Abstract
Accumulation of single stranded DNA (ssDNA) gaps in the nascent strand during DNA replication has been associated with cytotoxicity and hypersensitivity to genotoxic stress, particularly ...upon inactivation of the BRCA tumor suppressor pathway. However, how ssDNA gaps contribute to genotoxicity is not well understood. Here, we describe a multi-step nucleolytic processing of replication stress-induced ssDNA gaps which converts them into cytotoxic double stranded DNA breaks (DSBs). We show that ssDNA gaps are extended bidirectionally by MRE11 in the 3’−5’ direction and by EXO1 in the 5’−3’ direction, in a process which is suppressed by the BRCA pathway. Subsequently, the parental strand at the ssDNA gap is cleaved by the MRE11 endonuclease generating a double strand break. We also show that exposure to bisphenol A (BPA) and diethylhexyl phthalate (DEHP), which are widespread environmental contaminants due to their use in plastics manufacturing, causes nascent strand ssDNA gaps during replication. These gaps are processed through the same mechanism described above to generate DSBs. Our work sheds light on both the relevance of ssDNA gaps as major determinants of genomic instability, as well as the mechanism through which they are processed to generate genomic instability and cytotoxicity.
Abstract
The inability to protect stalled replication forks from nucleolytic degradation drives genome instability and underlies chemosensitivity in BRCA-deficient tumors. An emerging hallmark of ...BRCA-deficiency is the inability to suppress replication-associated single-stranded DNA (ssDNA) gaps. Here, we report that lagging strand ssDNA gaps interfere with the ASF1-CAF-1 nucleosome assembly pathway, and drive fork degradation in BRCA-deficient cells. We show that CAF-1 function at replication forks is lost in BRCA-deficient cells, due to defects in its recycling during replication stress. This CAF-1 recycling defect is caused by lagging strand gaps which preclude PCNA unloading, causing sequestration of PCNA-CAF-1 complexes on chromatin. Importantly, correcting PCNA unloading defects in BRCA-deficient cells restores CAF-1-dependent fork stability. We further show that the activation of a HIRA-dependent compensatory histone deposition pathway restores fork stability to BRCA-deficient cells. We thus define lagging strand gap suppression and nucleosome assembly as critical enablers of BRCA-mediated fork stability.
Abstract
Dysembryoplastic neuroepithelial tumors (DNT) lacking key diagnostic criteria are challenging to diagnose and sometimes fall into the broader category of mixed neuronal-glial tumors (MNGT) ...or the recently described polymorphous low-grade neuroepithelial tumor of the young (PLNTY). We examined 41 patients with DNT, MNGT, or PLNTY for histologic features, genomic findings, and progression-free survival (PFS). Genomic analysis included sequence and copy number variants and RNA-sequencing. Classic DNT (n = 26) was compared with those with diffuse growth without cortical nodules (n = 15), 6 of which exhibited impressive CD34 staining classifying them as PLNTY. Genomic analysis was complete in 33, with sequence alterations recurrently identified in BRAF, FGFR1, NF1, and PDGFRA, as well as 7 fusion genes involving FGFR2, FGFR1, NTRK2, and BRAF. Genetic alterations did not distinguish between MNGTs, DNTs, or PLNTYs; however, FGFR1 alterations were confined to DNT, and PLNTYs contained BRAF V600E or FGFR2 fusion genes. Analysis of PFS showed no significant difference by histology or genetic alteration; however, numbers were small and follow-up time short. Further molecular characterization of a PLNTY-related gene fusion, FGFR2-CTNNA3, demonstrated oncogenic potential via MAPK/PI3K/mTOR pathway activation. Overall, DNT-MNGT spectrum tumors exhibit diverse genomic alterations, with more than half (19/33) leading to MAPK/PI3K pathway alterations.
