Alternative RNA Splicing Events Research Articles

Sustained cancer-relevant alternative RNA splicing events driven by PRMT5 in high-risk neuroblastoma.

Protein arginine methyltransferase 5 (PRMT5) is over-expressed in a wide variety of cancers and is implicated as having a key oncogenic role, achieved in part through its control of the master transcription regulator E2F1. We investigated the relevance of PRMT5 and E2F1 in neuroblastoma (NB) and found that elevated expression of PRMT5 and E2F1 occurs in poor prognosis high-risk disease and correlates with an amplified Myelocytomatosis viral-related oncogene, neuroblastoma-derived (MYCN) gene. Our results show that MYCN drives the expression of splicing factor genes that, together with PRMT5 and E2F1, lead to a deregulated alternative RNA splicing programme that impedes apoptosis. Pharmacological inhibition of PRMT5 or inactivation of E2F1 restores normal splicing and renders NB cells sensitive to apoptosis. Our findings suggest that a sustained cancer-relevant alternative RNA splicing programme desensitises NB cells to apoptosis, and identify PRMT5 as a potential therapeutic target for high-risk disease.

AEP-cleaved DDX3X induces alternative RNA splicing events to mediate cancer cell adaptation in harsh microenvironments.

Oxygen and nutrient deprivation are common features of solid tumors. Although abnormal alternative splicing (AS) has been found to be an important driving force in tumor pathogenesis and progression, the regulatory mechanisms of AS that underly the adaptation of cancer cells to harsh microenvironments remain unclear. Here, we found that hypoxia- and nutrient deprivation-induced asparagine endopeptidase (AEP) specifically cleaved DDX3X in a HIF1A-dependent manner. This cleavage yields truncated carboxyl-terminal DDX3X (tDDX3X-C), which translocates and aggregates in the nucleus. Unlike intact DDX3X, nuclear tDDX3X-C complexes with an array of splicing factors and induces AS events of many pre-mRNAs; for example, enhanced exon skipping (ES) in exon 2 of the classic tumor suppressor PRDM2 leads to a frameshift mutation of PRDM2. Intriguingly, the isoform ARRB1-Δexon 13 binds to glycolytic enzymes and regulates glycolysis. By utilizing in vitro assays, glioblastoma organoids, and animal models, we revealed that AEP/tDDX3X-C promoted tumor malignancy via these isoforms. More importantly, high AEP/tDDX3X-C/ARRB1-Δexon 13 in cancerous tissues was tightly associated with poor patient prognosis. Overall, our discovery of the effect of AEP-cleaved DDX3X switching on alternative RNA splicing events identifies a mechanism in which cancer cells adapt to oxygen and nutrient shortages and provides potential diagnostic and/or therapeutic targets.

Abstract A001: Differential alternative RNA splicing and transcription events between Black and White prostate cancer patients involve genes promoting cancer aggressiveness and associate with patient survival

