Case Report: Differential Genomics and Evolution of a Meningeal Melanoma Treated With Ipilimumab and Nivolumab

Primary melanocytic tumors of the CNS are extremely rare conditions, encompassing different disease processes including meningeal melanoma and meningeal melanocytosis. Its incidence range between 3-5%, with approximately 0.005 cases per 100,000 people. Tumor biological behavior is commonly aggressive, with poor prognosis and very low survivability, and a high recurrence rate, even after disease remission with multimodal treatments. Specific genetic alterations involving gene transcription, alternative splicing, RNA translation, and cell proliferation are usually seen, affecting genes like BRAF, TERT, GNAQ, SF3B1, and EIF1AX. Here we present an interesting case of a 59-year-old male presenting with neurologic symptoms and a further confirmed diagnosis of primary meningeal melanoma. Multiple therapy lines were used, including radiosurgery, immunotherapy, and chemotherapy. The patient developed two relapses and an evolving genetic makeup that confirmed the disease’s clonal origin. We also provide a review of the literature on the genetic basis of primary melanocytic tumors of the CNS.

Ribosome Profiling Reveals Novel Regulation of C9ORF72 GGGGCC Repeat-Containing RNA Translation

GGGGCC (G4C2) repeat expansion in the first intron of C9ORF72 causes amyotrophic lateral sclerosis and frontotemporal dementia. Repeat-containing RNA is translated into dipeptide repeat (DPR) proteins, some of which are neurotoxic. Using dynamic ribosome profiling, we identified three translation initiation sites in the intron upstream of (G4C2) repeats; these sites are detected irrespective of the presence or absence of the repeats. During translocation, ribosomes appear to be stalled on the repeats. An AUG in the preceding C9ORF72 exon initiates a uORF that inhibits downstream translation. Polysome isolation indicates that unspliced (G4C2) repeat-containing RNA is a substrate for DPR protein synthesis. (G4C2) repeat-containing RNA translation is 5’ cap-independent but inhibited by the initiation factor DAP5, suggesting an interplay with uORF function. These results define novel translational mechanisms of expanded (G4C2) repeat-containing RNA in disease.

Targeting PRMT9 Suppresses Acute Myeloid Leukemia Maintenance

AML is a heterogenous disease in which prognosis and treatment is determined by recurrent genetic mutations and chromosomal abnormalities. Some genetic alterations result in aberrant RNA translation, which is exploited by leukemia stem cells (LSCs) to produce short-lived oncoproteins (c-Myc, Mcl-1) to promote cell survival. Since LSCs are considered as the source of treatment failure and relapse, it is critical to understand how LSCs hijack the translational machinery in order to develop effective therapeutics in AML. Arginine methylation catalyzed by protein arginine methyltransferases 1-9 (PRMT1-9) regulates various activities, including RNA translation. We revealed that PRMT1 over activation contributes to leukemia maintenance (Blood, 2019; Blood, 2019). Unlike PRMT1, the recently described PRMT9, is not defined in leukemia. Follow up of AML patients from existing datasets (GSE12417, TARGET) confirms that patients with higher levels of PRMT9 correlates with decreased overall survival. In our AML cohort, we observed significantly increased PRMT9 mRNA levels in AML CD34 + cells relative to normal counterparts (Fig. 1A), spurring our interest in evaluating its function in AML. We thus developed a Prmt9 conditional KO mouse (Mx1-Cre/Prmt9 f/f) and crossed it with an MLL-AF9 (MA9) knock-in mouse to generate Prmt9-KO/MA9 mice for further transplant assay. As a result, Prmt9-KO significantly delayed leukemogenesis in recipient mice carrying MA9 transplants evidenced by prolonged survival (Fig. 1B). Prmt9-KO impaired leukemia-initiating activity evidenced by secondary transplantation that significant less residual CD45.2 + MA9 leukemia cells were found in BM of secondary recipients receiving Prmt9-KO cells relative to those of Prmt9-WT controls. We next validated PRMT9 function in human AML. PRMT9-KD potentially impaired survival of primary AML CD34 + cells, whereas large sparing normal counterparts (Fig. 1C). Moreover, we designed a WT PRMT9 construct and corresponding catalytically dead mutant, both resistant to shPRMT9 (WT-R and MUT-R). Unlike MUT-R, WT-R expression rescued survival effects seen following shPRMT9 treatment, indicating that PRMT9 catalytic activity is required for AML survival (Fig. 1D). To define PRMT9 downstream effectors, we searched for methylated substrates in Molm13 with inducible PRMT9-KD or corresponding controls by performing SILAC analysis coupled with quantitative Mass-Spec (MS) (Fig. 1E). Complete analyses of normalized methyl peptides SILAC ratios revealed more prominent down-regulation of R-methylation in PRMT9-KD cells, with 49 methyl sites downregulated. Notably, methylated PAPB1 C-terminus peptide containing R493 was most significantly depleted upon PRMT9-KD. PABP1 potentiates translation initiation by binding to the poly(A) mRNA tail and interacting with factors like eIF4G. We thus generated an anti-R493 methylation antibody. Indeed, PRMT9 was confirmed to catalyze R493 methylation through in-vitro and cellular methylation assays (Fig. 1F, G). To define the function of R493 methylation, we ectopically expressed either WT PABP1 or the R493K mutant in Molm13 cells and then engineered those cells to express shPABP1 to KD endogenous PABP1. Notably, unlike WT PABP1, expression of R493K suppressed protein synthesis and increased apoptosis after endogenous PABP1-KD, suggesting that PRMT9 mediated PABP1-R493 methylation promotes AML viability (Fig. 1H, I). To discover PRMT9 inhibitors, we conducted a structure-based virtual screen of 960,000 compounds from NCI and Zinc compound libraries (Fig. 1J). We requested the top 300 candidates to assess their anti-leukemia activity in Molm13 cells (Fig. 1K). The top 20 most effective compounds were further analyzed via PRMT9 methylation assay (R493 antibody detection). NSC641396 exhibited the most potent PRMT9 inhibitory effects, as evidenced by decreased PABP1 R493 methylation levels at a dose <1 µΜ (Fig. 1L). NSC641396 treatment on AML CD34 + cells altered polysome profiling, decreased protein biosynthesis and reduced levels of short-lived proteins, suggesting translation inhibition (Fig. 1M). Taken together, our results suggest that PRMT9 plays an oncogenic role in AML or LSC maintenance, by promoting PABP1 methylation mediated translation activity. Further studies are needed to explore if targeting PRMT9 with newly identified lead compound ablates LSCs activity. Figure 1 Figure 1. Disclosures Marcucci: Novartis: Other: Speaker and advisory scientific board meetings; Agios: Other: Speaker and advisory scientific board meetings; Abbvie: Other: Speaker and advisory scientific board meetings.

