Genetic fusions favor tumorigenesis through degron loss in oncogenes

Chromosomal rearrangements can generate genetic fusions composed of two distinct gene sequences, many of which have been implicated in tumorigenesis and progression. Our study proposes a model whereby oncogenic gene fusions frequently alter the protein stability of the resulting fusion products, via exchanging protein degradation signal (degron) between gene sequences. Computational analyses of The Cancer Genome Atlas (TCGA) identify 2,406 cases of degron exchange events and reveal an enrichment of oncogene stabilization due to loss of degrons from fusion. Furthermore, we identify and experimentally validate that some recurrent fusions, such as BCR-ABL, CCDC6-RET and PML-RARA fusions, perturb protein stability by exchanging internal degrons. Likewise, we also validate that EGFR or RAF1 fusions can be stabilized by losing a computationally-predicted C-terminal degron. Thus, complementary to enhanced oncogene transcription via promoter swapping, our model of degron loss illustrates another general mechanism for recurrent fusion proteins in driving tumorigenesis.

Simulating fusion alpha heating in a stellarator reactor

Gyrocenter following simulations of fusion born alpha particles in a stellarator reactor are preformed using the BEAMS3D code. The Wendelstein 7-X high mirror configuration is scaled in geometry and magnetic field to reactor relevant parameters. A 2×1020 m−3 density plasma with 20 keV core temperatures is assumed and fusion birth rates calculated for various fusion products assuming a 50/50 deuterium-tritium mixture. It is found that energetic He4 ions comprise the vast majority of the energetic particle inventory. Slowing down simulations of the He4 population suggest plasma heating consistent with scaled energy confinement times for a stellarator reactor. Losses for this configuration appear large suggesting optimization beyond the scope of the W7-X device is key to a future fusion reactor. These first simulations are designed to demonstrate the capability of the BEAMS3D code to provide fusion alpha birth and heating profiles for stellarator reactor designs.

Presence of an EML4-ALK gene fusion detected by microfluidic chip DNA hybridization

ABSTRACT Non-small cell lung cancer (NSCLC) accounts for ∼80-85% of all lung cancer cases, and the EML4-ALK fusion oncogene is a well-known contributor to NSCLC cases. Expensive methods such as FISH, IHC, and NGS have been used to detect the EML4-ALK fusion oncogene. Here, a cost-effective and facile method of detecting and differentiating an EML4-ALK fusion oncogene from the wild-type gene has been accomplished by DNA hybridization using the microfluidic biochip. First, oligonucleotide probes were confirmed for successful detection of immobilized sense strands. Second, capture of the sense PCR product strands (fusion and WT) and their subsequent detection and differentiation were accomplished. Our proof-of-concept study shows the ability to detect 1% fusion products, among WT ones.

Characterization of NRG1 gene fusion events in solid tumors.

3113 Background: NRG1 fusions are actionable genomic alterations detected across tumor types. The NRG1 gene encode for neuregulin, which serves as a ligand for ERBB3 and ERBB4 receptors and activates downstream signaling through the MAPK and PI3K pathways. Here, we update the detection of NRG1 gene fusions across tumor types and further describe fusion characteristics. Methods: Samples submitted for clinical molecular profiling that included RNA-sequencing (Archer Dx or Caris MI transcriptome) were retrospectively analyzed for NRG1 fusion events. All NRG1 fusions with ≥ 3 junction reads were identified for manual review and for characterization of fusion class, intact functional domains, domain prediction, breakpoints, frame retention and co-occurring alterations by NGS. Results: A total of 82 NRG1 fusion events (0.2% of 44,570) were identified. Among the fusions identified, the distribution across tumor types was as follows: non-small cell lung cancer (NSCLC, 54%), breast cancer (11%), ovarian cancer (7%), pancreatic cancer (7%), cholangiocarcinoma (6%), colorectal cancer (5%), and other (10%). Forty-two unique fusion partners were identified, the most common being CD74 (23%), ATP1B1 (9%), SLC3A2 (7%), RBPMS (6%) and SDC4 (4%). Almost half (47%) of all fusion events are expected to include the transmembrane domain contributed by the NRG1 fusion partner. Lung and pancreatobilliary cancers had the highest rates of transmembrane domain retention from their fusion partners (63.6% and 54.5%, respectively). In all other tumor groups, most fusion partners lacked transmembrane domains. In 15% of cases, the chimeric transcripts are predicted to lead to increased expression of NRG1. The most commonly reported breakpoints in NRG1 occur in exon 6 and exon 2. While fusions with the NRG1 breakpoint at exon 2 retain the immunoglobulin (Ig) domain and all downstream portions (including EGF-like domain), those at exon 6 do not contain the Ig portion and result in shorter chimeric proteins. The breakpoints in all CD74:NRG1 fusions, the most common fusions in NSCLC, occur at exon 5 or 6 and cause truncation of domains upstream of the EGF-like domain. In ATP1B1:NRG1 fusions, the most common fusions in pancreatobilliary cancers, the breakpoints are at exon 1 or 2 and retain the Ig domain. Conclusions: NRG1 fusion products are diverse across tumor types, but the significance of these variations is not clear. The biological and clinical implications of retaining certain domains of NRG1 (such as the Ig domain) and of fusion partners warrants further investigation.

Outgoing Longwave Radiation and Its Diurnal Variation from Combined FY3D and FY4A

<p>The outgoing longwave radiation (OLR) is a crucial parameter for studying many areas in the atmospheric science, including the investigations of the cloud/water vapor/radiative interaction processes, climate variability, and for climate change monitoring and numerical model evaluation and diagnostics, etc. The OLR has continued being observed or estimated from Fengyun meteorological satellites, including solar orbit satellites (such as FY3D/MERSI) and geostationary satellites (such as FY4A/AGRI).</p><p>The advantage of solar orbiting satellites is global coverage. Thus it is difficult to reflect the diurnal variation of OLR for twice observations a day. While geostationary satellites are observed 24 times a day, which can accurately describe the diurnal variation of OLR. But its coverage is limited. Therefore, the development of OLR fusion products combined with solar orbit satellite and geostationary satellite, can improve product accuracy without losing coverage advantage. In this study, we use OLR from FY4A and FY3D to build a fusion OLR product to correct the diurnal variation of OLR, and get good results.</p>

Immunotherapy in soft-tissue sarcoma

Soft-tissue sarcoma (STS) is a rare mesenchymal malignancy that accounts for less than 1% of all adult tumours. Despite the successful advancement of localized therapies such as surgery and radiotherapy, these tumours can, for many, recur—often with metastatic disease. In the advanced setting, the role of systemic therapies is modest and is associated with poor survival. With the discovery of immunotherapies in other tumour types such as melanoma and lung cancer, interest has been renewed in exploring immunotherapy in STS. The biology of some STSs makes them ripe for immunotherapy intervention; for example, some STSs might have chromosomal translocations resulting in pathognomonic fusion products that have been shown to express cancer/testis antigens. Here, we present a targeted review of the published data and ongoing clinical trials for immunotherapies in patients with sarcoma, which comprise immune checkpoint inhibitors, adoptive cell therapies, and cancer vaccines.