Abstract Black patients suffer disproportionately from prostate cancer (PCa) progression to lethal disease compared with Asian and White patients. Comparing the molecular landscape of PCa in Black and White men has the potential to identify targets for development of new precision medicine interventions. Alternative RNA splicing and transcription events (ARS/Ts) can alter gene function. Cancer may exploit ARS/Ts to enhance proliferation, metastasis, and drug resistance. Here, we isolated RNA from fresh frozen PCa specimens and tumor-associated normal (TAN) specimens from 35 self-reported Black and 37 self-reported White patients diagnosed with Gleason-high or -low PCa and undergoing radical prostatectomy or biopsy. Analysis of follow-up clinical data for patients participating in our study show an increased hazard ratio of PCa progression among Black patients compared to White patients (HR = 2.13 and p < 0.05). We performed comparative transcriptomic analysis between Gleason-high or -low tumor and TAN samples among Blacks, among Whites, or between Blacks and Whites with Gleason-high or –low PCa. Among differential ARS/Ts identified between tumors and TANs among Blacks, 532 are unique to Gleason-high and 673 are unique to Gleason-low. Among differential ARS/Ts between Blacks and Whites, 360 are unique to Gleason-high and 242 are unique to Gleason-low. Interestingly, we found that even in TANs, there are 802 differential ARS/Ts between Blacks and Whites, with 459 and 343 in Gleason-high and Gleason-low, respectively. Among the genes undergoing differential ARS/Ts between Blacks and Whites are FGFR1, AKT1, H6PD, MDM2, and RAD51D in Gleason-high and CDK7 and VEGFA in Gleason-low. Notably, the number of genes undergoing ARS/Ts between Blacks and Whites with Gleason-high or -low tumors was higher than the number of genes undergoing differential aggregate gene expression between Blacks and Whites. Using gene set enrichment analysis, we found that genes undergoing ARS/Ts function in cancer relevant pathways. For example, the genes undergoing ARS/Ts between Blacks and Whites with Gleason-high or -low tumors were enriched in spermatogenesis and P53 hallmark pathways, respectively. Importantly, survival analysis shows a number of differential ARS/Ts between Blacks and Whites with Gleason-high or -low tumors are individually associated with progression-free survival. In summary, we have investigated the biology of PCa and TAN tissue between Black and White patients at the exon level. A number of genes undergoing newly identified differential ARS/Ts between Blacks and Whites are in genes reported to promote cancer aggressiveness and a number are in genes whose function in cancer was unreported prior to our findings, and a number are associated with patient progression-free survival. Our findings have identified novel targets with potential for precision oncology for PCa. Estimation of genetic ancestry of study participants and in vitro and in vivo validation of prioritized targets for PCa biology are underway. Citation Format: Muthana Al Abo, Wen-Chi Foo, Lauren Howard, Monika Anand, Daniel J. George, Steven R. Patierno, Jennifer A Freedman. Differential alternative RNA splicing and transcription events between Black and White prostate cancer patients involve genes promoting cancer aggressiveness and associate with patient survival [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A001.

Emerging roles of alternative RNA splicing in oral squamous cell carcinoma.

Alternative RNA splicing (ARS) is an essential and tightly regulated cellular process of post-transcriptional regulation of pre-mRNA. It produces multiple isoforms and may encode proteins with different or even opposite functions. The dysregulated ARS of pre-mRNA contributes to the development of many cancer types, including oral squamous cell carcinoma (OSCC), and may serve as a biomarker for the diagnosis and prognosis of OSCC and an attractive therapeutic target. ARS is mainly regulated by splicing factors, whose expression is also often dysregulated in OSCC and involved in tumorigenesis. This review focuses on the expression and roles of splicing factors in OSCC, the alternative RNA splicing events associated with OSCC, and recent advances in therapeutic approaches that target ARS.

RNA splicing: a dual-edged sword for hepatocellular carcinoma.

RNA splicing is the fundamental process that brings diversity at the transcriptome and proteome levels. The spliceosome complex regulates minor and major processes of RNA splicing. Aberrant regulation is often associated with different diseases, including diabetes, stroke, hypertension, and cancer. In the majority of cancers, dysregulated alternative RNA splicing (ARS) events directly affect tumor progression, invasiveness, and often lead to poor survival of the patients. Alike the rest of the gastrointestinal malignancies, in hepatocellular carcinoma (HCC), which alone contributes to ~ 75% of the liver cancers, a large number of ARS events have been observed, including intron retention, exon skipping, presence of alternative 3'-splice site (3'SS), and alternative 5'-splice site (5'SS). These events are reported in spliceosome and non-spliceosome complexes genes. Molecules such as MCL1, Bcl-X, and BCL2 in different isoforms can behave as anti-apoptotic or pro-apoptotic, making the spliceosome complex a dual-edged sword. The anti-apoptotic isoforms of such molecules bring in resistance to chemotherapy or cornerstone drugs. However, in contrast, multiple malignant tumors, including HCC that target the pro-apoptotic favoring isoforms/variants favor apoptotic induction and make chemotherapy effective. Herein, we discuss different splicing events, aberrations, and antisense oligonucleotides (ASOs) in modulating RNA splicing in HCC tumorigenesis with a possible therapeutic outcome.

