BRAF Point Mutations Research Articles

S100 and CD34 positive spindle cell tumors of the uterine cervix with EGFR mutation: a hitherto unrecognized neoplasm phenotypically and epigenetically overlapping with "NTRK-rearranged spindle cell neoplasms" of the uterus.

NTRK-rearranged spindle cell neoplasm represents an emerging entity included in the latest 5th edition of WHO classification of both soft tissue and female genital tumors. By immunohistochemistry, they are commonly positive for CD34, S100 protein, and CD30 and typically harbor fusions of kinase genes such as NTRK1/2/3, RET, and BRAF. In the gynecological tract, they typically affect the uterine cervix or uterine body. Most of the reported cases had fibrosarcoma-like morphology, occasionally showing perivascular and stromal hyalinization with only a few cases showing a less cellular spindle cell proliferation. Except for one case with RET fusion, all other gynecological cases harbored exclusively NTRK1/2/3 fusions. Besides kinase gene fusions, the analogous tumors in soft tissues may also harbor activating EGFR or BRAF point mutations, but no such case has been described in the uterus. Herein we are reporting two cases from the uterine cervix showing morphology and molecular features previously unreported at this anatomic site. The patients were 46 and 34years old and clinically presented with unremarkable cervical polyps each measuring 8mm in diameter. Histologically, both cases had a rounded polypoid outline and were composed of hypocellular proliferation of bland spindle cells lacking mitotic activity and growing in a fibrotic stroma which was punctuated by prominent small vessels with thick hyalinized walls. Immunohistochemically, both showed a diffuse expression of CD34, CD30, and S100 protein, whereas SOX10 was negative. Both cases harbored exon 20 EGFR mutation and did not reveal any fusions or significant copy number changes. The patient in case 1 was treated by hysterectomy with salpingectomy with no other residual tumor detected, and she was alive and well 27months after the diagnosis. The patient in case 2 had no other known tumors at the time of diagnosis, but no follow-up is available. We believe the reported cases represent a hitherto unrecognized variant of "NTRK-rearranged spindle cell neoplasms" of the uterine cervix with novel EGFR mutations.

The Gundersen Precision Oncology Cohort: A biospecimen resource for mutation characterization and target discovery.

e15184 Background: The generation and widespread sharing of large somatic mutation datasets has revolutionized our understanding of genetic mechanisms driving cancer initiation and progression. For well-understood mutations, this has created the opportunity for individualized therapeutic intervention in a wide range of malignancies. Beyond these well-characterized mutations, there exists a wide range of alterations that remain poorly understood and which require some kind of functional genomics analysis to determine whether such patients are eligible for the targeted therapy used for more typical mutations in that gene, whether these alterations are passenger mutations that don’t affect throughput on the associated signaling pathway, or reflect another more nuanced phenomenon. Whether using ectopic overexpression in cell lines or generation of genetically modified mice, addressing this problem at scale using functional genomics approaches is challenging. A key limitation is the absence of the original tissue context in which that variant co-evolved with other genetic alterations as well as data on the clinical response of the patient to successive lines of therapy. This can be addressed, in part, by the banking of tissue from patient cohorts who have had comprehensive genomic profiling as part of their routine clinical care. For this purpose, we have established the Gundersen Precision Oncology Cohort. Methods: The Gundersen Precision Oncology Cohort is a retrospective collection of tissue specimens, NGS reports and associated clinical data from deceased patients who received cancer care at the Gundersen Health System. The cohort is updated twice per year and banked tissue specimens are available for collaborative research studies. Results: At November 20, 2023 there were data from 780 patients in the cohort, with specimens tested between 2015 and 2023. 54 tumor types were represented, of which lung (n = 196), colorectal (n = 79), pancreas (n = 65), esophageal (n = 58) and breast (n = 46) were most common. The most common diagnostic companies were STRATA Oncology (n = 463) and Tempus (n = 248). Most patients had testing at a single timepoint, but longitudinal testing is available for 13 patients. We present data from some of the studied subgroups, including atypical point mutations in BRAF as well as fusions affecting BRAF and ROS1. Conclusions: This cohort, available for collaborative studies via the Gundersen Cancer Biobank, illustrates the value of banking well-annotated biospecimens to address outstanding questions in oncology.

