Search Results (161)

Circulating tumor DNA (ctDNA) analysis offers a non-invasive approach to molecular profiling. While RAS mutations are well-established predictive biomarkers in metastatic colorectal cancer (mCRC), the prognostic value of their variant allele frequency (VAF) remains unclear. We retrospectively analyzed individual patient data with mCRC who underwent ctDNA testing using the FoundationOne^® Liquid CDx assay. The primary objective was to determine the optimal RAS VAF cutoff for overall survival (OS) prognostication. Between November 2020 and July 2024, 282 patients were enrolled. Among 265 eligible patients, 134 (50.6%) were ctRAS mutant, 25 (9.4%) ctBRAF^V600E mutant, and 106 (40.0%) were ctRAS/BRAF wild-type. A RAS VAF threshold of 5% yielded the highest prognostic discrimination for OS (HR = 2.41; 95% CI 1.65–3.55; p < 0.0001; C-index = 0.601). ctRAS-high mutant tumors (VAF ≥ 5%) were associated with synchronous metastatic disease, multiple metastatic sites, higher blood tumor mutational burden, and elevated tumor fraction. ctRAS-low mutant tumors (VAF < 5%) were more frequently metachronous, presented with a single metastatic site, and showed liver involvement. High RAS VAF in ctDNA is a strong and independent prognostic marker for OS in mCRC. Quantitative ctDNA profiling may enhance risk stratification and guide personalized management strategies. Full article

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with a five-year survival rate of 3–15% and limited effective treatment options for most patients. Approximately 5–10% of cases are wild-type KRAS and are more likely to harbor rare alterations, including gene fusions involving anaplastic lymphoma kinase (ALK), ROS Proto-Oncogene 1 (ROS1), neurotrophic tyrosine receptor kinase (NTRK), Rearranged During Transfection (RET), Fibroblast Growth Factor Receptor (FGFR), or Neuregulin 1 (NRG1) genes, as well as germline mutations in DNA repair genes. This review integrates current evidence on the prevalence, molecular profile, and clinical significance of gene fusions, amplification, and somatic/germline mutations in PDAC, with a particular focus on the wild-type KRAS subgroup. Clinical trial data and case reports indicate that these alterations can enhance patient susceptibility to targeted therapies. Currently, selpercatinib, larotrectinib, and repotrectinib are approved by the FDA for the treatment of certain solid tumors harboring specific gene fusions. Recent studies on zenocutuzumab resulted in the FDA-accelerated approval for NGR1 fusion-positive NSCLC and PDAC. Germline mutations may specifically increase responsiveness to poly(ADP-ribose) polymerase (PARP) inhibitors or platinum-based treatments. Comprehensive genomic profiling, incorporating fusion detection and germline testing, is essential to identify patients who may benefit from precision-based approaches. Full article

Colorectal cancer (CRC) classification has progressed from consensus molecular subtypes (CMS) to epithelial–intrinsic consensus molecular subtypes (iCMS) and the layered intrinsic subtype-MSI-fibrosis (IMF) system that combines intrinsic state, MSI status, and fibrosis. This article reviews biological underpinnings of iCMS/IMF, their relationships to tumor-microenvironment crosstalk, and how single-cell and spatial transcriptomics refine therapeutic stratification by resolving tumor microenvironment heterogeneity and its impact on fibrosis. Prognostic and therapeutic implications are covered, including PD-1 blockade in MSI-high (MSI-H), MAPK-directed therapy in BRAF-mutant disease, and EGFR targeting in selected RAS wild-type (WT) left-sided tumors, and we suggest decision points specifically informed by the activity of the fibrosis axis. A step-by-step procedure is presented for the analysis of bulk and single-cell RNA and formalin-fixed, paraffin-embedded (FFPE) resources, along with open-source tools and reporting standards to make iCMS/IMF calling reproducible in clinics and trials. Future outlooks are outlined with near-term biomarker–drug hypotheses for microsatellite-stable (MSS)-iCMS3 and high fibrosis tumors and key gaps to close for clinical translation. This review outlines a roadmap for precision medicine in colorectal cancer by leveraging the iCMS/IMF framework to integrate pathology and digital pathology, molecular diagnostics, and therapy mapping with FAP-targeted imaging and therapy. Full article