Abstract PO-137: Comparative transcriptomic analysis of prostate cancer from African American and Caucasian American men by Gleason score and race

Abstract African American (AA) men exhibit 2-3 times higher mortality from prostate cancer compared with Caucasian American (CA) men. Factors contributing to the disparity include societal-, neighborhood- and institutional-level determinants of health. In addition, a number of studies have reported individual-level ancestry-related biological differences, including in mutations, copy number variation, aggregate gene expression and response to treatment between AA and CA prostate cancer patients. Previously, by comparing the transcriptome between 20 AA and 15 CA prostate cancer patients, we identified a large number of race-related Alternative RNA Splicing (ARS) events. Among these, we further demonstrated that an exon skipping event involving exon 20 within PIK3CD increased tumor growth rate, metastatic potential and drug resistance in prostate cancer. To expand our previous findings, we collected non-neoplastic and tumor-paired tissue from 37 AA and 40 CA prostate cancer patients with different Gleason score categories: 14 high grade (4 AA and 10 CA), 22 low grade (10 AA and 12 CA), and 41 intermediate grade (23 AA and 18 CA). DNA and RNA were isolated for ancestral genotyping and RNA seq analysis, respectively. To achieve RNA sequencing depth adequate for ARS analysis, we performed RNA seq of 150 bp paired-end and an average of 5 × 106 reads per sample. The read alignment was done using Star 2 TwoPass pipeline. The rMATS pipeline was used for ARS annotation and quantification. We identified 105,403 ARS events, including 60,657 exon skipping, 17,439 alternative acceptor, 12,737 alternative donor, 9,555 retained intron and 5,015 mutually exclusive exon. Using the Wilcoxon rank-sum test, we compared the Percent Spliced In (PSI) between AA and CA of the same Gleason score category and identified ARS events exhibiting ΔPSI > 15% and p-value < 0.05. Specifically, we identified 536 race-related ARS events in high grade, 492 race-related ARS events in low grade, and 447 race-related ARS events in intermediate grade. Gene Ontology analysis demonstrated that the genes undergoing race-related ARS events function in cellular processes relevant to cancer biology, including metabolic processes in low grade, NF-kappaB signaling in intermediate grade and cell motility in high grade. Specific examples of these genes include ERG and PARP2 in high grade, KLK2 and DNMT1 in intermediate grade, and AURKA and SEMA3A in low grade. These findings support a potential role for the ARS process in diversifying gene expression, potentially contributing to prostate cancer aggressiveness in AA patients. The race-related ARS events identified in our work represent potential biomarkers and/or therapeutic targets for precision oncology in the context of prostate cancer. Further analysis of the function of prioritized race-related ARS events and their association with local ancestry is ongoing. Funding: DoD Prostate Cancer Research Program Health Disparity Research Award. NIH Basic Research in Cancer Health Disparities R01 Award. Prostate Cancer Foundation Movember Challenge Award. Citation Format: Muthana Al Abo, Wen-Chi Foo, Daniel J. George, Steven R. Patierno, Jennifer A. Freedman. Comparative transcriptomic analysis of prostate cancer from African American and Caucasian American men by Gleason score and race [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-137.

MiRNA-Based Regulation of Alternative RNA Splicing in Metazoans.