Abstract
Pediatric low-grade gliomas (PLGGs) are the most common brain tumors in children, with varying degrees of brain invasion. Recent whole-genome sequencing has identified a rare gene fusion ...involving RAF1, a RAF isoform. Unlike other RAF fusions, RAF1 fusions are resistant to existing RAF inhibitors. Therefore, aside from surgical resection with adjuvant chemotherapy and radiation therapy, there are few targeted therapeutic alternatives for RAF1-fusion-driven PLGGs. Despite the prevalence and challenges this disease presented, our understanding of PLGGs was limited by a lack of genetic models. We ultimately picked Drosophila melanogaster as our model organism due to the conservation of major signaling pathways between flies and humans. Furthermore, this connection between humans and flies, coupled with other technical advantages associated with this model organism, like short generation cycle and its powerful genetic toolbox, makes Drosophila melanogaster an ideal organism to study the genesis and progression of PLGGs. With the help of the GAL4/UAS system, we established four fusion-driven PLGG fly genetic models and found that glial overexpression of QKI-RAF1, a fusion gene in pilocytic astrocytomas, induces an invasion-like phenotype with aberrant glial migration. This migration defect was suppressed by glial overexpression of repulsive guidance signaling receptors Robo2 or PlexA/B, indicating the dysregulation of repulsive guidance signaling pathways. Immunostaining coupled with quantitative analysis revealed that Robo2 expression is downregulated in migrating tumor cells in flies, which is recapitulated in mouse astrocytes overexpressing QKI-RAF1 and PLGG patients with RAF fusions. We further broaden our findings by profiling the tumor transcriptomes, revealing potential downstream effectors, including the G protein-coupled receptor GPR180/CG9304, and inhibition of which suppresses tumor invasion in flies. Taken together, we present the PLGG fly model system, leading to the discovery of Robo2, Plexins, and GPR180/CG9304 as potential therapeutic targets.
Sclerosing epithelioid fibrosarcoma (SEF) is an uncommon neoplasm that rarely presents in bone. It is characterized by epithelioid cells arranged in nests and single-file cords within a sclerotic ...stromal background which may mimic neoplastic bone. SEF harbors an EWSR1 translocation, which may complicate its distinction from Ewing sarcoma in cases with histomorphologic overlap. We present a diagnostically challenging case of SEF in the mandible of a 16-year-old girl. Our experience highlights the lack of specificity of traditional morphology and EWSR1 break-apart fluorescent in situ hybridization. Open-ended RNA-based fusion gene testing coupled with MUC4 immunohistochemistry aided the eventual diagnosis in this case. Herein, we report the third case of SEF with EWSR1-CREB3L3 translocation and show that this fusion leads to aberrant upregulation of the phosphoinositide 3-kinase/mammalian target of rapamycin signaling pathway in heterologous cell models.
Pediatric histiocytic neoplasms are hematopoietic disorders frequently driven by the BRAF‐V600E mutation. Here, we identified two BRAF gene fusions (novel MTAP‐BRAF and MS4A6A‐BRAF) in two aggressive ...histiocytic neoplasms. In contrast to previously described BRAF fusions, MTAP‐BRAF and MS4A6A‐BRAF do not respond to the paradox breaker RAF inhibitor (RAFi) PLX8394 due to stable fusion dimerization mediated by the N‐terminal fusion partners. This highlights a significant and clinically relevant shift from the current dogma that BRAF‐fusions respond similarly to BRAF‐inhibitors. As an alternative, we show suppression of fusion‐driven oncogenic growth with the pan‐RAFi LY3009120 and MEK inhibition.
