NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1

PURPOSE

Gliomas and their surrounding microenvironment constantly interact to promote tumorigenicity, yet the underlying posttranscriptional regulatory mechanisms that govern this interplay are poorly understood.

METHODS

Utilizing our established PAC-seq approach and PolyAMiner bioinformatic analysis pipeline, we deciphered the NUDT21-mediated differential APA dynamics in glioma cells.

RESULTS

We identified LAMC1 as a critical NUDT21 alternative polyadenylation (APA) target, common in several core glioma-driving signaling pathways. qRT-PCR analysis confirmed that NUDT21-knockdown in glioma cells results in the preferred usage of the proximal polyA signal (PAS) of LAMC1. Functional studies revealed that NUDT21-knockdown-induced 3'UTR shortening of LAMC1 is sufficient to cause translational gain, as LAMC1 protein is upregulated in these cells compared to their respective controls. We demonstrate that 3'UTR shortening of LAMC1 after NUDT21 knockdown removes binding sites for miR-124/506, thereby relieving potent miRNA-based repression of LAMC1 expression. Remarkably, we report that the knockdown of NUDT21 significantly promoted glioma cell migration and that co-depletion of LAMC1 with NUDT21 abolished this effect. Lastly, we observed that LAMC1 3'UTR shortening predicts poor prognosis of low-grade glioma patients from The Cancer Genome Atlas.

CONCLUSION

This study identifies NUDT21 as a core alternative polyadenylation factor that regulates the tumor microenvironment through differential APA and loss of miR-124/506 inhibition of LAMC1. Knockdown of NUDT21 in GBM cells mediates 3'UTR shortening of LAMC1, contributing to an increase in LAMC1, increased glioma cell migration/invasion, and a poor prognosis.

Zika Virus Infection Alters Gene Expression and Poly-Adenylation Patterns in Placental Cells

Flaviviruses are small RNA viruses that are mainly transmitted via arthropod vectors and are found in tropic and sub-tropical regions. Most infections are asymptomatic (90-95%), but symptoms can be as severe as hemorrhagic fever and encephalitis. One recently emerged flavivirus is Zika virus (ZIKV), which was originally isolated from rhesus monkeys in Uganda roughly 70 years ago but has recently spread east, reaching S. America in 2015-2016. This outbreak was associated with the development of Guillain-Barré syndrome in adults and microcephaly in infants born to expectant mothers infected early in pregnancy. ZIKV must traverse the placenta to impact the development of the fetus, but the mechanisms responsible are unknown. While flaviviruses are known to disrupt splicing patterns in host cells, little is known about how flaviviruses such as ZIKV impact the alternative polyadenylation (APA) of host transcripts. This is important as APA is well-established as a mechanism in the regulation of mRNA metabolism and translation. Thus, we sought to characterize transcriptomic changes including APA in human placental (JEG3) cells in response to ZIKV infection using Poly(A)-ClickSeq (PAC-Seq). We used our differential Poly(A)-cluster (DPAC) analysis pipeline to characterize changes in differential gene expression, alternative poly-adenylation (APA) and the use of alternative terminal exons. We identified 98 upregulated genes and 28 downregulated genes. Pathway enrichment analysis indicated that many RNA processing and immune pathways were upregulated in ZIKV-infected JEG3 cells. We also updated DPAC to provide additional metrics of APA including the percentage-distal usage index (PDUI), which revealed that APA was extensive and the 3' UTRs of 229 genes were lengthened while 269 were shortened. We further found that there were 214 upregulated and 59 downregulated poly(A)-clusters (PACs). We extracted the nucleotide sequences surrounding these PACs and found that the canonical signals for poly-adenylation (binding site for poly-A binding protein (PABP) upstream and a GU-rich region down-stream of the PAC) were only enriched in the downregulated PACs. These results indicate that ZIKV infection makes JEG3 cells more permissive to non-canonical poly-adenylation signals.

Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation

We previously showed that NUDT21-spanning copy-number variations (CNVs) are associated with intellectual disability (Gennarino et al., 2015). However, the patients' CNVs also included other genes. To determine if reduced NUDT21 function alone can cause disease, we generated Nudt21+/- mice to mimic NUDT21-deletion patients. We found that although these mice have 50% reduced Nudt21 mRNA, they only have 30% less of its cognate protein, CFIm25. Despite this partial protein-level compensation, the Nudt21+/- mice have learning deficits, cortical hyperexcitability, and misregulated alternative polyadenylation (APA) in their hippocampi. Further, to determine the mediators driving neural dysfunction in humans, we partially inhibited NUDT21 in human stem cell-derived neurons to reduce CFIm25 by 30%. This induced APA and protein level misregulation in hundreds of genes, a number of which cause intellectual disability when mutated. Altogether, these results show that disruption of NUDT21-regulated APA events in the brain can cause intellectual disability.

Abstract 321: RBFOX2 is critical for maintaining alternative polyadenylation patterns in cardiomyoblasts

Background: The RNA binding protein RBFOX2 is implicated in human heart diseases. However, RBFOX2-regulated RNA networks are not well defined. RBFOX2 has a well-characterized role in alternative splicing (AS) while accumulating evidence suggests that RBFOX2 may also have a role in alternative polyadenylation (APA). Recent studies showed that RBFOX2 binds to regions close to poly(A) sites in the 3’UTR of pre-mRNAs. In addition, RBFOX2 binds to the cleavage and polyadenylation specificity factors. Therefore, we aimed to determine whether RBFOX2 has a role in regulating APA.

