Core-binding factor fusion downregulation of ADAR2 RNA editing contributes to AML leukemogenesis.

Adenosine-to-inosine RNA editing, which is catalyzed by adenosine deaminases acting on RNA (ADAR) family of enzymes, ADAR1 and ADAR2, has been shown to contribute to multiple cancers. However, other than the chronic myeloid leukemia blast crisis, relatively little is known about its role in other types of hematological malignancies. Here, we found that ADAR2, but not ADAR1 and ADAR3, was specifically downregulated in the core-binding factor (CBF) acute myeloid leukemia (AML) with t(8;21) or inv(16) translocations. In t(8;21) AML, RUNX1-driven transcription of ADAR2 was repressed by the RUNX1-ETO additional exon 9a fusion protein in a dominant-negative manner. Further functional studies confirmed that ADAR2 could suppress leukemogenesis specifically in t(8;21) and inv16 AML cells dependent on its RNA editing capability. Expression of 2 exemplary ADAR2-regulated RNA editing targets coatomer subunit α and component of oligomeric Golgi complex 3 inhibits the clonogenic growth of human t(8;21) AML cells. Our findings support a hitherto, unappreciated mechanism leading to ADAR2 dysregulation in CBF AML and highlight the functional relevance of loss of ADAR2-mediated RNA editing to CBF AML.

Aberrant hyperediting of the myeloma transcriptome by ADAR1 confers oncogenicity and is a marker of poor prognosis.

DNA alterations have been extensively reported in multiple myeloma (MM); however, they cannot yet fully explain all the biological and molecular abnormalities in MM, which remains to this day an incurable disease with eventual emergence of refractory disease. Recent years have seen abnormalities at the RNA levels being reported to possess potential biological relevance in cancers. ADAR1-mediated A-to-I editing is an important posttranscriptional mechanism in human physiology, and the biological implication of its abnormality, especially at the global level, is underexplored in MM. In this study, we define the biological implications of A-to-I editing and how it contributes to MM pathogenesis. Here, we identified that the MM transcriptome is aberrantly hyperedited because of the overexpression of ADAR1. These events were associated with patients' survival independent of 1q21 amplifications and could affect patients' responsiveness to different treatment regimes. Our functional assays established ADAR1 to be oncogenic, driving cellular growth and proliferation in an editing-dependent manner. In addition, we identified NEIL1 (base-excision repair gene) as an essential and a ubiquitously edited ADAR1 target in MM. The recoded NEIL1 protein showed defective oxidative damage repair capacity and loss-of-function properties. Collectively, our data demonstrated that ADAR1-mediated A-to-I editing is both clinically and biologically relevant in MM. These data unraveled novel insights into MM molecular pathogenesis at the global RNA level.

Pan-cancer pervasive upregulation of 3' UTR splicing drives tumourigenesis.

Most mammalian genes generate messenger RNAs with variable untranslated regions (UTRs) that are important post-transcriptional regulators. In cancer, shortening at 3' UTR ends via alternative polyadenylation can activate oncogenes. However, internal 3' UTR splicing remains poorly understood as splicing studies have traditionally focused on protein-coding alterations. Here we systematically map the pan-cancer landscape of 3' UTR splicing and present this in SpUR ( http://www.cbrc.kaust.edu.sa/spur/home/ ). 3' UTR splicing is widespread, upregulated in cancers, correlated with poor prognosis and more prevalent in oncogenes. We show that antisense oligonucleotide-mediated inhibition of 3' UTR splicing efficiently reduces oncogene expression and impedes tumour progression. Notably, CTNNB1 3' UTR splicing is the most consistently dysregulated event across cancers. We validate its upregulation in hepatocellular carcinoma and colon adenocarcinoma, and show that the spliced 3' UTR variant is the predominant contributor to its oncogenic functions. Overall, our study highlights the importance of 3' UTR splicing in cancer and may launch new avenues for RNA-based anti-cancer therapeutics.

NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing.

The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are still constrained by their high sequencing error rates and low sequencing throughput. Here, we present NanoVar, an optimized structural variant caller utilizing low-depth (8X) whole-genome sequencing data generated by Oxford Nanopore Technologies. NanoVar exhibits higher structural variant calling accuracy when benchmarked against current tools using low-depth simulated datasets. In patient samples, we successfully validate structural variants characterized by NanoVar and uncover normal alternative sequences or alleles which are present in healthy individuals.

