RAS oncogenic activity predicts response to chemotherapy and outcome in lung adenocarcinoma

Activating mutations in KRAS occur in 32% of lung adenocarcinomas (LUAD). Despite leading to aggressive disease and resistance to therapy in preclinical studies, the KRAS mutation does not predict patient outcome or response to treatment, presumably due to additional events modulating RAS pathways. To obtain a broader measure of RAS pathway activation, we developed RAS84, a transcriptional signature optimised to capture RAS oncogenic activity in LUAD. We report evidence of RAS pathway oncogenic activation in 84% of LUAD, including 65% KRAS wild-type tumours, falling into four groups characterised by coincident alteration of STK11/LKB1, TP53 or CDKN2A, suggesting that the classifications developed when considering only KRAS mutant tumours have significance in a broader cohort of patients. Critically, high RAS activity patient groups show adverse clinical outcome and reduced response to chemotherapy. Patient stratification using oncogenic RAS transcriptional activity instead of genetic alterations could ultimately assist in clinical decision-making.

CDK13 cooperates with CDK12 to control global RNA polymerase II processivity

The RNA polymerase II (POLII)-driven transcription cycle is tightly regulated at distinct checkpoints by cyclin-dependent kinases (CDKs) and their cognate cyclins. The molecular events underpinning transcriptional elongation, processivity, and the CDK-cyclin pair(s) involved remain poorly understood. Using CRISPR-Cas9 homology-directed repair, we generated analog-sensitive kinase variants of CDK12 and CDK13 to probe their individual and shared biological and molecular roles. Single inhibition of CDK12 or CDK13 induced transcriptional responses associated with cellular growth signaling pathways and/or DNA damage, with minimal effects on cell viability. In contrast, dual kinase inhibition potently induced cell death, which was associated with extensive genome-wide transcriptional changes including widespread use of alternative 3' polyadenylation sites. At the molecular level, dual kinase inhibition resulted in the loss of POLII CTD phosphorylation and greatly reduced POLII elongation rates and processivity. These data define substantial redundancy between CDK12 and CDK13 and identify both as fundamental regulators of global POLII processivity and transcription elongation.

Regulation of the RNAPII Pool Is Integral to the DNA Damage Response

In response to transcription-blocking DNA damage, cells orchestrate a multi-pronged reaction, involving transcription-coupled DNA repair, degradation of RNA polymerase II (RNAPII), and genome-wide transcription shutdown. Here, we provide insight into how these responses are connected by the finding that ubiquitylation of RNAPII itself, at a single lysine (RPB1 K1268), is the focal point for DNA-damage-response coordination. K1268 ubiquitylation affects DNA repair and signals RNAPII degradation, essential for surviving genotoxic insult. RNAPII degradation results in a shutdown of transcriptional initiation, in the absence of which cells display dramatic transcriptome alterations. Additionally, regulation of RNAPII stability is central to transcription recovery-persistent RNAPII depletion underlies the failure of this process in Cockayne syndrome B cells. These data expose regulation of global RNAPII levels as integral to the cellular DNA-damage response and open the intriguing possibility that RNAPII pool size generally affects cell-specific transcription programs in genome instability disorders and even normal cells.

ECG interpretation skill acquisition: A review of learning, teaching and assessment

The recording of 12 lead electrocardiograms (ECG) is one of the most useful and commonly performed medical procedures. ECGs are used in diagnosis, risk-stratification management decision-making, and assessment in response to therapy. The correct interpretation of 12 lead ECG recordings is complex and clinically challenging with misinterpretation having the potential to result in poor outcomes or even patient fatality. Despite its widespread use, several studies have highlighted deficiencies in ECG interpretation skills among health professionals. The literature suggests that up to 33% of ECG interpretations have some error when compared to the expert reference and up to 11% resulted in inappropriate management. The pedagogy of ECG interpretation lacks universal establishment; time allocation, faculty training and teaching format vary considerably within the literature. This review of the literature reports how a lack of established ECG reporting methods may contribute to the variation in reported ECG interpretation competence across many healthcare professionals. The ubiquity of the ECG in clinical practice and an over reliance on computer assisted ECG interpretation are additionally explored as factors affecting acquisition and retention of this clinical skill.

UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene

The transcription-related DNA damage response was analyzed on a genome-wide scale with great spatial and temporal resolution. Upon UV irradiation, a slowdown of transcript elongation and restriction of gene activity to the promoter-proximal ∼25 kb is observed. This is associated with a shift from expression of long mRNAs to shorter isoforms, incorporating alternative last exons (ALEs) that are more proximal to the transcription start site. Notably, this includes a shift from a protein-coding ASCC3 mRNA to a shorter ALE isoform of which the RNA, rather than an encoded protein, is critical for the eventual recovery of transcription. The non-coding ASCC3 isoform counteracts the function of the protein-coding isoform, indicating crosstalk between them. Thus, the ASCC3 gene expresses both coding and non-coding transcript isoforms with opposite effects on transcription recovery after UV-induced DNA damage.

Multiomic Analysis of the UV-Induced DNA Damage Response

In order to facilitate the identification of factors and pathways in the cellular response to UV-induced DNA damage, several descriptive proteomic screens and a functional genomics screen were performed in parallel. Numerous factors could be identified with high confidence when the screen results were superimposed and interpreted together, incorporating biological knowledge. A searchable database, bioLOGIC, which provides access to relevant information about a protein or process of interest, was established to host the results and facilitate data mining. Besides uncovering roles in the DNA damage response for numerous proteins and complexes, including Integrator, Cohesin, PHF3, ASC-1, SCAF4, SCAF8, and SCAF11, we uncovered a role for the poorly studied, melanoma-associated serine/threonine kinase 19 (STK19). Besides effectively uncovering relevant factors, the multiomic approach also provides a systems-wide overview of the diverse cellular processes connected to the transcription-related DNA damage response.

Mutation of cancer driver MLL2 results in transcription stress and genome instability

Genome instability is a recurring feature of tumorigenesis. Mutation in MLL2, encoding a histone methyltransferase, is a driver in numerous different cancer types, but the mechanism is unclear. Here, we present evidence that MLL2 mutation results in genome instability. Mouse cells in which MLL2 gene deletion can be induced display elevated levels of sister chromatid exchange, gross chromosomal aberrations, 53BP1 foci, and micronuclei. Human MLL2 knockout cells are characterized by genome instability as well. Interestingly, MLL2 interacts with RNA polymerase II (RNAPII) and RECQL5, and, although MLL2 mutated cells have normal overall H3K4me levels in genes, nucleosomes in the immediate vicinity of RNAPII are hypomethylated. Importantly, MLL2 mutated cells display signs of substantial transcription stress, and the most affected genes overlap with early replicating fragile sites, show elevated levels of γH2AX, and suffer frequent mutation. The requirement for MLL2 in the maintenance of genome stability in genes helps explain its widespread role in cancer and points to transcription stress as a strong driver in tumorigenesis.

RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress

RECQL5 is the sole member of the RECQ family of helicases associated with RNA polymerase II (RNAPII). We now show that RECQL5 is a general elongation factor that is important for preserving genome stability during transcription. Depletion or overexpression of RECQL5 results in corresponding shifts in the genome-wide RNAPII density profile. Elongation is particularly affected, with RECQL5 depletion causing a striking increase in the average rate, concurrent with increased stalling, pausing, arrest, and/or backtracking (transcription stress). RECQL5 therefore controls the movement of RNAPII across genes. Loss of RECQL5 also results in the loss or gain of genomic regions, with the breakpoints of lost regions located in genes and common fragile sites. The chromosomal breakpoints overlap with areas of elevated transcription stress, suggesting that RECQL5 suppresses such stress and its detrimental effects, and thereby prevents genome instability in the transcribed region of genes.