Method: We employed poly(A)click sequencing (PAC-seq) and DPAC (Differential Poly(A) Cluster analysis) computational pipeline to identify differential poly(A) usage and mRNA abundance. We also used nanopore sequencing to identify different spliced variants and the coordinated AS and APA events.

Results: We report that knockdown of RBFOX2 in embryonic rat heart derived cells leads to altered alternative polyadenylation (APA) of hundreds of genes. RBFOX2-mediated APA changes impacted both mRNA levels and generation of different gene isoforms. Nanopore sequencing identified full-length transcripts regulated by RBFOX2 and revealed RBFOX2-mediated isoform switches via both APA and AS in cardiac cells. Notably, RBFOX2-regulated APA networks affect genes such as Tpm1 and Tnnt1 involved in cardiac contractility. Identification of RBFOX2-regulated RNA networks provides novel insights into the pathogenesis of heart diseases in which RBFOX2 is involved and pave the way for designing therapeutics.

Conclusions: RBFOX2 regulates alternative polyadenylation via splicing dependent and independent mechanisms. RBFOX2-mediated APA affects mRNA levels of contractile genes.

Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients

Alternative polyadenylation (APA) has emerged as a prevalent feature associated with cancer development and progression. The advantage of APA to tumor progression is to induce oncogenes through 3'-UTR shortening, and to inactivate tumor suppressor genes via the re-routing of microRNA competition. We previously identified the Mammalian Cleavage Factor I-25 (CFIm25) (encoded by Nudt21 gene) as a master APA regulator whose expression levels directly impact the tumorigenicity of glioblastoma (GBM) in vitro and in vivo. Despite its importance, the role of Nudt21 in GBM development is not known and the genes subject to Nudt21 APA regulation that contribute to GBM progression have not been identified. Here, we find that Nudt21 is reduced in low grade glioma (LGG) and all four subtypes of high grade glioma (GBM). Reduced expression of Nudt21 associates with worse survival in TCGA LGG cohorts and two TCGA GBM cohorts. Moreover, although CFIm25 was initially identified as biochemically associated with both CFIm59 and CFIm68, we observed three CFIm distinct subcomplexes exist and CFIm59 protein level is dependent on Nudt21 expression in GBM cells, but CFIm68 is not, and that only CFIm59 predicts prognosis of GBM patients similar to Nudt21. Through the use of Poly(A)-Click-Seq to characterize APA, we define the mRNAs subject to 3'-UTR shortening upon Nudt21 depletion in GBM cells and observed enrichment in genes important in the Ras signaling pathway, including Pak1. Remarkably, we find that Pak1 expression is regulated by Nudt21 through its 3'-UTR APA, and the combination of Pak1 and Nudt21 expression generates an even stronger prognostic indicator of GBM survival versus either value used alone. Collectively, our data uncover Nudt21 and its downstream target Pak1 as a potential "combination biomarker" for predicting prognosis of GBM patients.

Abstract 435: Post-transcriptional Regulation of Tropomyosin Isoforms Altered in Human Heart Diseases

Background: Tropomyosin 1 (TPM1) is a coiled coil protein that forms polymers along with the actin filament, and it is required for myofibril organization, myocardial contraction, and cardiac development. TPM1 has cardiac muscle and non-muscle specific protein isoforms that dictate its function in cardiac muscle contraction or in cytoskeleton. TPM1 mutations in exon 2b, 5, 6b or 8 are associated with cardiovascular diseases including familial hypertrophic cardiomyopathy, dilated cardiomyopathy and left ventricular non-compaction. Thus, it is of great importance to investigate the mechanisms that control tropomyosin isoforms in order to identify novel therapeutic targets for cardiovascular diseases in which TPM1 is mutated.

Method: We used nanopore sequencing technology using MinION and poly(A)click seq (PAC-seq) to identify different TPM1 transcripts generated in rat heart derived H9c2 cells. RT-PCR and western blotting were conducted to measure mRNA and protein levels of TPM1 respectively.

Results: We identified 10 different isoforms of TPM1 using nanopore sequencing and determined several exons that are extensively spliced and favored in cardiac cells. We further identified an RNA binding protein that controls cardiac specific isoforms of TPM1 via alternative splicing and polyadenylation. Importantly, we found that this RNA binding protein regulates alternative splicing of exon 6b of TPM1, which is mutated in patients with cardiomyopathies.

Conclusions: We identified an RNA binding protein, which controls expression of cardiac specific TPM1 isoforms by alternative polyadenylation and alternative splicing.

[Anna Freud exposes herself to criticism. "The ego and and the mechanisms of defense" under the magnifying glass]

In the early 1970's members and guests of the Hampstead Clinic, under the guidance of Joseph Sandler, discussed Anna Freud's The Ego and the Mechanisms of Defence, which had been published in 1936, with its author. Elrod presents this discussion in excerpts and emphasizes the undogmatic approach to psychoanalytic theory evident in Anna Freud's and Joseph Sandler's contributions.