MYB Alterations Research Articles

Comprehensive analysis of MYB/MYBL1-altered pediatric-type diffuse low-grade glioma.

Pediatric-type diffuse low-grade gliomas (pLGG) harboring recurrent genetic alterations involving MYB or MYBL1 are closely related tumors. Detailed treatment and outcome data of large cohorts are still limited. This study aimed to comprehensively evaluate pLGG with these alterations to define optimal therapeutic strategies. We retrospectively reviewed details of pLGG with MYB or MYBL1 alterations from patients treated or referred for pathologic review at St. Jude Children's Research Hospital. Tumor specimens were centrally reviewed, and clinical data were collated. Thirty-three patients (18 male; median age, 5 years) were identified. Two tumors had MYBL1 alterations; 31 had MYB alterations, MYB::QKI fusion being the most common (n = 10, 30%). Most tumors were in the cerebral hemispheres (n = 22, 67%). Two patients (6%) had metastasis at diagnosis. The median follow-up was 6.1 years. The 5-year event-free survival (EFS) rate was 81.3% ± 8.3%; the 5-year overall survival (OS) rate was 96.4% ± 4.1%. Patients receiving a near-total or gross-total resection had a 5-year EFS of 100%; those receiving a biopsy or subtotal resection had a 5-year EFS rate of 56.6% ± 15.2% (P < .01). No difference in EFS was observed based on location, histology, or molecular alterations. However, the tumors that progressed or metastasized may have distinct methylation profiles with evidence of activation of the MAPK and PI3K/AKT/mTOR pathways. pLGG with MYB/MYBL1 alterations have good outcomes. Our findings suggest that surgical resectability is a crucial determinant of EFS. Further characterization is required to identify optimal treatment strategies for progressive tumors.

The Role of Novel Immunohistochemical Markers for Special Types of Breast Carcinoma.

Some histologic special types of breast carcinoma harbor specific recurrent genetic alterations that are not seen in other types of breast carcinoma (no special type), namely adenoid cystic carcinoma, secretory carcinoma, and tall cell carcinoma with reversed polarity. These tumors have unique morphologic features, are triple-negative, that is, do not express hormone receptors or HER2, and are generally associated with a favorable prognosis. Adenoid cystic carcinoma, like its counterpart in other organs, shows a MYB-NFIB fusion gene that is the result of a recurrent t(6;9)(q22-23;p23-24) translocation. Other MYB alterations have been described that result in overexpression of MYB . Secretory carcinoma is characterized by an ETV6-NTRK3 gene fusion that is the result of recurrent (12;15);(p13;q25) translocation, which is also seen in mammary analog secretory carcinoma of the salivary gland. Tall cell carcinoma with reversed polarity shows IDH2 p.Arg172 hotspot mutations. Immunohistochemical antibodies have emerged that identify the underlying genetic alterations in these tumors and serve as useful diagnostic tools. This review will provide an update on the molecular features and diagnostic immunohistochemical markers that have become increasingly popular to aid in diagnosing these uncommon triple-negative breast tumors.

MYB RNA detection by in situ hybridisation has high sensitivity and specificity for the diagnosis of adenoid cystic carcinoma

Adenoid cystic carcinoma (ACC) is one of the most common primary salivary gland cancers. ACC has several benign and malignant mimics amongst salivary gland neoplasms. An accurate diagnosis of ACC is essential for optimal management of the patients and their follow-up. Upregulation of MYB has been described in 85-90% of ACC, but not in other salivary gland neoplasms. In ACC, MYB upregulation can occur as a result of a genetic rearrangement t(6;9) (q22-23;p23-24), MYB copy number variation (CNV), or enhancer hijacking of MYB. All mechanisms of MYB upregulation result in increased RNA transcription that can be detected using RNA in situ hybridisation (ISH) methods. In this study, utilising 138 primary salivary gland neoplasms including 78 ACC, we evaluate the diagnostic utility of MYB RNA ISH for distinguishing ACC from other primary salivary gland neoplasms with a prominent cribriform architecture including pleomorphic adenoma, basal cell adenoma, basal cell adenocarcinoma, epithelial myoepithelial carcinoma, and polymorphous adenocarcinoma. Fluorescent in situ hybridisation and next generation sequencing were also performed to evaluate the sensitivity and specificity of RNA ISH for detecting increased MYB RNA when MYB gene alterations were present. Detection of MYB RNA has 92.3% sensitivity and 98.2% specificity for a diagnosis of ACC amongst salivary gland neoplasms. The sensitivity of MYB RNA detection by ISH (92.3%) is significantly higher than that of the FISH MYB break-apart probe (42%) for ACC. Next generation sequencing did not demonstrate MYB alterations in cases that lacked MYB RNA overexpression indicating high sensitivity of MYB RNA ISH for detecting MYB gene alterations. The possibility that the sensitivity may be higher in clinical practice with contemporary samples as compared with older retrospective tissue samples with RNA degradation is not entirely excluded. In addition to the high sensitivity and specificity, MYB RNA testing can be performed using standard IHC platforms and protocols and evaluated using brightfield microscopy making it a time and cost-efficient diagnostic tool in routine clinical practice.