A global insight into a cancer transcriptional space using pancreatic data: importance, findings and flaws

Despite the increasing wealth of available data, the structure of cancer transcriptional space remains largely unknown. Analysis of this space would provide novel insights into the complexity of cancer, assess relative implications in complex biological processes and responses, evaluate the effectiveness of cancer models and help uncover vital facets of cancer biology not apparent from current small-scale studies. We conducted a comprehensive analysis of pancreatic cancer-expression space by integrating data from otherwise disparate studies. We found (i) a clear separation of profiles based on experimental type, with patient tissue samples, cell lines and xenograft models forming distinct groups; (ii) three subgroups within the normal samples adjacent to cancer showing disruptions to biofunctions previously linked to cancer; and (iii) that ectopic subcutaneous xenografts and cell line models do not effectively represent changes occurring in pancreatic cancer. All findings are available from our online resource for independent interrogation. Currently, the most comprehensive analysis of pancreatic cancer to date, our study primarily serves to highlight limitations inherent with a lack of raw data availability, insufficient clinical/histopathological information and ambiguous data processing. It stresses the importance of a global-systems approach to assess and maximise findings from expression profiling of malignant and non-malignant diseases.

RAF gene fusion breakpoints in pediatric brain tumors are characterized by significant enrichment of sequence microhomology

Gene fusions involving members of the RAF family of protein kinases have recently been identified as characteristic aberrations of low-grade astrocytomas, the most common tumors of the central nervous system in children. While it has been shown that these fusions cause constitutive activation of the ERK/MAPK pathway, very little is known about their formation. Here, we present a detailed analysis of RAF gene fusion breakpoints from a well-characterized cohort of 43 low-grade astrocytomas. Our findings show that the rearrangements that generate these RAF gene fusions may be simple or complex and that both inserted nucleotides and microhomology are common at the DNA breakpoints. Furthermore, we identify novel enrichment of microhomologous sequences in the regions immediately flanking the breakpoints. We thus provide evidence that the tandem duplications responsible for these fusions are generated by microhomology-mediated break-induced replication (MMBIR). Although MMBIR has previously been implicated in the pathogenesis of other diseases and the evolution of eukaryotic genomes, we demonstrate here that the proposed details of MMBIR are consistent with a recurrent rearrangement in cancer. Our analysis of repetitive elements, Z-DNA and sequence motifs in the fusion partners identified significant enrichment of the human minisatellite conserved sequence/χ-like element at one side of the breakpoint. Therefore, in addition to furthering our understanding of low-grade astrocytomas, this study provides insights into the molecular mechanistic details of MMBIR and the sequence of events that occur in the formation of genomic rearrangements.

FANCJ is a structure-specific DNA helicase associated with the maintenance of genomic G/C tracts

Fanconi anemia (FA) is a heritable human cancer-susceptibility disorder, delineating a genetically heterogenous pathway for the repair of replication-blocking lesions such as interstrand DNA cross-links. Here we demonstrate that one component of this pathway, FANCJ, is a structure-specific DNA helicase that dissociates guanine quadruplex DNA (G4 DNA) in vitro. Moreover, in contrast with previously identified G4 DNA helicases, such as the Bloom's helicase (BLM), FANCJ unwinds G4 substrates with 5'-3' polarity. In the FA-J human patient cell line EUFA0030 the loss of FANCJ G4 unwinding function correlates with the accumulation of large genomic deletions in the vicinity of sequences, which match the G4 DNA signature. Together these findings support a role for FANCJ in the maintenance of potentially unstable genomic G/C tracts during replication.

Cohesin relocation from sites of chromosomal loading to places of convergent transcription

Sister chromatids, the products of eukaryotic DNA replication, are held together by the chromosomal cohesin complex after their synthesis. This allows the spindle in mitosis to recognize pairs of replication products for segregation into opposite directions. Cohesin forms large protein rings that may bind DNA strands by encircling them, but the characterization of cohesin binding to chromosomes in vivo has remained vague. We have performed high resolution analysis of cohesin association along budding yeast chromosomes III-VI. Cohesin localizes almost exclusively between genes that are transcribed in converging directions. We find that active transcription positions cohesin at these sites, not the underlying DNA sequence. Cohesin is initially loaded onto chromosomes at separate places, marked by the Scc2/Scc4 cohesin loading complex, from where it appears to slide to its more permanent locations. But even after sister chromatid cohesion is established, changes in transcription lead to repositioning of cohesin. Thus the sites of cohesin binding and therefore probably sister chromatid cohesion, a key architectural feature of mitotic chromosomes, display surprising flexibility. Cohesin localization to places of convergent transcription is conserved in fission yeast, suggesting that it is a common feature of eukaryotic chromosomes.