Alternative RNA splicing is an important regulatory process used by genes to increase their diversity. This process is mainly executed by specific classes of RNA binding proteins that act in a dosage-dependent manner to include or exclude selected exons in the final transcripts. While these processes are tightly regulated in cells and tissues, little is known on how the dosage of these factors is achieved and maintained. Several recent studies have suggested that alternative RNA splicing may be in part modulated by microRNAs (miRNAs), which are short, non-coding RNAs (~22 nt in length) that inhibit translation of specific mRNA transcripts. As evidenced in tissues and in diseases, such as cancer and neurological disorders, the dysregulation of miRNA pathways disrupts downstream alternative RNA splicing events by altering the dosage of splicing factors involved in RNA splicing. This attractive model suggests that miRNAs can not only influence the dosage of gene expression at the post-transcriptional level but also indirectly interfere in pre-mRNA splicing at the co-transcriptional level. The purpose of this review is to compile and analyze recent studies on miRNAs modulating alternative RNA splicing factors, and how these events contribute to transcript rearrangements in tissue development and disease.

Differential alternative RNA splicing and transcription events between tumors from African American and White patients in The Cancer Genome Atlas

Individuals of African ancestry suffer disproportionally from higher incidence, aggressiveness, and mortality for particular cancers. This disparity likely results from an interplay among differences in multiple determinants of health, including differences in tumor biology. We used The Cancer Genome Atlas (TCGA) SpliceSeq and TCGA aggregate expression datasets and identified differential alternative RNA splicing and transcription events (ARS/T) in cancers between self-identified African American (AA) and White (W) patients. We found that retained intron events were enriched among race-related ARS/T. In addition, on average, 12% of the most highly ranked race-related ARS/T overlapped between any two analyzed cancers. Moreover, the genes undergoing race-related ARS/T functioned in cancer-promoting pathways, and a number of race-related ARS/T were associated with patient survival. We built a web-application, CanSplice, to mine genomic datasets by self-identified race. The race-related targets have the potential to aid in the development of new biomarkers and therapeutics to mitigate cancer disparity.

Dissecting the impact of regional identity and the oncogenic role of human-specific NOTCH2NL in an hESC model of H3.3G34R-mutant glioma

H3.3G34R-mutant gliomas are lethal tumors of the cerebral hemispheres with unknown mechanisms of regional specificity and tumorigenicity. We developed a human embryonic stem cell (hESC)-based model of H3.3G34R-mutant glioma that recapitulates the key features of the tumors with cell-type specificity to forebrain interneuronal progenitors but not hindbrain precursors. We show that H3.3G34R, ATRX, and TP53 mutations cooperatively impact alternative RNA splicing events, particularly suppression of intron retention. This leads to increased expression of components of the Notch pathway, notably NOTCH2NL, a human-specific gene family. We also uncover a parallel mechanism of enhanced NOTCH2NL expression via genomic amplification of its locus in some H3.3G34R-mutant tumors. These findings demonstrate a novel mechanism whereby evolutionary pathways that lead to larger brain size in humans are co-opted to drive tumor growth.

Two-step mixed model approach to analyzing differential alternative RNA splicing.

Changes in gene expression can correlate with poor disease outcomes in two ways: through changes in relative transcript levels or through alternative RNA splicing leading to changes in relative abundance of individual transcript isoforms. The objective of this research is to develop new statistical methods in detecting and analyzing both differentially expressed and spliced isoforms, which appropriately account for the dependence between isoforms and multiple testing corrections for the multi-dimensional structure of at both the gene- and isoform- level. We developed a linear mixed effects model-based approach for analyzing the complex alternative RNA splicing regulation patterns detected by whole-transcriptome RNA-sequencing technologies. This approach thoroughly characterizes and differentiates three types of genes related to alternative RNA splicing events with distinct differential expression/splicing patterns. We applied the concept of appropriately controlling for the gene-level overall false discovery rate (OFDR) in this multi-dimensional alternative RNA splicing analysis utilizing a two-step hierarchical hypothesis testing framework. In the initial screening test we identify genes that have differentially expressed or spliced isoforms; in the subsequent confirmatory testing stage we examine only the isoforms for genes that have passed the screening tests. Comparisons with other methods through application to a whole transcriptome RNA-Seq study of adenoid cystic carcinoma and extensive simulation studies have demonstrated the advantages and improved performances of our method. Our proposed method appropriately controls the gene-level OFDR, maintains statistical power, and is flexible to incorporate advanced experimental designs.