Rearrangements, Expression, and Clinical Significance of MYB and MYBL1 in Adenoid Cystic Carcinoma: A Multi-Institutional Study.

Simple SummaryAdenoid cystic carcinoma (ACC) is an aggressive glandular cancer with poor prognosis that preferentially occurs in the head and neck. The MYB and MYBL1 oncogenes are main oncogenic drivers, but the true frequency and clinical significance of these alterations are unclear. Here, we have used tissue microarrays to study these genes in a multi-institutional study of close to 400 ACCs, the largest study to date. We found alterations of MYB/MYBL1 in 78% of the cases and overexpression of the MYB/MYBL1 proteins in 93% of the cases. Importantly, we show that patients with loss of one part of the MYB gene and its neighboring sequences on chromosome 6 have a significantly shorter overall survival compared to those without loss. Our study provides new knowledge about the frequency and clinical significance of MYB/MYBL1 alterations and identifies genes with tumor suppressive functions on chromosome 6 that contribute to poor prognosis in ACC.Adenoid cystic carcinoma (ACC) is an aggressive head and neck malignancy characterized by a t (6;9) translocation resulting in an MYB–NFIB gene fusion or, more rarely, an MYBL1 fusion. The true frequency and clinical significance of these alterations are still unclear. Here, we have used tissue microarrays and analyzed 391 ACCs and 647 non-ACC salivary neoplasms to study the prevalence, expression, and clinical significance of MYB/MYBL1 alterations by FISH and immunohistochemistry. Alterations of MYB or MYBL1 were found in 78% of the cases, of which 62% had MYB alterations and 16% had MYBL1 rearrangements. Overexpression of MYB/MYBL1 oncoproteins was detected in 93% of the cases. MYB split signal, seen in 39% of the cases, was specific for ACC and not encountered in non-ACC salivary tumors. Loss of the 3′-part of MYB was enriched in grade 3 tumors and was a significant independent prognostic biomarker for overall survival in multivariate analyses. We hypothesize that loss of the 3′-part of MYB results from an unbalanced t(6;9) leading to an MYB–NFIB fusion with concomitant loss of the segment distal to the MYB breakpoint in 6q23.3. Our study provides new knowledge about the prevalence and clinical significance of MYB/MYBL1 alterations and indicates the presence of genes with tumor suppressive functions in 6q23.3-qter that contribute to poor prognosis and short overall survival in ACC.

The landscape of common genetic drivers and DNA methylation in low-grade (epilepsy-associated) neuroepithelial tumors: A review.