Abstract 950: Functional characterization of atypical somatic variants in the Gundersen Precision Oncology Cohort

Abstract The generation and widespread sharing of large somatic mutation datasets has revolutionized our understanding of genetic mechanisms driving cancer initiation and progression. For well-understood mutations, this has created the opportunity for individualized therapeutic intervention in a wide range of malignancies. Beyond these well-characterized mutations, there exists a wide range of alterations that remain poorly understood and which require some kind of functional genomics analysis to determine whether such patients are eligible for the targeted therapy used for more typical mutations in that gene, whether these alterations are passenger mutations that don’t affect throughput on the associated signaling pathway, or reflect another more nuanced phenomenon. Whether using ectopic overexpression in cell lines or generation of genetically modified mice, addressing this problem at scale using functional genomics approaches is challenging. A key limitation is the absence of the original tissue context in which that variant co-evolved with other genetic alterations as well as data on the clinical response of the patient to successive lines of therapy. This can be addressed, in part, by the banking of tissue from patient cohorts who have had comprehensive genomic profiling as part of their routine clinical care. The Gundersen Precision Oncology Cohort is a growing dataset of FFPE specimens and longitudinal clinical data from more than 750 patients who have had comprehensive cancer genome profiling using assays from a wide range of diagnostic companies. We use this resource for biomarker discovery and functional classification of many atypical cancer variants. Current subgroups include atypical point mutations in BRAF, ERBB2 and ERBB3, as well as fusions affecting BRAF, PIK3CA and ROS1. We present examples illustrating the value of this approach for classification of variants detected in a range of tumor types. Citation Format: Peter Feiszt, Paraic A. Kenny. Functional characterization of atypical somatic variants in the Gundersen Precision Oncology Cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 950.

In-house molecular diagnosis of diffuse glioma updating the revised WHO classification by a platform of the advanced medical care system, Senshin-Iryo.

Since the World Health Organization (WHO) 2016 revision, the number of molecular markers required for diffuse gliomas has increased, placing a burden on clinical practice. We have established an in-house, molecular diagnostic platform using Senshin-Iryo, a feature of Japan's unique healthcare system, and partially modified the analysis method in accordance with the WHO 2021 revision. Herein, we review over a total 5 years of achievements using this platform. Analyses of IDH, BRAF, and H3 point mutations, loss of heterozygosity (LOH) on 1p/19q and chromosomes 10 and 17, and MGMT methylation were combined into a set that was submitted to Senshin-Iryo as "Drug resistance gene testing for anticancer chemotherapy" and was approved in August 2018. Subsequently, in October 2021, Sanger sequencing for the TERT promoter mutation was added to the set, and LOH analysis was replaced with multiplex ligation-dependent probe amplification (MLPA) to analyze 1p/19q codeletion and newly required genetic markers, such as EGFR, PTEN, and CDKN2A from WHO 2021. Among the over 200 cases included, 54 were analyzed after the WHO 2021 revision. The laboratory has maintained a diagnostic platform where molecular diagnoses are confirmed within 2 weeks. Initial expenditures exceeded the income from patient copayments; however, it has gradually been reduced to running costs alone and is approaching profitability. After the WHO 2021 revision, diagnoses were confirmed using molecular markers obtained from Senshin-Iryo in 38 of 54 cases (70.1%). Among the remaining 16 patients, only four (7.4%) were diagnosed with diffuse glioma, not elsewhere classified, which was excluded in 12 cases where glioblastoma was confirmed by histopathological diagnosis. Our Senshin-Iryo trial functioned as a salvage system to overcome the transition period between continued revisions of WHO classification that has caused a clinical dilemma in the Japanese healthcare system.

10098-MPC-10 HOW SHOULD WE RESPOND TO REPEATED WHO REVISIONS? IN-HOUSE MOLECULAR DIAGNOSIS SYSTEM BY ADVANCED MEDICAL SYSTEM

Abstract BACKGROUND Since the WHO2016 revision, required molecular markers has been increasing, placing a burden on clinical practice of diffuse gliomas. We established an in-house molecular diagnostic platform by Senshin-Iryo (meaning advanced medical care system) and have since been partially modifying the analysis method in accordance with the WHO2021 revision. We review our achievements in total 5 years. METHODS Analyses of IDH, BRAF, and H3 point mutations, loss of heterozygosity on 1p19q and chromosomes 10 and 17, and MGMT methylation were combined into a set and submitted as a Senshin-Iryo "Drug resistance gene testing for anticancer chemotherapy" and approved in August 2018. Subsequently, in October 2021, Sanger sequencing for TERT promotor mutation was added to the set and the LOH analysis was replaced to MLPA, in order to analyze 1p19q codeletion and newly required genetic markers; EGFR, PTEN, CDKN2A, etc. in WHO2021. RESULTS The cumulative number of cases has reached over 200. Among them, 54 cases were analyzed after WHO2021 revision. The laboratory has maintained the diagnostic platform in which molecular diagnoses are steadily confirmed generally within two weeks. The initial expenditure was exceeded the income obtained from the patient co-payment, however, it has gradually been reduced to running costs alone, then is approaching profitability. After WHO2021 revision, diagnoses could be confirmed by molecular markers obtained from Senshin-Iryo in 38 of 54 cases (70.1%). Among the remaining 16, only 4 (7.4%) cases remained diagnosed as diffuse glioma, NEC, exclusionary after 12 cases in which glioblastoma was confirmed by histopathological diagnosis. CONCLUSIONS Our Senshin-Iryo trial has functioned as a salvage system to overcome the current transition period in which the continuing revision of WHO classification causing a clinical dilemma of healthcare system.