Background: KRAS mutations are detected in ~40% of colorectal cancer (CRC), yet their prognostic value is heterogeneous across specific substitutions; the impact of uncommon variants, particularly in non-metastatic disease, remains uncertain. Methods: We evaluated the prognostic role of the relatively infrequent KRAS G12A substitution in two independent retrospective cohorts of stage II–III CRC treated with surgical resection without neoadjuvant therapy: an institutional series (FMU; n = 299) and a public dataset (AC-ICAM; n = 178). Tumors were genotyped for KRAS (and BRAF in AC-ICAM), and relapse-free survival (RFS) and overall survival (OS) were investigated. Results: KRAS G12A comprised 3.0% (FMU) and 3.4% (AC-ICAM). Across genotypes, G12A showed the highest univariable hazards compared to wild-type (WT) references for both RFS and OS in each cohort. Notably, RFS events among G12A clustered within 12 months of surgery. In multivariable Cox models, G12A remained independently associated with worse RFS and OS in each cohort, whereas non-G12A KRAS mutations did not differ significantly from the WT references. Conclusions: Across two cohorts, KRAS G12A identified a small but clinically meaningful high-risk subset of stage II–III CRC characterized by early recurrence and inferior survival. Recognition of this variant may inform postoperative risk stratification in the adjuvant setting. Full article

Background: BRAF mutations are found in 10% of colon cancers (CCs) and are associated with poor prognosis in metastatic disease. BRAF V600E predicts sensitivity to cetuximab + encorafenib in the metastatic setting. With new trials testing encorafenib-containing regimens for early-stage CC, we sought to characterize the clinical outcomes of early-stage BRAF V600E CC. Methods: We performed a systematic review and meta-analysis. Key inclusion criteria were a diagnosis of stage 2/3 BRAF V600E CC. Co-primary endpoints were overall survival (OS) and recurrence/disease-free survival (DFS). Meta-analysis was performed with a random-effects model incorporating sample size, hazard ratio (HR), and 95% confidence intervals (CIs). Results: A total of 206 studies underwent full-text review. Of these, six randomized controlled trials were included, comprising 6836 and 843 patients with wild-type (WT) and BRAF V600E, respectively. BRAF V600E was associated with inferior OS (HR 1.49, CI 1.21–1.75) and DFS (HR 1.17, CI 1.03–1.33). This finding remains in patients with microsatellite instability—low/stable or proficient mismatch repair (OS: HR 1.66, CI 1.36–2.02, DFS: HR 1.45, CI 1.22–1.72). Conclusions: BRAF V600E is associated with inferior prognoses compared to BRAF WT in early-stage CC. This finding will help optimize trial design for this population. Full article

Background/Objectives: BRAF mutation is the most frequent somatic mutation in melanoma. The BRAF mutational status is crucial in selecting systemic therapy for advanced melanoma. Another important consideration is whether a melanoma is in situ or invasive. If this aspect could be known before the first surgical intervention, the appropriate surgical margins could be chosen from the beginning and a second surgical step could be avoided. Could the dermoscopic image predict the BRAF mutational status? Could it also predict if a melanoma is in situ or invasive? Methods: This retrospective study included 50 patients with 52 melanomas. The mutational status of the BRAF gene was determined, and the dermoscopic images were analysed. Results: There were no statistically significant differences between the BRAF-mutant melanoma group and the BRAF wild-type melanoma group. However, there were statistically significant differences between the dermoscopic images of melanomas in situ and thin invasive melanomas (≤1 mm Breslow thickness). Irregular dots or globules (p = 0.008), a blue-white veil (p = 0.011), milky red areas (p = 0.008), dotted vessels (p = 0.04), and linear irregular vessels (p = 0.016) were all more frequently present in thin invasive melanomas compared to melanomas in situ. Conclusions: Dermoscopy could predict whether a melanoma is in situ or invasive, but it could not predict the mutational BRAF status in the present study. Full article

