Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays

<p>Abstract</p> <p>Background</p> <p>Tumor-predominant splice isoforms were identified during comparative <it>in silico </it>sequence analysis of EST clones, suggesting that global aberrant alternative pre-mRNA splicing may be an epigenetic phenomenon in cancer. We used an exon expression array to perform an objective, genome-wide survey of glioma-specific splicing in 24 GBM and 12 nontumor brain samples. Validation studies were performed using RT-PCR on glioma cell lines, patient tumor and nontumor brain samples.</p> <p>Results</p> <p>In total, we confirmed 14 genes with glioma-specific splicing; seven were novel events identified by the exon expression array (<it>A2BP1, BCAS1, CACNA1G, CLTA, KCNC2, SNCB</it>, and <it>TPD52L2</it>). Our data indicate that large changes (> 5-fold) in alternative splicing are infrequent in gliomagenesis (< 3% of interrogated RefSeq entries). The lack of splicing changes may derive from the small number of splicing factors observed to be aberrantly expressed.</p> <p>Conclusion</p> <p>While we observed some tumor-specific alternative splicing, the number of genes showing exclusive tumor-specific isoforms was on the order of tens, rather than the hundreds suggested previously by <it>in silico </it>mining. Given the important role of alternative splicing in neural differentiation, there may be selective pressure to maintain a majority of splicing events in order to retain glial-like characteristics of the tumor cells.</p

Low-Molecular-Weight Cyclin E Deregulates DNA Replication and Damage Repair To Promote Genomic Instability in Breast Cancer

Low-molecular-weight cyclin E (LMW-E) is an N-terminus deleted (40 amino acid) form of cyclin E detected in breast cancer, but not in normal cells or tissues. LMW-E overexpression predicts poor survival in breast cancer patients independent of tumor proliferation rate, but the oncogenic mechanism of LMW-E and its unique function(s) independent of full-length cyclin E (FL-cycE) remain unclear. In the current study, we found LMW-E was associated with genomic instability in early-stage breast tumors (n = 725) and promoted genomic instability in human mammary epithelial cells (hMECs). Mechanistically, FL-cycE overexpression inhibited the proliferation of hMECs by replication stress and DNA damage accumulation, but LMW-E facilitated replication stress tolerance by upregulating DNA replication and damage repair. Specifically, LMW-E interacted with chromatin and upregulated the loading of minichromosome maintenance complex proteins (MCMs) in a CDC6 dependent manner and promoted DNA repair in a RAD51- and C17orf53-dependent manner. Targeting the ATR-CHK1-RAD51 pathway with ATR inhibitor (ceralasertib), CHK1 inhibitor (rabusertib), or RAD51 inhibitor (B02) significantly decreased the viability of LMW-E-overexpressing hMECs and breast cancer cells. Collectively, our findings delineate a novel role for LMW-E in tumorigenesis mediated by replication stress tolerance and genomic instability, providing novel therapeutic strategies for LMW-E-overexpressing breast cancers

SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems

Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone. SMRT-software detected N6-methyl-adenine (m6A) at GATC and CATG recognition sites, motifs previously shown to be targeted by PBCV-1 DNA methyltransferases M.CviAI and M. CviAII, respectively. At the same time, PacBio analyses indicated that 10.9% of the PBCV-1 genome had large interpulse duration ratio (ipdRatio) values, the primary metric for DNA modification identification. These events represent 20.6x more sites than can be accounted for by all available adenines in GATC and CATG motifs, suggesting base or backbone modifications other than methylation might be present. To define methylation stability, we cross-compared methylation status of each GATC and CATG sequence in three biological replicates and found ∼81% of sites were stably methylated, while ∼2% consistently lack methylation. The remaining 17% of sites were stochastically methylated. When methylation status was analyzed for both strands of each target, we show that palindromes existed in completely non-methylated states, fully-methylated states, or hemi-methylated states, though GATC sites more often lack methylation than CATG sequences. Given that both sequences are targeted by not just methyltransferases, but by restriction endonucleases that are together encoded by PBCV-1 as virus-originating restriction modification (RM) systems, there is strong selective pressure to modify all target sites. The finding that most instances of non-methylation are associated with hemi-methylation is congruent with observations that hemi-methylated palindromes are resistant to cleavage by restriction endonucleases. However, sites where hemi-methylation is conserved might represent a unique regulatory function for PBCV-1. This study serves as a baseline for future investigation into the epigenomics of chloroviruses and their giant virus relatives

Bite-sized and peer-assisted video-based learning in statistics education: benefits on attainment, attitudes and preferences of university students

The use and acceptance of online learning have increased following the COVID-19 pandemic. This mixed-methods study examined learners' preferences and performance in online learning interactions in relation to two factors: 'bite-sized' learning and 'presenter status' in instructional videos. University students (N = 18) without a mathematical background utilised bite-sized online learning episodes focusing on statistics. Each episode included a 10-minute instructional video followed by an assessment. The videos implemented three alternative 'presenter-status' conditions: lecturer, student-imitating-lecturer or student-peer-tutor. Individual students completed three episodes, one from each presenter-status condition (counterbalanced). Participants presented high performance in the post-episode assessments, irrespective of presenter status. Students also reported remarkably positive views towards bite-sized learning in user-satisfaction questionnaires. Finally, qualitative analysis of open-ended responses and interviews uncovered three main themes: positive learning experiences, divergent attitudes towards video-based learning, and differential preferences for presenter status. These findings have clear implications for teaching and learning in higher education

Recommendations for In Vitro and In Vivo Testing of Magnetic Nanoparticle Hyperthermia Combined with Radiation Therapy

Magnetic nanoparticle (MNP)-mediated hyperthermia (MH) coupled with radiation therapy (RT) is a novel approach that has the potential to overcome various practical difficulties encountered in cancer treatment. In this work, we present recommendations for the in vitro and in vivo testing and application of the two treatment techniques. These recommendations were developed by the members of Working Group 3 of COST Action TD 1402: Multifunctional Nanoparticles for Magnetic Hyperthermia and Indirect Radiation Therapy (“Radiomag”). The purpose of the recommendations is not to provide definitive answers and directions but, rather, to outline those tests and considerations that a researcher must address in order to perform in vitro and in vivo studies. The recommendations are divided into 5 parts: (a) in vitro evaluation of MNPs; (b) in vitro evaluation of MNP-cell interactions; (c) in vivo evaluation of the MNPs; (d) MH combined with RT; and (e) pharmacokinetic studies of MNPs. Synthesis and characterization of the MNPs, as well as RT protocols, are beyond the scope of this wor

Exploring the impact of group identity at university on psychological and behavioural outcomes

With respect to supporting student well-being and success, the current research developed a peer support scheme, built on the principles of Social Identity Theory (SIT). This was targeted towards first year undergraduate psychology students, in which measures of collective identity, sense of belonging, group efficacy, happiness and resilience were obtained, along with attendance and academic attainment. Following one academic year of being part of our peer support scheme, participants (N= 90) completed a questionnaire and consented to their attendance and attainment data to be used. It was found that students’ collective identity was positively related to their sense of belonging, group efficacy beliefs and happiness. Further, the sense of belonging was a reliable predictor of happiness, but not attendance or academic attainment. Therefore, there is some evidence to suggest that a SIT-driven peer support scheme can support students’ psychosocial well-being, although more is needed to ascertain whether this could be developed further to observe any course-related outcomes. Theoretical contributions to SIT are therefore presented, in which the insights can be applied to Higher Education beyond the UK