Pediatric Pleomorphic Xanthoastrocytoma with Neoplastic Meningitis: A Case Report with Cytopathological Evidence with Literature Review

AbstractPleomorphic xanthoastrocytoma (PXA) was regarded as grade II tumor and considered to be associated with favorable outcome. The World Health Organization Central Nervous System 5 (WHO CNS5) has classified PXA under circumscribed astrocytic gliomas and graded 2 or 3 depending on histology. Cerebrospinal fluid (CSF) and leptomeningeal spread are observed rarely in these tumors. The present case report describes a PXA, grade 3 tumor in a young male with neoplastic meningitis. This 17-year-old male child presented with history of seizure, signs of raised intracranial pressure, and meningeal irritation. Well-defined, T2 heterogeneously hyperintense lesion (5.5*4.8 cm) was seen in right frontal lobe with mild heterogenous contrast enhancement and adjacent pachy-meningeal enhancement. Right frontal craniotomy and near total excision were done. Postoperative hydrocephalus was treated with CSF diversion. Histopathology showed epithelioid and rhabdoid morphology with significant cellular pleomorphism and atypical mitosis consistent with the PXA, grade 3. The CSF cytology showed numerous tumor cells with marked nuclear and cytoplasmic pleomorphism. PXA is a rare malignancy of children and young adults, commonly seen in the temporal lobes. BRAF point mutations of V600E type are most common in PXA, grade 2. Meningeal dissemination is uncommon in PXA and its presence marks poor outcome. PXA, grade 2 tumors could be followed with serial imaging following gross total resection. PXA, grade 3 tumors are managed with maximal-safe resection, radiotherapy, and/ or chemotherapy. PXA, grade 3 with CSF spread tends to have rapid decline in the clinical course and it is advisable to get routine baseline and follow-up craniospinal screening and needs aggressive management.

Disseminated Xanthogranuloma with BRAF Gene Fusion and Profound Response to MEK Inhibitor Therapy

Background: Histiocytic neoplasms represent a diverse group of clonal hematopoietic disorders, varying in severity from xanthogranuloma to multisystemic Erdheim-Chester Disease (ECD). Both Langerhans cell histiocytosis (LCH) and non-Langerhans cell histiocytosis (nLCH) are characterized by activating mutations in the MAPK pathway, primarily involving BRAF point mutations. In this report, we present a compelling case of disseminated xanthogranuloma with a unique BRAF fusion, which exhibited a remarkable therapeutic response to MEK inhibition. This finding adds to our understanding of the molecular heterogeneity within histiocytic neoplasms and highlights the potential significance of targeted therapies in managing these rare but clinically significant disorders Clinical Observation: In this clinical observation, we present the case of a 71-year-old female who sought medical attention due to a 3-year history of progressive cutaneous lesions, accompanied by hoarseness and blurry vision. A biopsy of a lesion revealed characteristic features consistent with xanthogranuloma. Further examination through direct laryngoscopy unveiled lesions on the vocal cords and tracheal masses, which exhibited identical histologic findings as the skin biopsies. A comprehensive analysis involving massively parallel DNA sequencing revealed the presence of a GAB2-BRAF fusion, along with a tumor mutational burden of 1 mutation/megabase (Mb). Immunohistochemical testing of the endobronchial biopsy demonstrated a combined positive score of 10% for PDL-1 expression, suggesting the potential for immune checkpoint blockade. Given the implicated role of MAPK pathway activation due to the identified fusion, a therapeutic approach utilizing the MEK inhibitor Trametinib was initiated. Encouragingly, the patient exhibited a favorable response with a reduction in tumor burden, near-resolution of hoarseness, and improved vision. However, this treatment was accompanied by MEK inhibitor-associated cardiotoxicity, leading to the discontinuation of Trametinib. Regrettably, following the cessation of Trametinib, the patient's lesions rapidly progressed, and her disease worsened beyond the pre-treatment state. Taking into account the 10% PDL-1 positivity, immunotherapy with Pembrolizumab was commenced, resulting in partial improvement. Nonetheless, the patient developed immunotherapy-related cardiotoxicity. In light of the continued disease progression off therapy, the MEK inhibitor Cobimetinib was introduced. The patient responded rapidly to this therapeutic intervention; however, during a one-week break in Cobimetinib treatment, the disease worsened back to the baseline. Consequently, Cobimetinib was discontinued, and a continuously dosed MEK inhibitor, Binimetinib, was cautiously administered at a lower dose to mitigate the risk of cardiotoxicity. As of the time of this report, the patient remains on Binimetinib, achieving complete clinical remission, and there is no evidence of further cardiotoxicity. This clinical observation underscores the challenges and complexities in managing advanced xanthogranuloma with unique molecular alterations and highlights the importance of closely monitoring and tailoring therapies to optimize patient outcomes. Conclusion: To our knowledge, this is the first clinical trial documenting MEK inhibition for a patient with xanthoma disseminatum harboring a BRAF fusion. Seeking to target downstream of BRAF, MEK inhibition demonstrated a dramatic response, with rapid relapse upon cessation, supporting a central oncogenic role for BRAF fusion. Further studies should explore alterations in the RAS-BRAF-ERK pathway in nLCH and consider clinical trials with MEK inhibitors. Our clinical experience suggests continuous MEK inhibitor exposure may be necessary for effective disease control. These findings advance our understanding of therapeutic options in histiocytic neoplasms, paving the way for more precise and impactful treatments.