Low-grade-serous ovarian carcinomas (LGSOC) are rare tumors characterized by a high recurrence rate and limited treatment options. Most LGSOC are estrogen receptor (ER)-positive and demonstrate alterations in the RAS/MAPK pathway. Avutometinib is a dual RAF/MEK clamp, whereas defactinib and VS-4718 are focal adhesion kinase (FAK) inhibitors. Fulvestrant is an ER antagonist/degrader. We assessed the preclinical efficacy of fulvestrant, avutometinib + VS-4718 (FAKi), and the triple combination in a chemotherapy/aromatase inhibitor-resistant LGSOC patient-derived tumor xenograft (PDX) model. Tissue obtained from a LGSOC patient wild-type for KRAS/NRAS/BRAF mutations in progression after chemotherapy/anastrozole was transplanted into female CB17/lcrHsd-Prkdc/SCID mice (PDX-OVA(K)250). The animals were treated with either saline/control, fulvestrant, avutometinib/FAKi, or the triple combination of avutometinib/FAKi/fulvestrant. Avutometinib and FAKi were given five-days on and two-days off through oral gavage. Fulvestrant was administered subcutaneously weekly. Mechanistic studies were performed ex vivo using Western blot assays. Animals treated with the triple combination demonstrated stronger tumor growth inhibition compared to all the other experimental groups including control/saline (p < 0.001), single-agent fulvestrant (p = 0.04 from day eight and onwards), and avutometinib/FAKi (p = 0.02 from day 18). Median survival for mice treated with saline/control was 29 days while mice in all other experimental groups were alive at day 60 (p < 0.0001). Treatment was well tolerated across all experimental treatments. By Western blot, exposure of OVA(K)250 to the triple combination demonstrated a decrease in phosphorylated MEK (p-MEK) and p-ERK levels. The addition of fulvestrant to avutometinib/FAKi is well tolerated in vivo and enhances the antitumor activity of avutometinib/FAKi in a LGSOC-PDX model with acquired resistance to chemotherapy/aromatase inhibitors. These results support the clinical evaluation of avutometinib/defactinib in combination with fulvestrant or an aromatase inhibitor in patients with recurrent LGSOC. Full article

Epidermal growth factor receptor (EGFR) inhibitors remain a cornerstone in the treatment of metastatic colorectal cancer with RAS and BRAF wild-type cancer. Yet, primary and acquired resistance limit their benefit for many patients. A growing body of evidence reveals that resistance is not random but rather driven by a complex network of molecular alterations that sustain tumor growth independent of EGFR signaling. These include amplification of ERBB2 (HER2) and MET, activation of the PI3K and AKT pathways, EGFR extracellular domain mutations, and rare kinase fusions. The concept of negative hyperselection has emerged as a powerful strategy to refine patient selection by excluding tumors with these resistance drivers. Multiple clinical trials have consistently shown that patients who are hyperselected based on comprehensive molecular profiling achieve significantly higher response rates and improved survival compared to those selected by RAS and BRAF status alone. Liquid biopsy through circulating tumor DNA has further transformed this landscape, offering a noninvasive tool to capture tumor heterogeneity, monitor clonal evolution in real time, and guide rechallenge strategies after resistance emerges. Together, negative hyperselection, ctDNA-guided monitoring, and emerging therapeutics define a precision-oncology framework for identifying, tracking, and overcoming resistance to anti-EGFR therapy in mCRC, moving the field toward more effective and individualized care. Looking ahead, the development of innovative therapeutics such as bispecific antibodies, antibody drug conjugates, and RNA-based therapies promises to further expand in this challenging clinical scenario. These advances move precision oncology in colorectal cancer from concept to clinical reality, reshaping the standard of care through molecular insights. Full article