Low-grade neuroepithelial tumors (LNETs) represent an important group of central nervous system neoplasms, some of which may be associated to epilepsy. The concept of long-term epilepsy-associated tumors (LEATs) includes a heterogenous group of low-grade, cortically based tumors, associated to drug-resistant epilepsy, often requiring surgical treatment. LEATs entities can sometimes be poorly discriminated by histological features, precluding a confident classification in the absence of additional diagnostic tools. This study aimed to provide an updated review on the genomic findings and DNA methylation profiling advances in LNETs, including histological entities of LEATs. A comprehensive search strategy was conducted on PubMed, Embase, and Web of Science Core Collection. High-quality peer-reviewed original manuscripts and review articles with full-text in English, published between 2003 and 2022, were included. Results were screened based on titles and abstracts to determine suitability for inclusion, and when addressed the topic of the review was screened by full-text reading. Data extraction was performed through a qualitative content analysis approach. Most LNETs appear to be driven mainly by a single genomic abnormality and respective affected signaling pathway, including BRAF p.V600E mutations in ganglioglioma, FGFR1 abnormalities in dysembryoplastic neuroepithelial tumor, MYB alterations in angiocentric glioma, BRAF fusions in pilocytic astrocytoma, PRKCA fusions in papillary glioneuronal tumor, between others. However, these molecular alterations are not exclusive, with some overlap amongst different tumor histologies. Also, clustering analysis of DNA methylation profiles allowed the identification of biologically similar molecular groups that sometimes transcend conventional histopathological classification. The exciting developments on the molecular basis of these tumors reinforce the importance of an integrative histopathological and (epi)genetic classification, which can be translated into precision medicine approaches.

LGG-15. COMPREHENSIVE ANALYSIS OF MYB/MYB1-ALTERED GLIOMAS: A MULTI-INSTITUTIONAL EXPERIENCE OF 33 GLIOMAS

BackgroundPediatric diffuse gliomas harbor recurrent genetic alterations, including those in MYB and MYBL1. Regardless of histopathologic classification, low-grade diffuse gliomas with MYB/MYBL1 alterations represent a single disease entity. Additional insight is needed to define optimal therapeutic strategies for these tumors. MethodsWe retrospectively reviewed gliomas with MYB or MYB1L alterations treated or referred for pathologic review at St. Jude Children’s Research Hospital (St. Jude). Tumor specimens were centrally reviewed. Molecular characterization and clinical data were collated from St. Jude and referring institutions. ResultsThirty-three patients were identified. Two tumors had MYBL1 alterations, while 31 had MYB alterations. MYB-QKI fusion was the most common alteration. Eighteen (55%) were male. The median age at diagnosis was 5 years (range, 0–40 years). Most tumors were in the cerebral cortex (22/33), and the most common presentation was seizures (16/33). Three patients (9%) presented with hydrocephalus and required cerebrospinal fluid diversion. Two patients (6%) presented with metastatic disease. Gross-total resection was achieved in 15 patients (45%). Of the 7 patients receiving cytotoxic chemotherapy, no substantial response was observed. Of the 6 patients who received RT, one had disease progression. The median follow-up was 5.9 years. The 5-year event-free survival was 88.1%, while the 5-year overall survival was 96.3%. Two patients died, one of unclear cause and one of treatment-related acute myelogenous leukemia. Using log-rank tests, no difference in outcomes was observed based on molecular characteristics, degree of resection, metastatic status, or treatment modality. ConclusionsAlthough tumors with MYB and MYBL1 alterations present with varying molecular and clinical features, they represent a group of tumors with favorable outcomes. Further characterization is required to identify the subgroup of tumors with a higher propensity for progression.