Molecular features of thyroid cancer in children

Background. Malignant neoplasms of the thyroid gland are the most common endocrine malignant neoplasms in the children’s age group. Unlike adults, who most often have BRAF and RAS mutations, children have chromosomal displacements. The relevance is explained by the lack of comprehensive studies on thyroid cancer in children in the Russian-language literature.The aim of the study is — to summarize and systematize the literature data on the molecular features of thyroid cancer in children.Materials and methods. The authors conducted a search for publications in the PubMed electronic database using the following algorithm: Molecular AND Thyroid cancer AND pediatrics. We found 451 publications, and after reviewing the annotations, 111 studies describing the molecular features of thyroid cancer in the pediatric population were included in the review. Publications were excluded due to duplication and inconsistency with the subject of this study.Results. Instead of point mutations of BRAF and RAS, characteristic of adults, regardless of radiation status, chromosomal displacements are more common in children. Re-arrangement of RET/PTC genes is the most common, followed by BRAF fusions. Mutations of the TERT promoter, which are markers of the aggressive course of the disease in adults, are rare in children. DICER1 mutations appear to play a key role in pediatric cases of follicular and papillary thyroid cancer. Medullary thyroid cancer (MTC) in children requires the exclusion of multiple endocrine neoplasia syndrome (MEN type 2). Tumors originating from follicular cells other than MTC can rarely be familial. Literature data on the role of microRNA as a biomarker in thyroid carcinomas in children is currently limited.

Expression of NRP1, SMAD4 in correlation to mutational status of KRAS, NRAS in pancreatic cancer

Background: Pancreatic cancer is the second leading cause of death in tumor diseases worldwide. The expression of NRP1 and the presence of KRAS and BRAF point mutation lead to the cell survival by simultaneously with the SMAD2 and SMAD4 inactivation. In higher stages, we often find deletion of p53.

A Rapid Genotyping Assay for CSF Accelerates Diagnosis and Treatment Initiation for CNS Malignancies