Abstract
Dysembryoplastic neuroepithelial tumor (DNT) is a benign glioneuronal neoplasm classified by the 2016 WHO under the mixed neuronal-glial tumors. Compared to other low-grade neuroepithelial ...tumors (LGNTs) in this category, the genetic profile of DNTs is poorly understood. DNTs have been shown to exhibit mutational variability, ranging from stable genomes to occurrence of BRAF V600E (30% of cases), whole chromosome gains and FGFR1 mutations. To further expand our understanding of genetic drivers of DNTs, we performed clinical integrated genomic profiling and identified two novel FGFR2-associated gene fusions, FGFR2-INA and FGFR2-CTNNA3, in three patients with the histologic diagnosis of DNT. All three DNT cases harbored novel in-frame fusions between the kinase domain of FGFR2 and INA or CTNNA3. To functionally characterize the novel FGFR2 fusions, we cloned FGFR2-INA and stably expressed it in heterologous cell models. Soft agar proliferation assays showed significant increase in colony count in FGFR2-INA expressing cells over control (p<0.0005). In western blot assays, increased protein phosphorylation of both the MAPK and PI3K/mTOR pathways was observed in FGFR2-INA cells. Mechanistically, we found that FGFR2-INA dimerizes in co-immunoprecipitation assays suggesting dimerization induced activation of FGFR2 fusion proteins. We thereby identify and describe two novel FGFR2 fusions associated with DNT that aberrantly activate the MAPK and PI3K/mTOR signaling pathways. This oncogenic mechanism is similar to that of BRAF V600E mutations and may explain tumorigenesis in at least a subset of DNTs. In FGFR2 fusion positive DNTs, this genetic event is the likely driver of tumorigenesis and suggests a potential therapeutic target.
Angiosarcomas are rare, malignant soft tissue tumors in children that arise in a wide range of anatomical locations and have limited targeted therapies available. Here, we report a rare case of a ...pediatric angiosarcoma (pAS) with Li-Fraumeni syndrome (LFS) expressing a novel
gene fusion. Although both
and
are established proto-oncogenes, our study is the first to describe the mechanistic role of
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fusion arising via intrachromosomal rearrangement. NOTCH1-ROS1 displayed potent neoplastic transformation propensity in vitro, and harbors tumorigenic potential in vivo, where it induced oncogenic activation of the MAPK, PI3K/mTOR, and JAK-STAT signaling pathways in a murine allograft model. We found an unexpected contribution of the NOTCH1 extracellular region in mediating NOTCH1-ROS1 activation and oncogenic function, highlighting the contribution of both NOTCH1 and ROS1 fusion partners in driving tumorigenicity. Interestingly, neither membrane localization nor fusion protein dimerization were found to be essential for NOTCH1-ROS1 fusion oncogenicity. To target NOTCH1-ROS1-driven tumors, we tested both NOTCH1-directed inhibitors and ROS1-targeted tyrosine kinase inhibitors (TKI) in heterologous models (NIH3T3, Ba/F3). Although NOTCH1 inhibitors did not suppress NOTCH1-ROS1-driven oncogenic growth, we found that oral entrectinib treatment effectively suppressed the growth of NOTCH-ROS1-driven tumors. Taken together, we report the first known pAS case with a novel NOTCH1-ROS1 alteration along with a detailed report on the function and therapeutic targeting of NOTCH1-ROS1. Our study highlights the importance of genomic profiling of rare cancers such as pAS to reveal actionable drivers and improve patient outcomes.
While chronological age is a strong predictor for health-related risk factors, it is an incomplete metric that fails to fully characterize the unique aging process of individuals with different ...genetic makeup, neurodevelopment, and environmental experiences. Recent advances in epigenomic array technologies have made it possible to generate DNA methylation-based biomarkers of biological aging, which may be useful in predicting a myriad of cognitive abilities and functional brain network organization across older individuals. It is currently unclear which cognitive domains are negatively correlated with epigenetic age above and beyond chronological age, and it is unknown if functional brain organization is an important mechanism for explaining these associations. In this study, individuals with accelerated epigenetic age (i.e. AgeAccelGrim) performed worse on tasks that spanned a wide variety of cognitive faculties including both fluid and crystallized intelligence (N = 103, average age = 68.98 years, 73 females, 30 males). Additionally, fMRI connectome-based predictive models suggested a mediating mechanism of functional connectivity on epigenetic age acceleration-cognition associations primarily in medial temporal lobe and limbic structures. This research highlights the important role of epigenetic aging processes on the development and maintenance of healthy cognitive capacities and function of the aging brain.
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