Near normalization of peripheral blood markers in HIV-infected patients on long-term suppressive antiretroviral therapy: a case-control study.

To explore the differences in peripheral blood markers between HIV well controlled patients on long-term suppressive antiretroviral therapy (HIV-group) and age-matched healthy controls, to evaluate the benefits of virological suppression in those patients. We performed a case-control study in 22 individuals in the HIV-group and 14 in the healthy control-group. RNA-seq analysis was performed from peripheral blood mononuclear cells. Peripheral blood T-cell subsets were evaluated by flow cytometry and plasma biomarkers by immunoassays. All P values were corrected by the false discovery rate (q values). Only the serine/arginine repetitive matrix 4 gene, which is involved in alternative RNA splicing events, was differentially expressed between HIV and healthy control groups (q value ≤0.05 and fold-change ≥2). However, 147 differentially expressed genes were found with a more relaxed threshold (P value ≤0.05 and fold-change ≥1.5), of which 67 genes with values of variable importance in projection at least one were selected for pathway analysis. We found that six ribosomal genes represented significant ribosome-related pathways, all of them downregulated in the HIV-group, which may be a strategy to facilitate viral production. T cells subset and plasma biomarkers did not show significant differences after false discovery rate correction (q value >0.05), but a noncorrected analysis showed higher values of regulatory CD4 T cells (CD4CD25CD127), MCP-1, and sVEGF-R1 in the HIV-group (P value ≤0.05). T-cell subsets, plasma biomarkers, and gene expression were close to normalization in HIV-infected patients on long-term suppressive combination antiretroviral therapy compared with healthy controls. However, residual alterations remain, mainly at the gene expression, which still reveals the impact of HIV infection in these patients.

Abstract B050: Identification of differentially expressed and spliced genes between breast, colon, lung, and prostate cancer from African American and white patients

Abstract Racial/ethnic disparity in cancer refers to the disproportionate incidence of and/or mortality from various cancers among population groups. In addition to differences in social, lifestyle and structural determinants of health, there is accumulating evidence for a biologic contribution to racial/ethnic disparity in cancer. To understand further the biologic mechanisms underlying racial/ethnic disparity in cancer, the analysis of differential aggregate gene expression and mutation among cancer patients of different population groups is important. Our recently published work reported differential RNA splicing as a critical mechanism underlying prostate cancer aggressiveness and drug response in African American (AA) patients. Here, we use R to analyze the Genomic Data Commons for differential aggregate gene expression (2-fold mean change, p < 0.001, Wilcoxon rank sum test) and TCGASpliceSeq to analyze TCGA for differential RNA splicing (20% median change, percent spliced in) between breast (BRCA, 183 AA and 761 white), colon (COAD, 56 AA and 194 white), squamous and adenocarcinoma lung (LUSC and LUAD, 34 and 57 AA and 392 and 444 white, respectively), and prostate (PRAD, 49 AA and 307 white) cancer specimens from AA and white patients. Our analysis identified 698 differentially expressed genes (DEGs) and 114 alternative RNA splicing events (ARSs) in BRCA, 107 DEGs and 57 ARSs in COAD, 25 and 117 DEGs and 115 and 53 ARSs in LUSC and LUAD, respectively, and 25 DEGs and 71 ARSs in PRAD from AA and white patients. Notably, comparing the lists of DEGs or ARSs from each cancer type with each of the other cancer types yields a minority of overlapping DEGs or ARSs among cancer types, indicating that race-related DEGs and ARSs are largely specific to cancer type. Pathway analysis of DEGs and ARSs reveals that the majority of these genes function in pathways relevant to cancer development and progression, such as programmed cell death, DNA repair, signal transduction, gene expression and metabolism. These analyses increase understanding of molecular mechanisms underlying racial/ethnic disparity in cancer. Upon further study of the function of these variants, such DEGs and ARSs have the potential to become candidates for development of new precision medicine interventions. Citation Format: Muthana Al Abo, Daniel J. George, Jennifer A. Freedman, Steven R. Patierno. Identification of differentially expressed and spliced genes between breast, colon, lung, and prostate cancer from African American and white patients [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr B050.