The overlapping clinical and radiographic features of CNS neoplasms, combined with low yields of conventional CSF studies, complicate diagnostic workflows and delay treatment initiation. Neurosurgical biopsies of high-risk lesions are frequently required, and decisions regarding extent of surgical resection are challenging. In order to address these challenges, we previously developed the Targeted Rapid Sequencing (TetRS) assay to detect highly recurrent point mutations characteristic of CNS neoplasms from CSF, within 80 minutes of sample collection. This qPCR-based panel offers parallel detection of MYD88, TERT promoter, IDH1/2, BRAF and H3F3A point mutations. In this study, we describe the clinical performance and real-time utilization of this assay in a large, single-center prospective patient sample. We asked whether rapid point mutation detection from CSF liquid biopsies can (1) accelerate times to diagnosis and (2) provide a basis for safely initiating disease-directed therapies in the absence of solid tissue sampling. We collected CSF from 98 patients with new CNS lesions suspicious for neoplasms over an 18-month period. Patient enrollment, selection of specific assay variants, and utilization of results in clinical decision-making were at the discretion of providing physicians. IRB approval was obtained. In this diverse cohort, 40 of 98 patients ultimately established a diagnosis of a CNS neoplasm. A point mutation was detected by TetRS in 15 out of 40 patients with a neoplasm (37.5%); this included cases of primary and secondary CNS lymphoma (PCNSL), glioblastoma, IDH-mutant brainstem glioma and H3K27M-mutant diffuse midline glioma. In time-to-event analyses, we found that detection of a mutation by TetRS accelerated the return of diagnostic information from CSF sampling when compared to contemporaneous and historical control cases in which a mutation was not detected (median 0.5 vs 10.5 days, P<0.01). We found multiple cases in which mutation detection by TetRS helped to avoid neurosurgical biopsy. In one representative case, detection of the MYD88 L265P mutation established the diagnosis of PCNSL; methotrexate and rituximab were initiated within 3 days of CSF sampling. In this patient, TetRS results over serial CSF samplings correlated with treatment response and detecting disease recurrence. In another representative case, a lesion initially thought to be an H3K27M-mutant diffuse midline glioma on clinical and radiographic grounds was instead diagnosed as an IDH-mutant brainstem glioma based on TetRS detection of the IDH1 R132G mutation in CSF. This enabled rapid initiation of fractionated radiation, as well as targeted IDH inhibitor therapy; the patient experienced clinical and radiographic response over 10 months of follow-up. TetRS thus represents a novel, targeted point mutation panel that can rapidly and specifically diagnose a broad array of CNS neoplasms. We demonstrate the potential of this novel tool to accelerate diagnosis, follow treatment response and detect recurrence in selected patients without solid tissue sampling. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Epidemiology of Thyroid Cancer.

Epidemiology of Thyroid Cancer.

Abstract 2196: Oncogenic context drives the landscape of tumor suppression in lung cancer

Abstract Cooperative interactions between genomic alterations in oncogenes and tumor suppressors are a hallmark of cancer. While molecular characterization of tens of thousands of primary tumors has solidified estimates of how frequently specific genomic alterations occur, identifying genetic interactions from co-mutation rates alone remains limited by the vast number of possible combinations as well as inherent biases and confounding effects. Conversely, genetically engineered mouse models can reliably uncover causal effects of specific genetic alterations but are not sufficiently high throughput to generate broad insights into the interplay between genetic alterations in tumors. Therefore, how the effects of one alteration on tumor growth change in the context of other alterations remains largely unknown. We previously addressed these technical limitations by combining CRISPR/Cas9-mediated gene editing, tumor barcoding, and ultra-deep barcode sequencing methods with genetically engineered mouse models of human lung cancer, which together enable multiplexing of tumor genotypes in individual mice and precise, high-throughput quantification of in vivo tumor fitness. Here, we leverage this platform to systematically quantify the growth effects of over 45 known and putative tumor suppressor gene alterations across different common oncogenic point mutations in Kras and Braf. While the set of genes we identified as tumor suppressive in KrasG12D- and KrasG12C-driven lung cancers was largely consistent, inactivation of those genes typically resulted in larger tumor growth advantages in the KrasG12D model. Inactivation of most genes in BrafV600E-driven lung tumors had a strikingly different growth effect than in tumors with either Kras variant, and effects were generally far less pronounced in the BrafV600E context. Interestingly, loss of genes upstream of Braf within the Ras pathway often had strong effects in the KrasG12D or KrasG12C models—loss of Nf1, a negative regulator of Kras, or loss of the wildtype Kras allele enhanced oncogenic Kras-driven tumor growth, while loss of Shp2, a positive regulator of Kras, was mildly detrimental—but had little or no effects in the BrafV600E model. We assessed translatability of our experimental cause-and-effect data through comparisons to correlative data from publicly available human lung cancer genomics databases, and found that genetic interactions predicted by our models and gene co-mutation rates in patient tumors largely align. Together, these findings underscore the need for a contextual understanding of the ways in which tumors are influenced by their genetics and highlight the utility of high-throughput, quantitative autochthonous mouse models in pursuing this endeavor. Citation Format: Ian Winters, Lily Blair, Lafia Sebastian, Gabriel Grenot, Edwin Apilado, Wensheng Nie, Vy Tran, Ian Lai, Gregory Wall, Dmitri Petrov, Monte Winslow, Joseph Juan, Michael Rosen. Oncogenic context drives the landscape of tumor suppression in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2196.

Genomic landscape of sporadic pediatric differentiated thyroid cancers: a systematic review and meta-analysis.