Background/Objectives: The clinical, histopathological, and dermoscopic features may be associated with melanoma mutational status. The aims of the study were to assess the clinical, histopathological, and dermoscopic features of melanoma to identify their correlation with BRAF, NRAS, and cell cycle genes’ mutational status in melanoma. Methods: The clinical, histopathological information, dermoscopic images, and genomic DNA of 55 histopathologically diagnosed primary cutaneous melanomas were retrospectively analyzed. Next-generation sequencing (NGS) assays were conducted on the Ion GeneStudio S5 platform (Thermo Fisher Scientific, Waltham, MA, USA), using the Ion AmpliSeq™ Italian Melanoma Intergroup Somatic Panel. Results: Overall, 55 melanomas, including 30 superficial spreading, 24 nodular, and 1 naevoid, were analyzed. BRAF mutation was more frequently observed in ulcerated melanoma (16/23; 69.6%), with mitotic rate ≥ 5 n/mm² (8/11; 72.7%), while NRAS mutation was more common in amelanotic/hypomelanotic (8/17; 70.0%) and nodular melanoma (10/24; 41.7%). Dermoscopically, shiny white structures (OR = 3.50; 95% confidence interval: 1.13–10.84) were associated with BRAF-mutated melanomas, whereas a homogeneous disorganized pattern was associated with NRAS-mutated melanomas (OR = 6.96; 1.49–32.53). The risk of diagnosing cell cycle gene-mutated melanomas was significantly increased in presence of vascular patterns (OR = 4.50; 1.33–15.20), linear irregular (OR = 3.75; 1.18–11.92), polymorphous vessels (OR = 4.05; 1.27–12.97), and milky red globules/areas (OR = 3.14; 1.00–9.89). The blue-white veil was significantly associated with P53 mutation (OR = 35.84; 2.01–640.2). Conclusions: Conversely to Wild Type, BRAF, NRAS, and cell cycle gene-mutated melanomas were significantly associated with clinical and dermoscopic features underlying a more aggressive melanoma phenotype. The vascular pattern, linear irregular, polymorphous vessels, and milky-red globules/areas may be considered predictors of cell cycle mutated melanomas. Full article

BRAF inhibitors have a 50–70% response rate in melanoma but are less effective for thyroid cancer. Differential response may be from activation or expression of downstream mitogen-activated protein kinase (MAPK) pathway genes. Retrospective analysis compared whole exome and transcriptome sequencing in melanoma and thyroid cancers from April 2019 to October 2023. The MAPK Activation Score (MPAS) was calculated using Z-score normalized/log-transformed values indicating expression across 10 MAPK-associated genes. Our tumor registry provided outcome data. BRAF V600E mutations were identified in 33 of 200 (17%) melanomas and 14 (7%) had other BRAF mutations (V600K/R). Of 49 thyroid tumor samples, BRAF V600E mutations were found in 19 (39%). RNA expression of BRAF and the 10 MAPK-associated genes were increased in melanomas with V600E compared to wild-type BRAF (p = 0.02). Conversely, BRAF V600E mutation in thyroid cancer was not associated with increased expression nor MAPK pathway activation. No significant difference in overall survival based on BRAF mutation was observed in the subset of patients where data was available. The MAPK pathway is differentially affected by the different cancers, with increased MAPK activation observed in melanoma and not in thyroid cancer. This may account in part for the observed differential response to BRAF inhibitors. Full article