Asian Zika Virus Isolate Significantly Changes the Transcriptional Profile and Alternative RNA Splicing Events in a Neuroblastoma Cell Line.

The alternative splicing of pre-mRNAs expands a single genetic blueprint to encode multiple, functionally diverse protein isoforms. Viruses have previously been shown to interact with, depend on, and alter host splicing machinery. The consequences, however, incited by viral infection on the global alternative slicing (AS) landscape are under-appreciated. Here, we investigated the transcriptional and alternative splicing profile of neuronal cells infected with a contemporary Puerto Rican Zika virus (ZIKVPR) isolate, an isolate of the prototypical Ugandan ZIKV (ZIKVMR), and dengue virus 2 (DENV2). Our analyses revealed that ZIKVPR induced significantly more differential changes in expressed genes compared to ZIKVMR or DENV2, despite all three viruses showing equivalent infectivity and viral RNA levels. Consistent with the transcriptional profile, ZIKVPR induced a higher number of alternative splicing events compared to ZIKVMR or DENV2, and gene ontology analyses highlighted alternative splicing changes in genes associated with mRNA splicing. In summary, we show that ZIKV affects cellular RNA homeostasis not only at the transcriptional levels but also through the alternative splicing of cellular transcripts. These findings could provide new molecular insights into the neuropathologies associated with this virus.

Human ESC-Based Model of H3.3G34R-Mutant High-Grade Glioma Reveals the Oncogenic Role Of Human-Specific <i>NOTCH2NL</i> Genes

H3.3G34R-mutant gliomas are lethal tumors of the cerebral hemispheres, with unknown mechanisms of regional specificity and tumorigenicity. We developed a human embryonic stem cell-based model of H3.3G34R-mutant glioma that recapitulates the key features of the tumors, with anatomical specificity to forebrain but not hindbrain cells. We show that H3.3G34R, ATRX and TP53 mutations cooperatively impact alternative RNA splicing events, particularly suppression of intron retention. This leads to increased expression of components of the Notch pathway, notably NOTCH2NL, a human-specific gene family. We also uncover a parallel mechanism of enhanced NOTCH2NL expression via genomic amplification of its locus in some H3.3G34R-mutant tumors. These findings demonstrate a novel mechanism whereby evolutionary pathways that lead to larger brain size in humans are co-opted to drive tumor growth.

Abstract PL02-02: Spliceomics: Alternative RNA splicing as a source of ancestry-related molecular targets in precision oncology and cancer disparities

Abstract PL02-02: Spliceomics: Alternative RNA splicing as a source of ancestry-related molecular targets in precision oncology and cancer disparities

Splice-switching small molecules: A new therapeutic approach to modulate gene expression.

Manipulating alternative RNA splicing events with small molecules is emerging as a viable mechanism for the development of therapeutics. A salient challenge in the field is understanding the molecular determinants defining the selectivity of splice-switching events and their mechanisms of action. In this review, the current state-of-the-art in splice-switching small molecules is described. Three examples of splice-switching small molecules are presented, and the differences in their modes of action compared.

Alternative RNA Splicing as a Potential Major Source of Untapped Molecular Targets in Precision Oncology and Cancer Disparities.