Solution structure, hydrodynamics and thermodynamics of the UvrB C-terminal domain

The solution structure, thermodynamic stability and hydrodynamic properties of the 55-residue C-terminal domain of UvrB that interacts with UvrC during excision repair in E. coli have been determined using a combination of high resolution NMR, ultracentrifugation, 15N NMR relaxation, gel permeation, NMR diffusion, circular dichroism and differential scanning calorimetry. The subunit molecular weight is 7,438 kDa., compared with 14.5+/-1.0 kDa. determined by equilibrium sedimentation, indicating a dimeric structure. The structure determined from NMR showed a stable dimer of anti-parallel helical hairpins that associate in an unusual manner, with a small and hydrophobic interface. The Stokes radius of the protein decreases from a high plateau value (ca. 22 A) at protein concentrations greater than 4 microM to about 18 A at concentrations less than 0.1 microM. The concentration and temperature-dependence of the far UV circular dichroism show that the protein is thermally stable (Tm ca. 71.5 degrees C at 36 microM). The simplest model consistent with these data was a dimer dissociating into folded monomers that then unfolds co-operatively. The van't Hoff enthalpy and dissociation constant for both transition was derived by fitting, with deltaH1=23 kJ mol(-1). K1(298)=0.4 microM and deltaH2= 184 kJ mol(-1). This is in good agreement with direct calorimetric analysis of the thermal unfolding of the protein, which gave a calorimetric enthalpy change of 181 kJ mol(-1) and a van't Hoff enthalpy change of 354 kJ mol(-1), confirming the dimer to monomer unfolding. The thermodynamic data can be reconciled with the observed mode of dimerisation. 15N NMR relaxation measurements at 14.1 T and 11.75 T confirmed that the protein behaves as an asymmetric dimer at mM concentrations, with a flexible N-terminal linker for attachment to the remainder of the UvrB protein. The role of dimerisation of this domain in the excision repair mechanism is discussed.

Analysis of backbone dynamics in cytochrome b5 using 15N-NMR relaxation measurements

Determination of 15N-NMR relaxation rates has allowed the characterisation of the dynamic properties of 55 1H-15N bond vectors in a soluble haem-binding domain of bovine microsomal ferricytochrome b5 consisting of the first 104 amino acid residues. Measurements of heteronuclear [1H]-15N-NMR nuclear Overhauser effects, and 15N-NMR longitudinal and transverse relaxation rates have been analysed using both model-free and reduced spectral density mapping approaches, demonstrating the application of these methods to a paramagnetic system. Analysis reveals that, for those regions which have been assessed, the polypeptide backbone of ferricytochrome b5 is largely rigid (average S2 = 0.80), and that minimal internal backbone motion occurs on the sub-nanosecond timescale. In contrast, motions on the microsecond to millisecond timescale, especially pronounced for the loop region extending from residues 28 to 31, and which may be of biological relevance, are indicated.

The solution structure of bovine ferricytochrome b5 determined using heteronuclear NMR methods