Methyltransferase-Deficient Avian Flaviviruses Are Attenuated Due to Suppression of Viral RNA Translation and Induction of a Higher Innate Immunity

The 5’ end of the flavivirus genome contains a type 1 cap structure formed by sequential N-7 and 2’-O methylations by viral methyltransferase (MTase). Cap methylation of flavivirus genome is an essential structural modification to ensure the normal proliferation of the virus. Tembusu virus (TMUV) (genus Flavivirus) is a causative agent of duck egg drop syndrome and has zoonotic potential. Here, we identified the in vitro activity of TMUV MTase and determined the effect of K61-D146-K182-E218 enzymatic tetrad on N-7 and 2’-O methylation. The entire K61-D146-K182-E218 motif is essential for 2’-O MTase activity, whereas N-7 MTase activity requires only D146. To investigate its phenotype, the single point mutation (K61A, D146A, K182A or E218A) was introduced into TMUV replicon (pCMV-Rep-NanoLuc) and TMUV infectious cDNA clone (pACYC-TMUV). K-D-K-E mutations reduced the replication ability of replicon. K61A, K182A and E218A viruses were genetically stable, whereas D146A virus was unstable and reverted to WT virus. Mutant viruses were replication and virulence impaired, showing reduced growth and attenuated cytopathic effects and reduced mortality of duck embryos. Molecular mechanism studies showed that the translation efficiency of mutant viruses was inhibited and a higher host innate immunity was induced. Furthermore, we found that the translation inhibition of MTase-deficient viruses was caused by a defect in N-7 methylation, whereas the absence of 2’-O methylation did not affect viral translation. Taken together, our data validate the debilitating mechanism of MTase-deficient avian flavivirus and reveal an important role for cap-methylation in viral translation, proliferation, and escape from innate immunity.

The Potential Functions of Protein Domains during COVID Infection; an Analysis and a Review

Coronaviruses (CoVs) are a large viral family that can evolve rapidly emerging new strains that cause outbreaks and life-loss, including SARS-CoV, MERS-CoV, and SARS-CoV-2 (COVID-19). CoVs encode a diverse number of proteins, ranging from 5 proteins in bat CoV, to 14 in SARS CoV, which could have implication on viral tropism and pathogenicity. Here, we highlight the functional protein motifs (domains) that could contribute in the coronavirus infection and severity, including SARS-CoV-2. For this role, we used the experimentally validated domain (motif) datasets that are known to be crucial for viral infection. Then, we highlight the potential molecular pathways and interactions of SARS-CoV-2 proteins within human cells. Interestingly, the C-terminal of SARS-COV-2 nsp1 protein encodes MREL motif, which a signature motif of the tubulin superfamily, and regulate tubulin expression. The C-terminal region of nsp1 protein can bind to ribosome and regulation viral RNA translation.

Exploring Evidence of Non-coding RNA Translation With Trips-Viz and GWIPS-Viz Browsers

Detection of translation in so-called non-coding RNA provides an opportunity for identification of novel bioactive peptides and microproteins. The main methods used for these purposes are ribosome profiling and mass spectrometry. A number of publicly available datasets already exist for a substantial number of different cell types grown under various conditions, and public data mining is an attractive strategy for identification of translation in non-coding RNAs. Since the analysis of publicly available data requires intensive data processing, several data resources have been created recently for exploring processed publicly available data, such as OpenProt, GWIPS-viz, and Trips-Viz. In this work we provide a detailed demonstration of how to use the latter two tools for exploring experimental evidence for translation of RNAs hitherto classified as non-coding. For this purpose, we use a set of transcripts with substantially different patterns of ribosome footprint distributions. We discuss how certain features of these patterns can be used as evidence for or against genuine translation. During our analysis we concluded that the MTLN mRNA, previously misannotated as lncRNA LINC000116, likely encodes only a short proteoform expressed from shorter RNA transcript variants.