Differentiated thyroid cancers (DTCs) in the paediatric population differ from that of their adult counterparts in terms of clinicopathological characteristics and treatment outcomes. This systematic review and meta-analysis was conducted to comprehensively evaluate the prevalence of various genetic alterations underlying the pathogenesis of sporadic paediatric DTCs. This study followed the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) guidelines. Systematic searches were made on the PubMed and Embase databases using relevant keywords, and articles published until October 15, 2021 were selected. Data on the prevalence of various genetic alterations were extracted from the individual articles. Random-effects model was employed for meta-analysis to generate pooled estimates and their 95% confidence intervals (95% CIs). Thirty-three articles comprising 1,380 paediatric patients were included. RET rearrangement (pooled prevalence: 24.4%, 95% CI: 19.1-30.1) was observed to be the most common genetic alteration in sporadic paediatric DTCs, closely followed by BRAF point mutation (pooled prevalence: 21.2%, 95% CI: 17.2-25.5). Other common alterations included: NTRK rearrangement (pooled prevalence: 13.5%, 95% CI: 9.5-17.9) and DICER1 mutation (pooled prevalence: 12.5%, 95% CI: 3.6-25.7). RAS and TERT mutations were observed to be relatively uncommon (pooled prevalence: 5.7%, 95% CI: 2.9-9.3, and 2.2%, 95% CI: 0.4-5.5, respectively). There was no evidence of publication bias. Fusion oncogenes are noted to be the major oncogenic drivers in sporadic paediatric DTCs and underlie their unique behaviour. However, despite the relatively lower frequency of BRAF point mutation compared to adults, it remains a major player in childhood DTCs.

NTRK-fusions in pediatric thyroid tumors: Current state and future perspectives

Pediatric and adult papillary thyroid cancer (PTC) share many similar oncogenic drivers, but differ in the pathological features and outcomes of the disease. The most frequent genetic alterations in adult PTCs are mutually exclusive point mutations in BRAF or the RAS family. In pediatric PTC, fusion oncogenes involving chromosomal translocations in tyrosine kinase (TK) receptors, most commonly RET and NTRK, are the most common genetic alterations observed. This review of the literature describes the current state of translational research in pediatric NTRK-driven thyroid cancer and highlights opportunities to improve our understanding and current models of pediatric PTC.

PRKAR1A and Thyroid Tumors.

Simple SummaryIn 2021 it is estimated that there will be 44,280 new cases of thyroid cancer in the United States and the incidence rate is higher in women than in men by almost 3 times. Well-differentiated thyroid cancer is the most common subtype of thyroid cancer and includes follicular (FTC) and papillary (PTC) carcinomas. Over the last decade, researchers have been able to better understand the molecular mechanisms involved in thyroid carcinogenesis, identifying genes including but not limited to RAS, BRAF, PAX8/PPARγ chromosomal rearrangements and others, as well as several tumor genes involved in major signaling pathways regulating cell cycle, differentiation, growth, or proliferation. Patients with Carney complex (CNC) have increased incidence of thyroid tumors, including cancer, yet little is known about this association. CNC is a familial multiple neoplasia and lentiginosis syndrome cause by inactivating mutations in the PRKAR1A gene which encodes the regulatory subunit type 1α of protein kinase A. This work summarizes what we know today about PRKAR1A defects in humans and mice and their role in thyroid tumor development, as the first such review on this issue.Thyroid cancer is the most common type of endocrine malignancy and the incidence is rapidly increasing. Follicular (FTC) and papillary thyroid (PTC) carcinomas comprise the well-differentiated subtype and they are the two most common thyroid carcinomas. Multiple molecular genetic and epigenetic alterations have been identified in various types of thyroid tumors over the years. Point mutations in BRAF, RAS as well as RET/PTC and PAX8/PPARγ chromosomal rearrangements are common. Thyroid cancer, including both FTC and PTC, has been observed in patients with Carney Complex (CNC), a syndrome that is inherited in an autosomal dominant manner and predisposes to various tumors. CNC is caused by inactivating mutations in the tumor-suppressor gene encoding the cyclic AMP (cAMP)-dependent protein kinase A (PKA) type 1α regulatory subunit (PRKAR1A) mapped in chromosome 17 (17q22–24). Growth of the thyroid is driven by the TSH/cAMP/PKA signaling pathway and it has been shown in mouse models that PKA activation through genetic ablation of the regulatory subunit Prkar1a can cause FTC. In this review, we provide an overview of the molecular mechanisms contributing to thyroid tumorigenesis associated with inactivation of the RRKAR1A gene.

Molecular Alterations in Relation to Histopathological Characteristics in a Large Series of Pediatric Papillary Thyroid Carcinoma from a Single Institution.