The solution structure of a recombinant form of cytochrome b5 containing 104 amino acid residues has been determined using three-dimensional NMR spectroscopy. Using protein enriched in 15N the majority of the polypeptide backbone resonances have been assigned to reveal numerous chemical shift differences to those reported previously for smaller fragments of cytochrome b5. By using 3D NMR methods the extensive spectral overlap of resonance cross-peaks in 2D NMR spectra could be satisfactorily resolved. The large number of sequence-specific assignments made for this form of the protein allowed the identification of over 1130 NOEs, giving an average of 14 NOEs per assigned residue, and 52 dihedral angles (phi). This data was used in an ab initio simulated annealing protocol to determine the solution structure for bovine microsomal cytochrome b5. A series of 50 structures was generated using distance restraints derived from the magnitude of the NOE and torsional angles based on the measured JHN-HA coupling constants. From an initial round of simulated annealing a family of 36 structures was selected on the basis of good covalent geometry and minimal restraint violations. A single cycle of simulated annealing refinement produced 36 converged structures that exhibited an average r.m.s.d. of 0.73 A for the backbone atoms. The determination of the solution structure of cytochrome b5 is the first using NMR methods for any form of this protein. It is also the only cytochrome whose structure has been determined in the oxidised or paramagnetic state. The results show that despite significant line broadening and pseudocontact shifts for resonances lying close to the paramagnetic haem centre, and despite extensive spectral overlap that prevents complete resonance assignment, the topology of the polypeptide backbone can be derived. The conformation for cytochrome b5 determined in this study reveals several small, but significant, differences in structure to that determined previously by crystallography for a smaller fragment of this protein. For example, NMR data do not support a short beta strand as the first element of secondary structure at the N terminus nor is it likely that a beta-bulge structure forms between residues 75 to 79. The data obtained in this study are more consistent with a turn in this region of the protein linking helices 5 and 6 and leads to cytochrome b5 containing only three clearly defined beta strands. Four of the six helices together with the antiparallel beta strands make up a haem binding pocket in which the solvent-accessible area of the protoporphyrin IX centre remains very similar to that found in the crystal structure. The remaining helices and the beta strands form a second structural domain on which the four helix bundle that surrounds the haem is based. THe derivation of the solution structure of cytochrome b5 will allow a greater understanding of the functional properties of cytochrome b5 including its role in biological electron transfer and molecular recognition together with insight into haem protein folding and stability.

Extraction of Light Filth from Oriental Sauces Containing Soy Sauce, Thickeners, and Spices: Collaborative Study

Results are reported for a collaborative study of a method for the extraction of light filth from oriental sauces containing soy sauce, thickeners, and spices. A100 g test portion is pretreated in a 2% solution of Tergitol Anionic 4 over a steam bath, and oils are removed by wet-sieving on No. 230 sieve. Filth is isolated from 40% isopropanol by using Na4EDTA and mineral oil. Average recoveries by 9 collaborators for 3 spike levels of rat hairs (5,10, and 15) were 84, 78, and 79%, respectively; for insect fragments (5,15, and 30), recoveries were 92, 95, and 96%, respectively. The method was adopted first action by AOAC International.

Radiographs in clinical periodontal trials

Fifty-eight patients were selected from an ongoing study of periodontal therapy at The University of Michigan. Pre-and post-treatment series of full mouth radiographs obtained by conventional paralleling long cone technique were available. Mesial and distal radiographic bone height was scored using the technique developed by Björn et al. A total of 1416 teeth were scored from the itial radiographs, and subsequently at one, two, three, and four years after the treatment. Radiographic bone height scores were compared with level of attachment and pocket depth scores for the same teeth at the same time. Statistical significance and correlation coefficients were derived using computer analysis of the data. The data were analyzed using three different data groupings: individual teeth, patient means, and half-mouth treatment methods. High positive correlations were found between initial measurements of radiographic bone height and attachment level as well as pocket depth. The correlations between changes in measurements of radiographic bone height and attachment level after treatment were markedly lower but are statistically significant. A highly significant correlation between radiographic bone heights and measurements of attachment level also appeared in follow-up data one to four years after treatment. The method of data grouping resulted in different correlation coefficients. Highest correlations were found if the data were pooled for patients. Lowest correlations were found if the data for individual teeth were analyzed. When the data were combined to produce patient scores, sample variation is reduced and correlations increase in magnitude. The generally high correlations between radiographic bone height and attachment level scores before and after treatment tend to confirm the fact that radiographic assessment of alveolar bone height using the method of Björn et al. can provide fairly accurate assessment of interproximal periodontal support.