Some pancreatic ductal-type (PDADK) and lung adenocarcinomas (LADK) lacking other molecular drivers are reported to harbor NRG1 fusions as potential novel therapeutic targets. We investigated the feasibility of a fluorescent in situ hybridization (FISH)-based diagnosis of NRG1 fusions in a case series of PDADK and LADK lacking other identified oncogenic drivers. First, among a case series of PDADK, KRAS analyses (PCR followed in PCR-negative cases by RNA sequencing—RNAseq) found 27/162 (16.7%) KRAS wild-type cases, among which 1/162 (0.6%) NRG1 fusion was diagnosed using FISH. Secondly, among a case series of LDAK, 191/446 (42.8%) cases had no molecular alterations in EGFR, KRAS, BRAF, HER2, MET, ALK, ROS1 and RET according to NGS and FISH analyses and, among them, 4/446 (0.9%) cases had NRG1 fusions using FISH. Finally, four additional cases out of the two previously mentioned cases series (1 PDADK and 3 LADK) with NRG1 fusions diagnosed by first-line RNAseq were also concluded as NRG1 FISH-positive. The NRG1 FISH tests for the nine NRG1 FISH-positive cases resulted in 50% to 80% of positive tumor nuclei, all with single 3′-NRG1 FISH signals. In our series, of the 22 cases analyzed with both NRG1 FISH (positivity criterion of at least 15% of tumor nuclei with a split between the 5′- and the 3′- parts of the probes and/or isolated single 3′-NRG1 signal) and RNAseq, 17 cases were FISH– RNAseq– and 5 cases were FISH+ RNAseq+ (no FISH+ RNAseq– or FISH– RNAseq+ cases in our study) resulting in 100% sensibility and specificity for the NRG1 FISH test. In the case of no access to RNAseq, NRG1 FISH consists of a valuable tool searching for NRG1 fusions in patients with advanced cancers. Full article

It has been more than a decade since anti-PD-1 and anti-CTLA-4 antibodies were first introduced for the treatment of unresectable melanoma. The advent of these immunotherapies has dramatically transformed the treatment landscape. In recent years, anti-PD-1 antibodies have become the cornerstone of melanoma therapy, and the development of new treatment regimens has advanced rapidly in both Eastern and Western countries. However, clinical practice has revealed lower response rates in East Asian melanoma patients compared to Caucasian populations. This discrepancy may be partially attributed to T cell immune exhaustion within the tumor microenvironment, although the detailed mechanisms remain unclear. Moreover, there is currently no established treatment for BRAF wild-type melanoma that is resistant to anti-PD-1 antibodies. This review discusses the currently available therapeutic strategies for advanced melanoma and addresses the aforementioned challenges, highlighting recent efforts in both Eastern and Western regions. Full article

Background: Anti-EGFR therapy, combined with chemotherapy, represents the standard therapeutic approach for triple wild-type (KRAS/NRAS and BRAF), left-sided, microsatellite stable (MSS) metastatic colorectal cancer (mCRC). However, acquired resistance develops in approximately 50% of patients. This study evaluated the efficacy of anti-EGFR therapy re-challenge and analyzed circulating tumor DNA (ctDNA) for potential resistance mechanisms. Methods: Eleven patients with triple wild-type, MSS, HER2-negative, left-sided mCRC were included. All patients received Cetuximab with chemotherapy as the first-line treatment, with three patients subsequently receiving Cetuximab re-challenge. Twenty-one plasma samples were collected at baseline and at each response assessment for retrospective ctDNA analysis using next-generation sequencing with a 16-gene panel. Results: Genetic alterations were detected in only 14.2% of ctDNA samples. In one re-challenge patient, the KRAS: c.35G>A mutation appeared during progression. No RAS mutations were identified in four patients who progressed on first-line Cetuximab treatment. Conclusions: This preliminary study suggests that clinically based anti-EGFR re-challenge may benefit selected mCRC patients. The low detection rate of resistance-conferring mutations indicates potential alternative resistance mechanisms beyond RAS pathway alterations. Our findings, while limited by sample size and the retrospective design of ctDNA testing, contribute to the growing evidence supporting anti-EGFR re-challenge strategies in mCRC management. Full article