Simple SummaryPapillary thyroid carcinoma (PTC) in pediatric patients shows different characteristics compared with PTC in adults. In this large mono-institutional cohort of pediatric PTCs, tumor tissue samples have been analyzed for point mutations and fusions. Overall, molecular alterations were detected in 131 out of 163 PTCs (80%). Fusion-driven PTCs showed more aggressive clinico-pathological features compared to mutation-driven and wild-type cases. These results highlight the importance of testing pediatric PTCs for gene rearrangement in routine characterization of tumors.Papillary thyroid carcinoma (PTC) presents distinct clinico-pathological and molecular differences in children compared with adult patients. Whether the presence of rearrangements or point mutations is associated with aggressive PTC clinical presentation is still controversial. In this study, PTCs diagnosed in patients aged less than 18 years were retrospectively searched from the institutional archive and tumor tissue was tested for point mutations in BRAF and RAS genes and for rearrangements in RET, NTRK1, NTRK3, ALK, PPARG, BRAF and THADA. A total of 163 PTCs were analyzed. Point mutations were found in 83 (51%) and gene fusions in 48 cases (30%). The most frequent alteration was the BRAFV600E mutation (36.8%), followed by NTRK3 fusion (11%), NRAS mutation (10.4%) and RET fusion (10.4%). Fusion-driven PTCs showed more frequently infiltrative growth, larger tumors, extrathyroidal extension and N1b disease. PTCs showing solid growth pattern were significantly enriched in gene fusions. This is one of the largest cohorts of pediatric PTCs. Fusion-driven tumors most frequently show aggressive pathological features; the search for rearrangements, especially in tumors with solid areas, could improve the characterization of pediatric PTCs and offer possible therapeutic options.

FIREFLY-1: A phase 2 study of the pan-RAF inhibitor DAY101 in pediatric patients with low-grade glioma.

TPS10056 Background: The mitogen-activated protein kinase (MAPK) signaling pathway is an essential pathway that regulates key cell functions such as growth, survival, and differentiation. Genomic alterations and dysregulation of the MAPK pathway including BRAF fusions, point mutations (e.g. BRAF V600) and in-frame deletions have been described in many different types of malignancies, including pediatric low-grade glioma (pLGG) and other pediatric cancers. The identification of the KIAA1549:BRAF fusion in 2008 led to deeper understanding of the genomic events driving growth of pLGG (Jones, Cancer Res 2008). Despite the low-grade histology and excellent long-term survival, pLGGs are often associated with tumor- and treatment-associated morbidity and significant late-effects that persist throughout the lifespan of the patient. DAY101 is an oral, highly selective, CNS-penetrant small-molecule, Type II pan-RAF kinase inhibitor that is being developed for patients with pLGG harboring an activating BRAF-alteration. DAY101 has demonstrated tumor inhibition in preclinical models and has achieved clinically meaningful and durable responses in 7/8 patients with RAF-altered LGG in a pediatric phase 1 trial, including 2 complete responses, 3 partial responses, 2 stable disease and 1 progressive disease with a median time to response of 10.5 weeks. Patients have been treated for up to two years with no discontinuations due to toxicity or disease progression (Wright, SNO 2020). Methods: FIREFLY-1 is an open-label, multi-center, international Phase 2 study with DAY101 in pediatric and young adult patients between the ages of 6 months and 25 years with LGG harboring a documented BRAF-alteration as determined by local laboratory testing. DAY101 is administered orally once a week on a continuous 28-day schedule. Patients who respond will be treated for a minimum of two years after which they may at any point, opt to enter a “drug holiday” discontinuation period. Dosing is based on body surface area. DAY101 is available in a pediatric-friendly oral liquid formulation and tablets. The primary endpoint is objective response rate based on Response Assessment for Neuro-Oncology (RANO) as determined by an independent review committee. Secondary endpoints include objective response rate based on Response Assessment in Pediatric Neuro-Oncology (RAPNO) working group criteria, duration of response and safety. Exploratory endpoints include quality-of-life measurements as well as functional outcomes. Molecular abnormalities will be characterized through the analysis of archival tissue. Enrollment began in February 2021 and is ongoing. Clinical trial information: NCT03429804.