Studies of alternative RNA splicing (ARS) have the potential to provide an abundance of novel targets for development of new biomarkers and therapeutics in oncology, which will be necessary to improve outcomes for patients with cancer and mitigate cancer disparities. ARS, a key step in gene expression enabling individual genes to encode multiple proteins, is emerging as a major driver of abnormal phenotypic heterogeneity. Recent studies have begun to identify RNA splicing-related genetic and genomic variation in tumors, oncogenes dysregulated by ARS, RNA splice variants driving race-related cancer aggressiveness and drug response, spliceosome-dependent transformation, and RNA splicing-related immunogenic epitopes in cancer. In addition, recent studies have begun to identify and test, preclinically and clinically, approaches to modulate and exploit ARS for therapeutic application, including splice-switching oligonucleotides, small molecules targeting RNA splicing or RNA splice variants, and combination regimens with immunotherapies. Although ARS data hold such promise for precision oncology, inclusion of studies of ARS in translational and clinical cancer research remains limited. Technologic developments in sequencing and bioinformatics are being routinely incorporated into clinical oncology that permit investigation of clinically relevant ARS events, yet ARS remains largely overlooked either because of a lack of awareness within the clinical oncology community or perceived barriers to the technical complexity of analyzing ARS. This perspective aims to increase such awareness, propose immediate opportunities to improve identification and analysis of ARS, and call for bioinformaticians and cancer researchers to work together to address the urgent need to incorporate ARS into cancer biology and precision oncology.

Transcriptome-wide analysis of alternative RNA splicing events in Epstein-Barr virus-associated gastric carcinomas.

Multiple human diseases including cancer have been associated with a dysregulation in RNA splicing patterns. In the current study, modifications to the global RNA splicing landscape of cellular genes were investigated in the context of Epstein-Barr virus-associated gastric cancer. Global alterations to the RNA splicing landscape of cellular genes was examined in a large-scale screen from 295 primary gastric adenocarcinomas using high-throughput RNA sequencing data. RT-PCR analysis, mass spectrometry, and co-immunoprecipitation studies were also used to experimentally validate and investigate the differential alternative splicing (AS) events that were observed through RNA-seq studies. Our study identifies alterations in the AS patterns of approximately 900 genes such as tumor suppressor genes, transcription factors, splicing factors, and kinases. These findings allowed the identification of unique gene signatures for which AS is misregulated in both Epstein-Barr virus-associated gastric cancer and EBV-negative gastric cancer. Moreover, we show that the expression of Epstein–Barr nuclear antigen 1 (EBNA1) leads to modifications in the AS profile of cellular genes and that the EBNA1 protein interacts with cellular splicing factors. These findings provide insights into the molecular differences between various types of gastric cancer and suggest a role for the EBNA1 protein in the dysregulation of cellular AS.

Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma.

BackgroundDysregulations in alternative splicing (AS) patterns have been associated with many human diseases including cancer. In the present study, alterations to the global RNA splicing landscape of cellular genes were investigated in a large-scale screen from 377 liver tissue samples using high-throughput RNA sequencing data.ResultsOur study identifies modifications in the AS patterns of transcripts encoded by more than 2500 genes such as tumor suppressor genes, transcription factors, and kinases. These findings provide insights into the molecular differences between various types of hepatocellular carcinoma (HCC). Our analysis allowed the identification of 761 unique transcripts for which AS is misregulated in HBV-associated HCC, while 68 are unique to HCV-associated HCC, 54 to HBV&HCV-associated HCC, and 299 to virus-free HCC. Moreover, we demonstrate that the expression pattern of the RNA splicing factor hnRNPC in HCC tissues significantly correlates with patient survival. We also show that the expression of the HBx protein from HBV leads to modifications in the AS profiles of cellular genes. Finally, using RNA interference and a reverse transcription-PCR screening platform, we examined the implications of cellular proteins involved in the splicing of transcripts involved in apoptosis and demonstrate the potential contribution of these proteins in AS control.ConclusionsThis study provides the first comprehensive portrait of global changes in the RNA splicing signatures that occur in hepatocellular carcinoma. Moreover, these data allowed us to identify unique signatures of genes for which AS is misregulated in the different types of HCC.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3029-z) contains supplementary material, which is available to authorized users.

477: Preeclampsia (PE) and global dysregulation of placental alternative RNA splicing events

477: Preeclampsia (PE) and global dysregulation of placental alternative RNA splicing events