Background/Objectives: According to recent reports, the BRAF^V600E mutation in serous borderline tumors (SBTs) plays a protective role against progression to low-grade serous carcinoma through oncogene-induced senescence. One consequence of this is the appearance of eosinophilic cells (ECs). The aim of the current study was to determine the interobserver reproducibility of ECs and their predictive significance for the detection of the BRAF^V600E mutation in SBTs. Methods: The study was conducted using 63 cases of ovarian SBTs. Three gynecological pathologists, blinded to each tumor’s mutation status, assessed the presence of ECs. Immunohistochemical staining with p16 and Ki-67 was performed to validate ECs. Mutational analysis was carried out using targeted NGS. Results: Genetic analysis revealed 30 BRAF-mutated, 1 NRAS-mutated, and 9 KRAS-mutated SBTs. ECs were identified by the majority of pathologists (two or three) in 78% of the BRAF^V600E-mutated and 11% of the wild-type tumors with other mutations (p < 0.0001). The interobserver reproducibility of the presence of ECs was substantial (κ = 0.66). ECs validated with p16/Ki-67 were identified in 92.6% of the BRAF^V600E-mutated and in 13.8% of the wild-type tumors with other mutations (p < 0.0001). For the ECs identified by the majority of pathologists, the sensitivity and specificity when predicting the BRAF^V600E mutation were 77.8% and 88.9%, respectively. For the ECs validated with p16/Ki-67, the sensitivity and specificity when predicting the BRAF^V600E mutation were 95.3% and 90.5%, respectively. Conclusions: Overall, these results suggest that ECs in SBTs have potential association with the BRAF^V600E mutation. Full article

The clinicopathological and molecular features of synchronous parathyroid carcinoma (PC) and thyroid carcinoma in a male patient are presented. At 11, he received mantle field radiotherapy for Hodgkin lymphoma. He had a 26-year adulthood history of recurrent nephrolithiasis treated five times with lithotripsy. At 52, he was referred to our clinic for hypercalcemia. Primary hyperparathyroidism was diagnosed (calcium: 3.46 mmol/L, parathormone: 150 pmol/L, preserved renal function, nephrolithiasis, and osteoporosis). Neck ultrasound revealed a 41 × 31 × 37 mm nodule in the left thyroid and smaller nodules in the right thyroid. Enlarged cervical lymph nodes were not observed. The large nodule was interpreted as parathyroid adenoma on 99Tc-pertechnetate scintigraphy/99Tc-MIBI scintigraphy with SPECT/CT. Total left-sided and subtotal right-sided thyroidectomy were performed. Histopathology confirmed locally invasive, low-grade PC (pT2; positive for parafibromin and E-cadherin, negative for galectin-3 and PGP9.5; wild-type expression for p53 and retinoblastoma protein; Ki-67 index 10%) and incidental papillary thyroid carcinoma (pT1b). Genetic profiling revealed no loss in CDC73, MEN1, CCND1, PIK3CA, CDH1, RB1, and TP53 genes. Deletions in CDKN2A, LATS1, ARID1A, ARID1B, RAD54L, and MUTYH genes and monosomies in nine chromosomes were identified. The tumor mutational burden and genomic instability score were low, and the tumor was microsatellite-stable. The thyroid carcinoma exhibited a TRIM24::BRAF fusion. Following surgery, the parathormone and calcium levels had normalized, and the patient underwent radioiodine treatment for thyroid cancer. The follow-up of 14 months was eventless. In summary, the clinical, laboratory, and imaging features of hyperparathyroidism taken together could have suggested malignancy, then confirmed histologically. The synchronous carcinomas were most likely caused by irradiation treatment diagnosed 41 years after exposure. It seems that the radiation injury initially induced parathyroid adenoma in young adulthood, which underwent a malignant transformation around age fifty. Full article