Injury patterns in patients presenting with a recurrent anterior cruciate ligament tear following primary reconstruction.

BACKGROUND: An anterior cruciate ligament (ACL) graft rupture or a primary ACL injury in the contralateral knee is one of the greatest concerns of patients following primary anterior cruciate ligament reconstruction (ACLR). Our study describes the epidemiology and presence of concomitant meniscal injuries of patients with a graft rupture following primary ACLR or a primary rupture of the contralateral ACL following primary ACLR of the ipsilateral knee. METHODS: We reviewed the medical records of 42 patients who underwent a second ACLR. ACLR was performed using the ipsilateral semitendinosus and gracilis autograft. Variables extracted included the presence of concomitant MM and LM injuries intra-operatively, the patients' level of intensity of sport (light, moderate, strenuous), duration of rehabilitation and mechanism of injury (contact, non-contact). RESULTS: Twenty-four (57.1%) patients had graft rupture of a previously reconstructed ACL of which 20 (83.3%) were male and 18 (42.9%) patients had a primary ACL tear of the contralateral knee following ACLR of the ipsilateral knee of which 18 (100%) were male. Patient who sustained a graft rupture were younger (29.5 vs. 31.9 years), had a higher body mass index (BMI) (26.42 vs. 25.10 kg/m(2)) and had a longer time before re-injury (6.18 vs. 4.94 years). Concomitant meniscal injury rates were comparable in both groups and the medial meniscus was injured more often. CONCLUSIONS: This study describes the demographics of 2(nd) ACL injuries in the Asian population. Additional studies that investigate the differences in knee anatomy of Asians and Caucasians and their impact on ACL injuries should be performed.

Effect of storage temperature and equilibration time on polymethyl methacrylate (PMMA) bone cement polymerization in joint replacement surgery.

BACKGROUND: In cemented joint arthroplasty, the handling characteristics (doughing, working, and setting times) of polymethyl methacrylate (PMMA) bone cement is important as it determines the amount of time surgeons have to optimally position an implant. Storage conditions (temperature and humidity) and the time given for PMMA cement to equilibrate to ambient operating theater (OT) temperatures are often unregulated and may lead to inconsistencies in its handling characteristics. This has not been previously studied. Hence, the purpose of this study was to investigate the effect of storage temperatures on the handling characteristics of PMMA cement and the duration of equilibration time needed at each storage temperature to produce consistent and reproducible doughing, setting, and working times. METHODS: SmartSet® HV cement was stored at three different controlled temperatures: 20 °C (control), 24 °C, and 28 °C for at least 24 h prior to mixing. The cement components were then brought into a room kept at 20 °C and 50 % humidity. Samples were allowed to equilibrate to ambient conditions for 15, 30, 45, and 60 min. The cement components were mixed and the dough time, temperature-versus-time curve (Lutron TM-947SD, Lutron Electronics, Inc., Coopersburg, PA), and setting time were recorded. Analysis was performed using the two-way ANOVA test (IBM SPSS Statistics V.22). RESULTS: At 20 °C (control) storage temperature, the mean setting time was 534 ± 17 s. At 24 °C storage temperature, the mean setting time was 414 ± 6 s (p < 0.001*) with 15 min of equilibration, 446 ± 11 s (p < 0.001*) with 30 min of equilibration, 501 ± 12 s (p < 0.001*) with 45 min of equilibration, and 528 ± 15 (p > 0.05) with 60 min of equilibration. At 28 °C storage temperature, the mean setting time was 381 ± 8 s (p < 0.001*) with 15 min of equilibration, 432 ± 30 s (p < 0.001*) with 30 min of equilibration, 487 ± 9 (p < 0.001*) with 45 min of equilibration, and 520 ± 16 s (p > 0.05) with 60 min of equilibration. CONCLUSIONS: This study reflects the extent to which storage temperatures and equilibration times can potentially affect the handling characteristics of PMMA cement. We recommend institutions to have a well-regulated temperature and humidity-controlled facility for storage of bone cements and a protocol to standardize the equilibration time of cements prior to use in the OT to improve consistency and reproducibility of the handling characteristics of PMMA cement.