Abstract 1611: MYB and the MYB-NFIB fusion induce adenoid cystic carcinoma

Abstract Adenoid cystic carcinoma (ACC) is the second most common malignancy of the salivary glands, also found at lower frequency rates in other secretory glands such as the mammary and lacrimal glands. Salivary ACCs are slow-growing but aggressive neoplasms, with propensity to perineural invasion and high recurrence rates. MYB is the most frequently altered gene in ACCs, as approximately 40% of the ACCs contain MYB-NFIB gene fusions, and the full-length MYB is overexpressed in over 50% of the fusion-negative ACCs. However, it is still unclear whether MYB activities promote ACC development. To assess the oncogenic potential of MYB in vivo, we generated transgenic mice that overexpress MYB using the TetO system. In these mice, focal MYB overexpression was directed to salivary and mammary glands using the activator line MMTV-tTA. We found that 25% of these mice developed tumors with an average latency of 23 months. Remarkably, all the tumors that developed in these mice were ACCs, and the three main phenotypic variants of human ACCs (cribriform, tubular and solid) were represented in this cohort. Using the same transgenic system, we found that the MYB-NFIB fusion also induced ACCs, with similar incidence and lower latency. Immunohistochemical analysis of these mouse ACCs for several biomarkers of human ACC, including p63 and c-kit, provided additional evidence of the similarity of the mouse ACCs that developed in these models, and human ACCs. RNAseq global expression profiling uncovered the activation of several cancer-associated pathways in MYB-induced mouse ACCs. Most notably, activation NOTCH signaling was highly enriched in these tumors. Additional analysis for the presence of the NOTCH intracellular domain demonstrated that all of the MYB- and MYB-NFIB-induced ACCs contain NOTCH activation. These findings, and the recent identification of activating mutations in NOTCH1 and NOTCH2 in human ACCs, suggest that NOTCH activities may contribute to ACC development. To test this hypothesis, ongoing studies in the lab are directed to assess the role of NOTCH signaling in ACC development, by generating mouse models in which constitutive activation of NOTCH is induced in mice alone or in combination with MYB alterations. Overall, these studies demonstrate that MYB activities are the main oncogenic driver of ACC. Genomic rearrangements that result in MYB-NFIB fusions may enhance the oncogenic potential of MYB. Citation Format: Yuan Hu, Xiaoyuan Zhu, Han Luo, Adel El-Naggar, Carlos Caulin. MYB and the MYB-NFIB fusion induce adenoid cystic carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1611.

Isomorphic diffuse glioma is a morphologically and molecularly distinct tumour entity with recurrent gene fusions of MYBL1 or MYB and a benign disease course.

The "isomorphic subtype of diffuse astrocytoma" was identified histologically in 2004 as a supratentorial, highly differentiated glioma with low cellularity, low proliferation and focal diffuse brain infiltration. Patients typically had seizures since childhood and all were operated on as adults. To define the position of these lesions among brain tumours, we histologically, molecularly and clinically analysed 26 histologically prototypical isomorphic diffuse gliomas. Immunohistochemically, they were GFAP-positive, MAP2-, OLIG2- and CD34-negative, nuclear ATRX-expression was retained and proliferation was low. All 24 cases sequenced were IDH-wildtype. In cluster analyses of DNA methylation data, isomorphic diffuse gliomas formed a group clearly distinct from other glial/glio-neuronal brain tumours and normal hemispheric tissue, most closely related to paediatric MYB/MYBL1-altered diffuse astrocytomas and angiocentric gliomas. Half of the isomorphic diffuse gliomas had copy number alterations of MYBL1 or MYB (13/25, 52%). Gene fusions of MYBL1 or MYB with various gene partners were identified in 11/22 (50%) and were associated with an increased RNA-expression of the respective MYB-family gene. Integrating copy number alterations and available RNA sequencing data, 20/26 (77%) of isomorphic diffuse gliomas demonstrated MYBL1 (54%) or MYB (23%) alterations. Clinically, 89% of patients were seizure-free after surgery and all had a good outcome. In summary, we here define a distinct benign tumour class belonging to the family of MYB/MYBL1-altered gliomas. Isomorphic diffuse glioma occurs both in children and adults, has a concise morphology, frequent MYBL1 and MYB alterations and a specific DNA methylation profile. As an exclusively histological diagnosis may be very challenging and as paediatric MYB/MYBL1-altered diffuse astrocytomas may have the same gene fusions, we consider DNA methylation profiling very helpful for their identification.

Genomic profiling of variant urinary tract tumor histologies.