LGG-46. MOLECULAR CHARACTERIZATION OF HEMISPHERIC LOW-GRADE GLIOMAS IN CHILDREN

BACKGROUNDHeterogeneous pathology in hemispheric low-grade gliomas (hemLGG) stress the importance of molecular testing in terms of prognosis prediction and targeted therapy options.METHODSDemographic data was collected and targeted genomic approach was employed in the single institutional study. RT-PCR was used to screen for KIAA1549-BRAF fusion and FGFR1 tyrosine-kinase domain duplication (FGFR1-ITD). Direct sequencing evaluated point mutations (BRAF ex15 and ex11, FGFR1 ex12 and ex14). Samples with no detected alteration were subjected to panel RNA-sequencing (FusionPlex Archer Diagnostics).RESULTSWithin 2000–2019 were diagnosed 76 patients with hemLGG (median age 11.1y, range 0.0y–18.5y) comprising predominantly of ganglioglioma, dysembryoplastic neuroepithelial tumors, and diffuse astrocytoma. 40 % of hemLGG were characterized by BRAF alterations with over 2/3 of those cases harboring BRAF point mutations (two BRAFex11, 12 BRAFV600E). Notably, BRAF fusions were uncommon and detected only in six patients (two KIAA-BRAF fusion, two minor oncogenic BRAF variants, two non-KIAA BRAF fusion). 25 % of alterations were found in genes for receptor tyrosine kinases, consisting of seven patients with FGFR1-ITD, three FGFR2/3 fusions, two FGFR1 mutations, two ALK fusions, and one ROS fusion. Out of MAP kinase pathway, the most frequent alteration was IDH1 mutations (n=9). Two angiocentric gliomas were characterized by MYB-QKI fusion.CONCLUSIONTargeted sequencing combined with RNA-sequencing is feasible to establish molecular diagnosis in majority of cases and reveal new and rare alterations. Significant prevalence of non-BRAF alterations explains heterogeneity among hemLGG.

BIOM-54. A RAPID GENOTYPING PANEL FOR SENSITIVE AND SPECIFIC SEGREGATION OF CNS PATHOLOGIES

Abstract Primary central nervous system lymphoma (PCNSL) remains challenging to diagnose due to nonspecific clinical and radiologic features and low diagnostic yields of cerebrospinal fluid (CSF) studies. We sought to characterize the diagnostic approach of suspected PCNSL, in order to improve clinical workflow. We first reviewed 1,007 new brain lesions of unknown etiology that included PCNSL in the radiologic differential diagnosis. The most common final diagnoses included high-grade glioma (28.2%) and PCNSL (14.6%). Diagnostic biopsies were frequently performed for high-grade glioma (100%) and PCNSL (94.4%), while CSF was frequently sampled for PCNSL (78.7%). We next identified 159 patients with an established new diagnosis of PCNSL. CSF studies were non-diagnostic in 86.7% of cases, whereas biopsy was positive in 93%. However, intraoperative histopathology was inconclusive for PNCSL in 54.5%, likely contributing to 22% of patients undergoing surgical resection. These challenges resulted in 12 days median time to treatment initiation, and readmission for further workup or treatment initiation in 27% of patients. These results indicated the need for a rapid, sensitive and specific platform to segregate PCNSL and glioma using CSF and tissue samples. We developed a qPCR-based assay to genotype the MYD88 L265P hotspot mutation from CSF and plasma within 80 minutes of sample acquisition. Results were concordant with orthogonal DNA sequencing in extracts from 87 archived specimens, with detection limits of 490pg of input genomic DNA and 0.15% mutant allele frequency. When performed simultaneously with assays for TERT promoter, IDH1/2, H3F3A and BRAF point mutations, the resulting panel accurately segregated PCNSL and adult diffuse glioma molecular diagnoses in 87 archived specimens and 19 prospective liquid biopsies, including cases of lymphoma and glioma. We propose that inclusion of targeted analysis of these mutually exclusive recurrent molecular alterations characterizing gliomas and PCNSL will facilitate rapid, sensitive diagnosis from solid and liquid biopsies.

Safety and efficacy evaluation of encorafenib plus binimetinib for the treatment of advanced BRAF-mutant melanoma patients

ABSTRACT Introduction Approximately 40–50% of patients with cutaneous melanoma harbor point mutations in BRAF. BRAF and MEK inhibitors in combination are now a standard therapy for advanced BRAF V600-mutated melanoma. Nevertheless, survival rates with the combination are limited, highlighting the need for further therapeutic improvement and strategies to overcome primary and acquired resistance. Areas covered Encorafenib, a highly selective BRAF inhibitor, was developed in combination with binimetinib, a potent, selective allosteric MEK1/2 inhibitor, to improve efficacy and tolerability over other approved combo-targeted therapies. This novel combination shows peculiar pharmacodynamic properties which translate in a higher on-target potency and paradox index. Consistent survival improvements for encorafenib and binimetinib in BRAF V600-mutated melanoma have been confirmed in clinical trials, with over 4 years of median follow up. Expert opinion the favorable survival results and the attractive toxicity profile suggest that encorafenib and binimetinib combination is an intriguing standard option when targeted therapies are considered as first line treatment in BRAF mutated melanoma patients. In the near future, results from ongoing clinical trials will provide information on the use of this novel combination in specific situation, including as adjuvant treatment or as a combination strategy.