]; 3.7% vs 8.9% [pMMR/MSS], q &lt; 0.0001), while MCL-1-low showed marginally increased rates of TMB-high (8.0% vs 7.0% [all CRC]; 3.3% vs 2.6% [pMMR/MSS], P &lt; 0.05). MCL-1-high expression was associated with a higher T-cell inflamed signature and IFN score ( q &lt; 0.0001). MCL-1 high was associated with higher mutation rates of CDKN2A, BRCA2, KRAS and GNAS, while lower mutation rates of TP53, PIK3CA, PTEN, BRAF, APC, FBXW7, AMER1, SOX9, and SMAD2 and copy number amplifications in several genes ( q &lt; 0.05). MCL-1 high TME had higher CI of M1 and M2 macrophages, monocytes, B cells, NK cells, and T-reg infiltration, while dendritic cells and CD4+ T-cell were lower ( q &lt; 0.05). Patients with high MCL-1 expressing CRC had longer survival (Q4 vs Q1: 33.5 vs 24.8 months, HR 0.72, 95% CI 0.67-0.77, P &lt; 0.0001) and longer time-on-treatment with regorafenib although with limited clinical benefit (Q4 vs Q1: 2.03 vs 1.06 months, HR: 0.67, 95% CI: 0.50-0.89, P = 0.005). Conclusions: Our data show a strong correlation between distinct immune biomarkers, TME cell infiltration and MCL-1 expression in CRC. Furthermore, increased tumor MCL-1 expression improved patient prognosis and treatment outcomes. These findings suggest a key clinical role for MCL-1 as an important modulator of anti-tumor immunity and TME and a potential biomarker in CRC.

Incidence of BRAF mutations in cutaneous melanoma: histopathological and molecular analysis of aUkrainian population.

This study aimed to investigate the incidence of BRAF mutation in cutaneous melanoma in the Ukrainian population with respect to clinical and histopathological data. This single-center retrospective cohort study enrolled 299 primary CM with known BRAF status assessed by RT-PCR. The overall BRAF mutation rate was 56.5% in CM and demonstrated a link with the younger age (p<0.001), anatomical site (p<0.001) and histological type of CM (p=0.022). BRAF-positive CM possessed a slightly higher mitotic rate (p=0.015) and Breslow thickness (p=0.028) but did not relate to tumor-infiltrating lymphocytes. The high rate of BRAF mutations in CM patients in the Ukrainian cohort was associated with superficial spreading histology, higher depth of invasion and proliferation.

Application of the Novel Grading System of Invasive Pulmonary Adenocarcinoma in a Real Diagnostic Scenario: A Brief Report of 9353 Cases

IntroductionThe International Association for the Study of Lung Cancer proposed a novel grading system of invasive pulmonary adenocarcinoma (IPA), but the application of this grading system and its genotypic characterization in the real diagnostic scenario has never been reported. MethodsWe prospectively collected and analyzed the clinicopathological and genotypic features of a cohort of 9353 consecutive patients with resected IPA, including 7134 patients with detection of common driver mutation. ResultsIn the entire cohort, 3 (0.3%) of lepidic, 1207 (19.0%) of acinar, and 126 (23.6%) of papillary predominant IPAs were diagnosed as grade 3. In chronological order, an evident downtrend of the proportion of grade 2 was observed in chronological order. Conversely, the diagnostic ratio of grade 1 (8.0%–14.5%) and grade 3 (27.9%–32.3%) experienced a gradual rise. EGFR mutation was more frequently detected in grade 2 (77.5%) and grade 1 (69.7%) IPA than grade 3 (53.7%, p < 0.001), whereas the mutation rates of KRAS, BRAF, ALK, and ROS1 were higher in grade 3 IPA. More importantly, the rate of EGFR mutation gradually fell as the proportion of high-grade components increased, to 24.3% in IPA with more than 90% high-grade components. ConclusionsThe grading system for IPA could be applied to stratify patients with different clinicopathological and genotypic features in a real diagnostic scenario.