450 Background: Little is known about the genomic features of rare histologic variants of urinary tract (UT) tumors. The purpose of this study is to compare the pattern of genetic alterations in UT tumors with adenocarcinoma (AD), small cell (SC), or squamous cell (SQ) histology to UT tumors with urothelial carcinoma (UC) histology. Methods: We identified patients with pure variant (AD, SC, or SQ) or UC histology evaluated at Dana Farber Cancer Institute (DFCI). Tumors with mixed histology were excluded. We employed Oncopanel, which assesses 275-447 cancer genes for somatic mutations and copy number variations (CNVs). Alterations observed at an allele frequency &gt; 0.1% in the ExAC database were assumed to be germline variants and were excluded. Mutation frequencies, CNVs, and tumor mutation burden (TMB) were determined for AD, SC, SQ, and UC, and were compared using the Fisher’s Exact test and Kruskall Wallis Test. Nominal p values were obtained, and fdr correction was employed (q &lt; 0.1). Results: Genetic data was available for 11 AD, 6 SC, 9 SQ, and 120 UC tumors. All patients had muscle-invasive disease. The mean age was 67.8 years and 74% of patients were male. Overall, UC had significantly higher TMB than AD (median = 9.5 vs median = 6 respectively, p = 0.03). There were no significant differences in the CNV count among the four subtypes. Statistically significant differences in genetic alterations by subtype are shown in the Table. ARID1A and KDM6A mutations were less common in the variant histologies; while DICER1, FBXW7, MAP2K4, and MYB alterations were higher in ≥1 variant histology. RB1 and TP53 mutations were enriched in SC tumors while SMAD4 alterations were enriched in AD tumors. Conclusions: Genetic features of variant histology UT tumors differ from those seen in UC, suggesting biological differences and possibly different therapies. Validation in larger datasets is warranted. [Table: see text]

Analysis of clinicopathological characteristics, MYB rearrangement and prognostic factors in salivary adenoid cystic carcinoma.

Recent studies have indicated that a recurrent t(6;9)(q22-23;p23-24) chromosomal translocation in salivary adenoid cystic carcinoma (ACC) results in a MYB proto-oncogene transcription factor-nuclear factor I/B (MYB-NFIB) gene fusion, which has not previously been detected in any non-ACC carcinomas of the head and neck. In the present study, data on clinical factors affecting the survival rate of patients with salivary ACC from a single institution was retrospectively analyzed, and the frequency of MYB gene rearrangement determined. A total of 97 patient cases were analyzed, and young adults presenting with ACC (<40 years old) accounted for 19.6% of all patients (n=19). A total of 70.1% (n=68) displayed neurological symptoms, including pain, paraesthesia, tongue deviation, and facial paralysis. A marked majority of the analyzed tumors (85.6%) displayed evidence of MYB rearrangement. MYB rearrangement was significantly higher in patients with late Tumor-Node-Metastasis (TNM) stage cancer compared with that in patients with early TNM stage (P=0.033), as detected by a dual color MYB break-apart fluorescence in situ hybridization probe. Kaplan-Meier analysis revealed significant differences in patient overall survival (OS) time with regard to age, gender, TNM stage, neurological symptoms, margin status and MYB rearrangement. Specifically, young age was significantly associated with a shorter OS time. In summary, the present study suggested that young patients with salivary ACC presented with a worse prognosis, in contrast to the majority of patients with salivary ACC. Moreover, MYB alterations exhibited a high positive rate in salivary ACC, and therefore, the absence of MYB rearrangements may be associated with a better prognosis.

Identification of Multiple Complex Rearrangements Associated with Deletions in the 6q23-27 Region in Sézary Syndrome

The 6q23-27 region, recurrently deleted in Sézary syndrome (SS), was characterized at the molecular level in 13 SS patients and SS cell line SeAx. Using fine-tiling comparative genomic hybridization, deletions within the 6q23-27 region were detected in half of the samples (six patients and SeAx). All samples with deletions were further analyzed by ligation-mediated PCR. In addition, in one patient sample and in SeAx, paired-end next-generation sequencing was performed on the HiSeq2000 Illumina platform. Using those techniques, 23 rearrangements associated with the deletions were identified. The majority of rearrangements showed enormous complexity and diversity, including eight inversions, three transpositions, and four translocations (with chromosomes 3, 17, 10, and 12). Fifteen genes were disrupted by those rearrangements, the MYB proto-oncogene three times and the interleukin-22 receptor subunit alpha-2 gene (IL22RA2) twice. All three patients with MYB alterations showed low MYB expression, whereas seven of the remaining patients showed overexpression. Most patients overexpressing MYB also presented increased expression of MYC, HSPA8, and BCL2. Five gene fusions were identified, of which two, CCDC28A-IL22RA2 and AIG1-GOSR1, both in SeAx, were in the same orientation and were expressed at the messenger RNA level.

Potential Targets Are Identified in Diffuse Low-Grade Pediatric Gliomas

Abstract Mutually exclusive FGFR1 or MYB alterations are frequent in diffuse low-grade pediatric gliomas.